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Xu L, Yue XL, Li HZ, Jian SL, Shu WS, Cui L, Xu XW. Aerobic Anoxygenic Phototrophic Bacteria in the Marine Environments Revealed by Raman/Fluorescence-Guided Single-Cell Sorting and Targeted Metagenomics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:7087-7098. [PMID: 38651173 DOI: 10.1021/acs.est.4c02881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Aerobic anoxygenic phototrophic bacteria (AAPB) contribute profoundly to the global carbon cycle. However, most AAPB in marine environments are uncultured and at low abundance, hampering the recognition of their functions and molecular mechanisms. In this study, we developed a new culture-independent method to identify and sort AAPB using single-cell Raman/fluorescence spectroscopy. Characteristic Raman and fluorescent bands specific to bacteriochlorophyll a (Bchl a) in AAPB were determined by comparing multiple known AAPB with non-AAPB isolates. Using these spectroscopic biomarkers, AAPB in coastal seawater, pelagic seawater, and hydrothermal sediment samples were screened, sorted, and sequenced. 16S rRNA gene analysis and functional gene annotations of sorted cells revealed novel AAPB members and functional genes, including one species belonging to the genus Sphingomonas, two genera affiliated to classes Betaproteobacteria and Gammaproteobacteria, and function genes bchCDIX, pucC2, and pufL related to Bchl a biosynthesis and photosynthetic reaction center assembly. Metagenome-assembled genomes (MAGs) of sorted cells from pelagic seawater and deep-sea hydrothermal sediment belonged to Erythrobacter sanguineus that was considered as an AAPB and genus Sphingomonas, respectively. Moreover, multiple photosynthesis-related genes were annotated in both MAGs, and comparative genomic analysis revealed several exclusive genes involved in amino acid and inorganic ion metabolism and transport. This study employed a new single-cell spectroscopy method to detect AAPB, not only broadening the taxonomic and genetic contents of AAPB in marine environments but also revealing their genetic mechanisms at the single-genomic level.
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Affiliation(s)
- Lin Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, P. R. China
- Collge of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, P. R. China
| | - Xiao-Lan Yue
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, P. R. China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
| | - Hong-Zhe Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P. R. China
| | - Shu-Ling Jian
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, P. R. China
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P. R. China
| | - Wen-Sheng Shu
- Institute of Ecological Science, School of Life Science, South China Normal University, Guangzhou 510631, P. R. China
| | - Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P. R. China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, P. R. China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
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Takebe H, Tominaga K, Isozaki T, Watanabe T, Yamamoto K, Kamikawa R, Yoshida T. Taxonomic difference in marine bloom-forming phytoplanktonic species affects the dynamics of both bloom-responding prokaryotes and prokaryotic viruses. mSystems 2024; 9:e0094923. [PMID: 38441030 PMCID: PMC11019789 DOI: 10.1128/msystems.00949-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/13/2024] [Indexed: 03/06/2024] Open
Abstract
The production of dissolved organic matter during phytoplankton blooms and consumption by heterotrophic prokaryotes promote marine carbon biogeochemical cycling. Although prokaryotic viruses presumably affect this process, their dynamics during blooms are not fully understood. Here, we investigated the effects of taxonomic difference in bloom-forming phytoplankton on prokaryotes and their viruses. We analyzed the dynamics of coastal prokaryotic communities and viruses under the addition of dissolved intracellular fractions from taxonomically distinct phytoplankton, the diatom Chaetoceros sp. (CIF) and the raphidophycean alga Heterosigma akashiwo (HIF), using microcosm experiments. Ribosomal RNA gene amplicon and viral metagenomic analyses revealed that particular prokaryotes and prokaryotic viruses specifically increased in either CIF or HIF, indicating that taxonomic difference in bloom-forming phytoplankton promotes distinct dynamics of not only the prokaryotic community but also prokaryotic viruses. Furthermore, combining our microcosm experiments with publicly available environmental data mining, we identified both known and novel possible host-virus pairs. In particular, the growth of prokaryotes associating with phytoplanktonic organic matter, such as Bacteroidetes (Polaribacter and NS9 marine group), Vibrio spp., and Rhodobacteriales (Nereida and Planktomarina), was accompanied by an increase in viruses predicted to infect Bacteroidetes, Vibrio, and Rhodobacteriales, respectively. Collectively, our findings suggest that changes in bloom-forming species can be followed by an increase in a specific group of prokaryotes and their viruses and that elucidating these tripartite relationships among specific phytoplankton, prokaryotes, and prokaryotic viruses improves our understanding of coastal biogeochemical cycling in blooms.IMPORTANCEThe primary production during marine phytoplankton bloom and the consumption of the produced organic matter by heterotrophic prokaryotes significantly contribute to coastal biogeochemical cycles. While the activities of those heterotrophic prokaryotes are presumably affected by viral infection, the dynamics of their viruses during blooms are not fully understood. In this study, we experimentally demonstrated that intracellular fractions of taxonomically distinct bloom-forming phytoplankton species, the diatom Chaetoceros sp. and the raphidophycean alga Heterosigma akashiwo, promoted the growth of taxonomically different prokaryotes and prokaryotic viruses. Based on their dynamics and predicted hosts of those viruses, we succeeded in detecting already-known and novel possible host-virus pairs associating with either phytoplankton species. Altogether, we propose that the succession of bloom-forming phytoplankton would change the composition of the abundant prokaryotes, resulting in an increase in their viruses. These changes in viral composition, depending on bloom-forming species, would alter the dynamics and metabolism of prokaryotes, affecting biogeochemical cycling in blooms.
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Affiliation(s)
- Hiroaki Takebe
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kento Tominaga
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | | | | | - Keigo Yamamoto
- Research Institute of Environment, Agriculture and Fisheries, Osaka Prefecture, Osaka, Japan
| | - Ryoma Kamikawa
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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Du S, Wu Y, Ying H, Wu Z, Yang M, Chen F, Shao J, Liu H, Zhang Z, Zhao Y. Genome sequences of the first Autographiviridae phages infecting marine Roseobacter. Microb Genom 2024; 10. [PMID: 38630615 DOI: 10.1099/mgen.0.001240] [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] [Indexed: 04/19/2024] Open
Abstract
The ubiquitous and abundant marine phages play critical roles in shaping the composition and function of bacterial communities, impacting biogeochemical cycling in marine ecosystems. Autographiviridae is among the most abundant and ubiquitous phage families in the ocean. However, studies on the diversity and ecology of Autographiviridae phages in marine environments are restricted to isolates that infect SAR11 bacteria and cyanobacteria. In this study, ten new roseophages that infect marine Roseobacter strains were isolated from coastal waters. These new roseophages have a genome size ranging from 38 917 to 42 634 bp and G+C content of 44.6-50 %. Comparative genomics showed that they are similar to known Autographiviridae phages regarding gene content and architecture, thus representing the first Autographiviridae roseophages. Phylogenomic analysis based on concatenated conserved genes showed that the ten roseophages form three distinct subgroups within the Autographiviridae, and sequence analysis revealed that they belong to eight new genera. Finally, viromic read-mapping showed that these new Autographiviridae phages are widely distributed in global oceans, mostly inhabiting polar and estuarine locations. This study has expanded the current understanding of the genomic diversity, evolution and ecology of Autographiviridae phages and roseophages. We suggest that Autographiviridae phages play important roles in the mortality and community structure of roseobacters, and have broad ecological applications.
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Affiliation(s)
- Sen Du
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Ying Wu
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Hanqi Ying
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Zuqing Wu
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Mingyu Yang
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Jiabing Shao
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - He Liu
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Zefeng Zhang
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Yanlin Zhao
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, PR China
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, PR China
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Zhang H, Tan Y, Zhou Y, Liu J, Xia X. Light-dark fluctuated metabolic features of diazotrophic and non-diazotrophic cyanobacteria and their coexisting bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 910:168702. [PMID: 37992836 DOI: 10.1016/j.scitotenv.2023.168702] [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: 09/06/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023]
Abstract
Cyanobacteria, the most abundant photosynthetic organisms in oceans, are tightly associated with diverse microbiota. However, the relationships between heterotrophic bacteria and cyanobacteria, particularly the diazotrophic group, are not fully understood. Here, we compared diel gene expressions of N2 fixing cyanobacteria Crocosphaera watsonii WH0003 and non-diazotrophic Synechococcus sp. RS9902 and their associated bacteria using metatranscriptomics approach. WH0003 showed significant up-regulation of O2 restriction and oxidative phosphorylation related genes at nighttime due to large carbon and energy investments for active N2 fixation. In contrast, RS9902 had higher expression for those genes at daytime. The two cyanobacteria hosted distinct bacterial communities with clear separate substrate utilization niches to reduce competition. Light-dark partitioning of nutrient acquisition among the dominant bacterial groups likely contributed to the dynamic balance for community coexistence. Moreover, particle-attached (PA) bacteria in RS9902 largely expressed glycoside hydrolases to hydrolyze complex carbohydrate compounds, while free-living (FL) bacteria priorly assimilated soluble, diffusible molecules. Spatial partitioning of nutrient acquisition between PA and FL bacteria implied that location initially influenced metabolic features of host associated bacteria. Our results advance knowledge on light-dark regulated metabolic activities of diazotrophic and non-diazotrophic cyanobacteria, and provide new insights into the coexisting strategies of different bacterial groups.
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Affiliation(s)
- Hao Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yehui Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Youping Zhou
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jiaxing Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China..
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China..
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Liu Y, Brinkhoff T, Berger M, Poehlein A, Voget S, Paoli L, Sunagawa S, Amann R, Simon M. Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster. MICROBIOME 2023; 11:265. [PMID: 38007474 PMCID: PMC10675870 DOI: 10.1186/s40168-023-01644-5] [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: 06/12/2023] [Accepted: 08/07/2023] [Indexed: 11/27/2023]
Abstract
BACKGROUND The RCA (Roseobacter clade affiliated) cluster belongs to the family Roseobacteracea and represents a major Roseobacter lineage in temperate to polar oceans. Despite its prevalence and abundance, only a few genomes and one described species, Planktomarina temperata, exist. To gain more insights into our limited understanding of this cluster and its taxonomic and functional diversity and biogeography, we screened metagenomic datasets from the global oceans and reconstructed metagenome-assembled genomes (MAG) affiliated to this cluster. RESULTS The total of 82 MAGs, plus five genomes of isolates, reveal an unexpected diversity and novel insights into the genomic features, the functional diversity, and greatly refined biogeographic patterns of the RCA cluster. This cluster is subdivided into three genera: Planktomarina, Pseudoplanktomarina, and the most deeply branching Candidatus Paraplanktomarina. Six of the eight Planktomarina species have larger genome sizes (2.44-3.12 Mbp) and higher G + C contents (46.36-53.70%) than the four Pseudoplanktomarina species (2.26-2.72 Mbp, 42.22-43.72 G + C%). Cand. Paraplanktomarina is represented only by one species with a genome size of 2.40 Mbp and a G + C content of 45.85%. Three novel species of the genera Planktomarina and Pseudoplanktomarina are validly described according to the SeqCode nomenclature for prokaryotic genomes. Aerobic anoxygenic photosynthesis (AAP) is encoded in three Planktomarina species. Unexpectedly, proteorhodopsin (PR) is encoded in the other Planktomarina and all Pseudoplanktomarina species, suggesting that this light-driven proton pump is the most important mode of acquiring complementary energy of the RCA cluster. The Pseudoplanktomarina species exhibit differences in functional traits compared to Planktomarina species and adaptations to more resource-limited conditions. An assessment of the global biogeography of the different species greatly expands the range of occurrence and shows that the different species exhibit distinct biogeographic patterns. They partially reflect the genomic features of the species. CONCLUSIONS Our detailed MAG-based analyses shed new light on the diversification, environmental adaptation, and global biogeography of a major lineage of pelagic bacteria. The taxonomic delineation and validation by the SeqCode nomenclature of prominent genera and species of the RCA cluster may be a promising way for a refined taxonomic identification of major prokaryotic lineages and sublineages in marine and other prokaryotic communities assessed by metagenomics approaches. Video Abstract.
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Affiliation(s)
- Yanting Liu
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl Von Ossietzky Str. 9-11, 26129, Oldenburg, Germany.
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China.
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl Von Ossietzky Str. 9-11, 26129, Oldenburg, Germany.
| | - Martine Berger
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl Von Ossietzky Str. 9-11, 26129, Oldenburg, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Sonja Voget
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zurich, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zurich, Switzerland
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl Von Ossietzky Str. 9-11, 26129, Oldenburg, Germany.
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstr. 231, 26129, Oldenburg, Germany.
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Li SH, Kang I, Cho JC. Metabolic Versatility of the Family Halieaceae Revealed by the Genomics of Novel Cultured Isolates. Microbiol Spectr 2023; 11:e0387922. [PMID: 36916946 PMCID: PMC10100682 DOI: 10.1128/spectrum.03879-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/16/2023] [Indexed: 03/16/2023] Open
Abstract
The family Halieaceae (OM60/NOR5 clade) is a gammaproteobacterial group abundant and cosmopolitan in coastal seawaters and plays an important role in response to phytoplankton blooms. However, the ecophysiology of this family remains understudied because of the vast gap between phylogenetic diversity and cultured representatives. Here, using six pure cultured strains isolated from coastal seawaters, we performed in-depth genomic analyses to provide an overview of the phylogeny and metabolic capabilities of this family. The combined analyses of 16S rRNA genes, genome sequences, and functional genes relevant to taxonomy demonstrated that each strain represents a novel species. Notably, two strains belonged to the hitherto-uncultured NOR5-4 and NOR5-12 subclades. Metabolic reconstructions revealed that the six strains likely have aerobic chemo- or photoheterotrophic lifestyles; five of them possess genes for proteorhodopsin or aerobic anoxygenic phototrophy. The presence of blue- or green-tuned proteorhodopsin in Halieaceae suggested their ability to adapt to light conditions varying with depth or coastal-to-open ocean transition. In addition to the genes of anaplerotic CO2 fixation, genes encoding a complete reductive glycine pathway for CO2 fixation were found in three strains. Putative polysaccharide utilization loci were detected in three strains, suggesting the association with phytoplankton blooms. Read mapping of various metagenomes and metatranscriptomes showed that the six strains are widely distributed and transcriptionally active in marine environments. Overall, the six strains genomically characterized in this study expand the phylogenetic and metabolic diversity of Halieaceae and likely serve as a culture resource for investigating the ecophysiological features of this environmentally relevant bacterial group. IMPORTANCE Although the family Halieaceae (OM60/NOR5 clade) is an abundant and cosmopolitan clade widely found in coastal seas and involved in interactions with phytoplankton, a limited number of cultured isolates are available. In this study, we isolated six pure cultured Halieaceae strains from coastal seawaters and performed a comparative physiological and genomic analysis to give insights into the phylogeny and metabolic potential of this family. The cultured strains exhibited diverse metabolic potential by harboring genes for anaplerotic CO2 fixation, proteorhodopsin, and aerobic anoxygenic phototrophy. Polysaccharide utilization loci detected in some of these strains also indicated an association with phytoplankton blooms. The cultivation of novel strains of Halieaceae and their genomic characteristics largely expanded the phylogenetic and metabolic diversity, which is important for future ecophysiological studies.
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Affiliation(s)
- Shan-Hui Li
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, Republic of Korea
| | - Ilnam Kang
- Center for Molecular and Cell Biology, Inha University, Incheon, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, Republic of Korea
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Hollensteiner J, Wemheuer F, Schneider D, Pfeiffer B, Wemheuer B. Extraction of Total DNA and RNA from Marine Filter Samples and Generation of a Universal cDNA as Universal Template for Marker Gene Studies. Methods Mol Biol 2023; 2555:13-21. [PMID: 36306076 DOI: 10.1007/978-1-0716-2795-2_2] [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] [Indexed: 06/16/2023]
Abstract
Microbial communities play an important role in marine ecosystem processes. Although the number of studies targeting marker genes such as the 16S rRNA gene has increased during the last years, the vast majority of marine diversity are rather unexplored. Moreover, most studies focused on the entire microbial community and thus do not assess the active fraction of the microbial community. Here, we describe a detailed protocol for the simultaneous extraction of DNA and RNA from marine water samples and the generation of cDNA from the isolated RNA that can be used as a universal template in various marker gene studies.
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Affiliation(s)
| | - Franziska Wemheuer
- Institute of Microbiology and Genetics, Georg August University Göttingen, Göttingen, Germany
| | - Dominik Schneider
- Institute of Microbiology and Genetics, Georg August University Göttingen, Göttingen, Germany
| | - Birgit Pfeiffer
- Institute of Microbiology and Genetics, Georg August University Göttingen, Göttingen, Germany
| | - Bernd Wemheuer
- Institute of Microbiology and Genetics, Georg August University Göttingen, Göttingen, Germany.
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Kumar S, Raj VS, Ahmad A, Saini V. Amoxicillin modulates gut microbiota to improve short-term high-fat diet induced pathophysiology in mice. Gut Pathog 2022; 14:40. [PMID: 36229889 PMCID: PMC9563906 DOI: 10.1186/s13099-022-00513-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/02/2022] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND A high-fat diet (HFD) induced perturbation of gut microbiota is a major contributory factor to promote the pathophysiology of HFD-associated metabolic syndrome. The HFD could also increase the susceptibility to the microbial infections warranting the use of antibiotics which are independently capable of impacting both gut microbiota and metabolic syndrome. Further, the usage of antibiotics in individuals consuming HFD can impact mitochondrial function that can be associated with an elevated risk of chronic conditions like inflammatory bowel disease (IBD). Despite this high propensity to infections in individuals on HFD, the link between duration of HFD and antibiotic treatment, and its impact on diversity of the gut microbiome and features of metabolic syndrome is not well established. In this study, we have addressed these knowledge gaps by examining how the gut microbiota profile changes in HFD-fed mice receiving antibiotic intervention in the form of amoxicillin. We also determine whether antibiotic treatment in HFD-fed mice may adversely impact the ability of immune cells to clear microbial infections. METHODS AND RESULTS We have subjected mice to HFD and chow diet (CD) for 3 weeks, and a subset of these mice on both diets received antibiotic intervention in the form of amoxicillin in the 3rd week. Body weight and food intake were recorded for 3 weeks. After 21 days, all animals were weighted and sacrificed. Subsequently, these animals were evaluated for basic haemato-biochemical and histopathological attributes. We used 16S rRNA sequencing followed by bioinformatics analysis to determine changes in gut microbiota in these mice. We observed that a HFD, even for a short-duration, could successfully induce the partial pathophysiology typical of a metabolic syndrome, and substantially modulated the gut microbiota in mice. The short course of amoxicillin treatment to HFD-fed mice resulted in beneficial effects by significantly reducing fasting blood glucose and skewing the number of thrombocytes towards a normal range. Remarkably, we observed a significant remodelling of gut microbiota in amoxicillin-treated HFD-fed mice. Importantly, some gut microbes associated with improved insulin sensitivity and recovery from metabolic syndrome only appeared in amoxicillin-treated HFD-fed mice reinforcing the beneficial effects of antibiotic treatment in the HFD-associated metabolic syndrome. Moreover, we also observed the presence of gut-microbiota unique to amoxicillin-treated HFD-fed mice that are also known to improve the pathophysiology associated with metabolic syndrome. However, both CD-fed as well as HFD-fed mice receiving antibiotics showed an increase in intestinal pathogens as is typically observed for antibiotic treatment. Importantly though, infection studies with S. aureus and A. baumannii, revealed that macrophages isolated from amoxicillin-treated HFD-fed mice are comparable to those isolated from mice receiving only HFD or CD in terms of susceptibility, and progression of microbial infection. This finding clearly indicated that amoxicillin treatment does not introduce any additional deficits in the ability of macrophages to combat microbial infections. CONCLUSIONS Our results showed that amoxicillin treatment in HFD-fed mice exert a beneficial influence on the pathophysiological attributes of metabolic syndrome which correlates with a significant remodelling of gut microbiota. A novel observation was the increase in microbes known to improve insulin sensitivity following amoxicillin treatment during short-term intake of HFD. Even though there is a minor increase in gut-resistant intestinal pathogens in amoxicillin-treated groups, there is no adverse impact on macrophages with respect to their susceptibility and ability to control infections. Taken together, this study provides a proof of principle for the exploration of amoxicillin treatment as a potential therapy in the people affected with metabolic syndrome.
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Affiliation(s)
- Suresh Kumar
- National Institute of Biologicals, Ministry of Health & Family Welfare, Govt. of India, Noida, 201309, India.
| | - V Samuel Raj
- Center for Drug, Design, Discovery and Development (C4D), SRM University, Delhi-NCR, 131029, Sonepat, Haryana, India
| | - Ayaan Ahmad
- Laboratory of Infection Biology and Translational Research, Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Vikram Saini
- Laboratory of Infection Biology and Translational Research, Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India.
- Biosafety Laboratory-3, Centralized Core Research Facility (CCRF), All India Institute of Medical Sciences (AIIMS), New Delhi, India.
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Godet A, Fortier A, Bannier E, Coquery N, Val-Laillet D. Interactions between emotions and eating behaviors: Main issues, neuroimaging contributions, and innovative preventive or corrective strategies. Rev Endocr Metab Disord 2022; 23:807-831. [PMID: 34984602 DOI: 10.1007/s11154-021-09700-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/29/2021] [Indexed: 12/13/2022]
Abstract
Emotional eating is commonly defined as the tendency to (over)eat in response to emotion. Insofar as it involves the (over)consumption of high-calorie palatable foods, emotional eating is a maladaptive behavior that can lead to eating disorders, and ultimately to metabolic disorders and obesity. Emotional eating is associated with eating disorder subtypes and with abnormalities in emotion processing at a behavioral level. However, not enough is known about the neural pathways involved in both emotion processing and food intake. In this review, we provide an overview of recent neuroimaging studies, highlighting the brain correlates between emotions and eating behavior that may be involved in emotional eating. Interaction between neural and neuro-endocrine pathways (HPA axis) may be involved. In addition to behavioral interventions, there is a need for a holistic approach encompassing both neural and physiological levels to prevent emotional eating. Based on recent imaging, this review indicates that more attention should be paid to prefrontal areas, the insular and orbitofrontal cortices, and reward pathways, in addition to regions that play a major role in both the cognitive control of emotions and eating behavior. Identifying these brain regions could allow for neuromodulation interventions, including neurofeedback training, which deserves further investigation.
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Affiliation(s)
- Ambre Godet
- Nutrition Metabolisms and Cancer (NuMeCan), INRAE, INSERM, Univ Rennes, St Gilles, France
| | - Alexandra Fortier
- Nutrition Metabolisms and Cancer (NuMeCan), INRAE, INSERM, Univ Rennes, St Gilles, France
| | - Elise Bannier
- CRNS, INSERM, IRISA, INRIA, Univ Rennes, Empenn Rennes, France
- Radiology Department, Rennes University Hospital, Rennes, France
| | - Nicolas Coquery
- Nutrition Metabolisms and Cancer (NuMeCan), INRAE, INSERM, Univ Rennes, St Gilles, France
| | - David Val-Laillet
- Nutrition Metabolisms and Cancer (NuMeCan), INRAE, INSERM, Univ Rennes, St Gilles, France.
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Wang M, Wang H, Wang P, Fu HH, Li CY, Qin QL, Liang Y, Wang M, Chen XL, Zhang YZ, Zhang W. TCA cycle enhancement and uptake of monomeric substrates support growth of marine Roseobacter at low temperature. Commun Biol 2022; 5:705. [PMID: 35835984 PMCID: PMC9283371 DOI: 10.1038/s42003-022-03631-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 06/24/2022] [Indexed: 11/29/2022] Open
Abstract
Members of the marine Roseobacter group are ubiquitous in global oceans, but their cold-adaptive strategies have barely been studied. Here, as represented by Loktanella salsilacus strains enriched in polar regions, we firstly characterized the metabolic features of a cold-adapted Roseobacter by multi-omics, enzyme activities, and carbon utilization procedures. Unlike in most cold-adapted microorganisms, the TCA cycle is enhanced by accumulating more enzyme molecules, whereas genes for thiosulfate oxidation, sulfate reduction, nitrate reduction, and urea metabolism are all expressed at lower abundance when L. salsilacus was growing at 5 °C in comparison with higher temperatures. Moreover, a carbon-source competition experiment has evidenced the preferential use of glucose rather than sucrose at low temperature. This selective utilization is likely to be controlled by the carbon source uptake and transformation steps, which also reflects an economic calculation balancing energy production and functional plasticity. These findings provide a mechanistic understanding of how a Roseobacter member and possibly others as well counteract polar constraints. The metabolic adaptation of Loktanella salsilacus strains to cold involves an increase of enzymes involved in the TCA cycle and preferential use of glucose rather than sucrose at low temperature, providing insights into how Roseobacter adapts in polar regions.
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Affiliation(s)
- Meng Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.,Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China.,State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Huan Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Peng Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Hui-Hui Fu
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Chun-Yang Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Qi-Long Qin
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.,State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Yantao Liang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Min Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266373, China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China. .,Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China. .,State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China. .,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266373, China.
| | - Weipeng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
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11
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Zhao G, He H, Wang H, Liang Y, Guo C, Shao H, Jiang Y, Wang M. Variations in Marine Bacterial and Archaeal Communities during an Ulva prolifera Green Tide in Coastal Qingdao Areas. Microorganisms 2022; 10:microorganisms10061204. [PMID: 35744722 PMCID: PMC9228619 DOI: 10.3390/microorganisms10061204] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 11/23/2022] Open
Abstract
Green tides caused by Ulva prolifera occur annually in the Yellow Sea, potentially influencing the marine microorganisms. Here, we focused on the variations in marine bacterial and archaeal communities during an U. prolifera green tide in coastal Qingdao areas with Illumina high-throughput sequencing analysis. Our results revealed that the diversity and structure of bacterial and archaeal communities, as well as the organization and structure of microbial co-occurrence networks, varied during the green tide. The decline phase may be favorable to the bacterial and archaeal diversity and richness. The bacterial community, as well as the archaeal community, showed clear variations between the outbreak and decline phases. A simpler and less connected microbial co-occurrence network was observed during the outbreak phase compared with the decline phase. Flavobacteriales and Rhodobacterales separately dominated the bacterial community during the outbreak and decline phase, and Marine Group II (MGII) dominated the archaeal community during the green tide. Combined with microbial co-occurrence network analysis, Flavobacteriales, Rhodobacterales and MGII may be important organisms during the green tide. Temperature, chlorophyll a content and salinity may have an important impact on the variations in bacterial and archaeal communities during the green tide.
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Affiliation(s)
- Guihua Zhao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
| | - Hui He
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
- Correspondence: (H.H.); (M.W.)
| | - Hualong Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
| | - Cui Guo
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
| | - Yong Jiang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
- The Affiliated Hospital of Qingdao University, Qingdao 266000, China
- OUC-UMT Joint Academic Centre for Marine Studies, Qingdao 266003, China
- Correspondence: (H.H.); (M.W.)
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12
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Dynamics of Planktonic Microbial Community Associated with Saccharina japonica Seedling. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10060726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Macroalgae interact with planktonic microbes in seawater. It remains unclear how planktonic microbes interact with the environment and each other during the cultivation processes of commercially important algal species. Such an interaction is important for developing environment-friendly mariculture methods. In this study, the dynamics of the planktonic microbial community associated with Saccharina japonica were profiled during the seedling production stage, with its environmental correlation and co-occurrence pattern determined simultaneously. Microbial richness increased and positively correlated with light intensity and contents of NO3− and PO43−. A clear temporal succession of the community was observed, which coincided with changes in light intensity, dissolved oxygen, pH, and NO3− content. α-Proteobacteria, Bacteroidetes, γ-Proteobacteria, and the genera prevalent in these taxa dominated the planktonic microbial community, and their relative abundance temporally changed. A profile of keystone taxa that is different from prevalent genera was identified based on betweenness centrality scores. A modularized co-occurrence pattern was determined, in addition to intensified species-to-species interactions at the core of the co-occurrence network. These findings expanded our cognization of the planktonic microbial community in response to S. japonica cultivation.
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13
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Availability of vitamin B 12 and its lower ligand intermediate α-ribazole impact prokaryotic and protist communities in oceanic systems. THE ISME JOURNAL 2022; 16:2002-2014. [PMID: 35585186 PMCID: PMC9296465 DOI: 10.1038/s41396-022-01250-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 04/28/2022] [Accepted: 05/06/2022] [Indexed: 01/22/2023]
Abstract
Genome analyses predict that the cofactor cobalamin (vitamin B12, called B12 herein) is produced by only one-third of all prokaryotes but almost all encode at least one B12-dependent enzyme, in most cases methionine synthase. This implies that the majority of prokaryotes relies on exogenous B12 supply and interacts with producers. B12 consists of a corrin ring centred around a cobalt ion and the lower ligand 5’6-dimethylbenzimidazole (DMB). It has never been tested whether availability of this pivotal cofactor, DMB or its intermediate α-ribazole affect growth and composition of prokaryotic microbial communities. Here we show that in the subtropical, equatorial and polar frontal Pacific Ocean supply of B12 and α-ribazole enhances heterotrophic prokaryotic production and alters the composition of prokaryotic and heterotrophic protist communities. In the polar frontal Pacific, the SAR11 clade and Oceanospirillales increased their relative abundances upon B12 supply. In the subtropical Pacific, Oceanospirillales increased their relative abundance upon B12 supply as well but also downregulated the transcription of the btuB gene, encoding the outer membrane permease for B12. Surprisingly, Prochlorococcus, known to produce pseudo-B12 and not B12, exhibited significant upregulation of genes encoding key proteins of photosystem I + II, carbon fixation and nitrate reduction upon B12 supply in the subtropical Pacific. These findings show that availability of B12 and α-ribazole affect growth and composition of prokaryotic and protist communities in oceanic systems thus revealing far-reaching consequences of methionine biosynthesis and other B12-dependent enzymatic reactions on a community level.
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14
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O'Brien J, McParland EL, Bramucci AR, Siboni N, Ostrowski M, Kahlke T, Levine NM, Brown MV, van de Kamp J, Bodrossy L, Messer LF, Petrou K, Seymour JR. Biogeographical and seasonal dynamics of the marine Roseobacter community and ecological links to DMSP-producing phytoplankton. ISME COMMUNICATIONS 2022; 2:16. [PMID: 37938744 PMCID: PMC9723663 DOI: 10.1038/s43705-022-00099-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 11/09/2023]
Abstract
Ecological interactions between marine bacteria and phytoplankton play a pivotal role in governing the ocean's major biogeochemical cycles. Among these, members of the marine Roseobacter Group (MRG) can establish mutualistic relationships with phytoplankton that are, in part, maintained by exchanges of the organosulfur compound, dimethylsulfoniopropionate (DMSP). Yet most of what is known about these interactions has been derived from culture-based laboratory studies. To investigate temporal and spatial co-occurrence patterns between members of the MRG and DMSP-producing phytoplankton we analysed 16S and 18S rRNA gene amplicon sequence variants (ASVs) derived from 5 years of monthly samples from seven environmentally distinct Australian oceanographic time-series. The MRG and DMSP-producer communities often displayed contemporaneous seasonality, which was greater in subtropical and temperate environments compared to tropical environments. The relative abundance of both groups varied latitudinally, displaying a poleward increase, peaking (MRG at 33% of total bacteria, DMSP producers at 42% of eukaryotic phototrophs) during recurrent spring-summer phytoplankton blooms in the most temperate site (Maria Island, Tasmania). Network analysis identified 20,140 significant positive correlations between MRG ASVs and DMSP producers and revealed that MRGs exhibit significantly stronger correlations to high DMSP producers relative to other DMSP-degrading bacteria (Pelagibacter, SAR86 and Actinobacteria). By utilising the power of a continental network of oceanographic time-series, this study provides in situ confirmation of interactions found in laboratory studies and demonstrates that the ecological dynamics of an important group of marine bacteria are shaped by the production of an abundant and biogeochemically significant organosulfur compound.
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Affiliation(s)
- James O'Brien
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia.
- School of Life Sciences, University of Technology Sydney, Broadway, NSW, Australia.
| | - Erin L McParland
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Anna R Bramucci
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia
| | - Nachshon Siboni
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia
| | - Martin Ostrowski
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia
| | - Tim Kahlke
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia
| | - Naomi M Levine
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Mark V Brown
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | | | | | - Lauren F Messer
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Katherina Petrou
- School of Life Sciences, University of Technology Sydney, Broadway, NSW, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia.
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15
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Assessment of Hydrocarbon Degradation Potential in Microbial Communities in Arctic Sea Ice. Microorganisms 2022; 10:microorganisms10020328. [PMID: 35208784 PMCID: PMC8879337 DOI: 10.3390/microorganisms10020328] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 02/04/2023] Open
Abstract
The anthropogenic release of oil hydrocarbons into the cold marine environment is an increasing concern due to the elevated usage of sea routes and the exploration of new oil drilling sites in Arctic areas. The aim of this study was to evaluate prokaryotic community structures and the genetic potential of hydrocarbon degradation in the metagenomes of seawater, sea ice, and crude oil encapsulating the sea ice of the Norwegian fjord, Ofotfjorden. Although the results indicated substantial differences between the structure of prokaryotic communities in seawater and sea ice, the crude oil encapsulating sea ice (SIO) showed increased abundances of many genera-containing hydrocarbon-degrading organisms, including Bermanella, Colwellia, and Glaciecola. Although the metagenome of seawater was rich in a variety of hydrocarbon degradation-related functional genes (HDGs) associated with the metabolism of n-alkanes, and mono- and polyaromatic hydrocarbons, most of the normalized gene counts were highest in the clean sea ice metagenome, whereas in SIO, these counts were the lowest. The long-chain alkane degradation gene almA was detected from all the studied metagenomes and its counts exceeded ladA and alkB counts in both sea ice metagenomes. In addition, almA was related to the most diverse group of prokaryotic genera. Almost all 18 good- and high-quality metagenome-assembled genomes (MAGs) had diverse HDGs profiles. The MAGs recovered from the SIO metagenome belonged to the abundant taxa, such as Glaciecola, Bermanella, and Rhodobacteracea, in this environment. The genera associated with HDGs were often previously known as hydrocarbon-degrading genera. However, a substantial number of new associations, either between already known hydrocarbon-degrading genera and new HDGs or between genera not known to contain hydrocarbon degraders and multiple HDGs, were found. The superimposition of the results of comparing HDG associations with taxonomy, the HDG profiles of MAGs, and the full genomes of organisms in the KEGG database suggest that the found relationships need further investigation and verification.
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16
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Isaac A, Francis B, Amann RI, Amin SA. Tight Adherence (Tad) Pilus Genes Indicate Putative Niche Differentiation in Phytoplankton Bloom Associated Rhodobacterales. Front Microbiol 2021; 12:718297. [PMID: 34447362 PMCID: PMC8383342 DOI: 10.3389/fmicb.2021.718297] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/19/2021] [Indexed: 11/14/2022] Open
Abstract
The multiple interactions of phytoplankton and bacterioplankton are central for our understanding of aquatic environments. A prominent example of those is the consistent association of diatoms with Alphaproteobacteria of the order Rhodobacterales. These photoheterotrophic bacteria have traditionally been described as generalists that scavenge dissolved organic matter. Many observations suggest that members of this clade are specialized in colonizing the microenvironment of diatom cells, known as the phycosphere. However, the molecular mechanisms that differentiate Rhodobacterales generalists and phycosphere colonizers are poorly understood. We investigated Rhodobacterales in the North Sea during the 2010–2012 spring blooms using a time series of 38 deeply sequenced metagenomes and 10 metaproteomes collected throughout these events. Rhodobacterales metagenome assembled genomes (MAGs) were recurrently abundant. They exhibited the highest gene enrichment and protein expression of small-molecule transporters, such as monosaccharides, thiamine and polyamine transporters, and anaplerotic pathways, such as ethylmalonyl and propanoyl-CoA metabolic pathways, all suggestive of a generalist lifestyle. Metaproteomes indicated that the species represented by these MAGs were the dominant suppliers of vitamin B12 during the blooms, concomitant with a significant enrichment of genes related to vitamin B12 biosynthesis suggestive of association with diatom phycospheres. A closer examination of putative generalists and colonizers showed that putative generalists had persistently higher relative abundance throughout the blooms and thus produced more than 80% of Rhodobacterales transport proteins, suggesting rapid growth. In contrast, putative phycosphere colonizers exhibited large fluctuation in relative abundance across the different blooms and correlated strongly with particular diatom species that were dominant during the blooms each year. The defining feature of putative phycosphere colonizers is the presence of the tight adherence (tad) gene cluster, which is responsible for the assembly of adhesive pili that presumably enable attachment to diatom hosts. In addition, putative phycosphere colonizers possessed higher prevalence of secondary metabolite biosynthetic gene clusters, particularly homoserine lactones, which can regulate bacterial attachment through quorum sensing. Altogether, these findings suggest that while many members of Rhodobacterales are competitive during diatom blooms, only a subset form close associations with diatoms by colonizing their phycospheres.
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Affiliation(s)
- Ashley Isaac
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Ben Francis
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Shady A Amin
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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17
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Feng X, Chu X, Qian Y, Henson MW, Lanclos VC, Qin F, Barnes S, Zhao Y, Thrash JC, Luo H. Mechanisms driving genome reduction of a novel Roseobacter lineage. ISME JOURNAL 2021; 15:3576-3586. [PMID: 34145391 DOI: 10.1038/s41396-021-01036-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 01/21/2023]
Abstract
Members of the marine Roseobacter group are key players in the global carbon and sulfur cycles. While over 300 species have been described, only 2% possess reduced genomes (mostly 3-3.5 Mbp) compared to an average roseobacter (>4 Mbp). These taxonomic minorities are phylogenetically diverse but form a Pelagic Roseobacter Cluster (PRC) at the genome content level. Here, we cultivated eight isolates constituting a novel Roseobacter lineage which we named 'CHUG'. Metagenomic and metatranscriptomic read recruitment analyses showed that CHUG members are globally distributed and active in marine pelagic environments. CHUG members possess some of the smallest genomes (~2.6 Mb) among all known roseobacters, but they do not exhibit canonical features of typical bacterioplankton lineages theorized to have undergone genome streamlining processes, like higher coding density, fewer paralogues and rarer pseudogenes. While CHUG members form a genome content cluster with traditional PRC members, they show important differences. Unlike other PRC members, neither the relative abundances of CHUG members nor their relative gene expression levels are correlated with chlorophyll a concentration across the global samples. CHUG members cannot utilize most phytoplankton-derived metabolites or synthesize vitamin B12, a key metabolite mediating the roseobacter-phytoplankton interactions. This combination of features is evidence for the hypothesis that CHUG members may have evolved a free-living lifestyle decoupled from phytoplankton. This ecological transition was accompanied by the loss of signature genes involved in roseobacter-phytoplankton symbiosis, suggesting that relaxation of purifying selection owing to lifestyle shift is likely an important driver of genome reduction in CHUG.
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Affiliation(s)
- Xiaoyuan Feng
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, SAR, Hong Kong.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Xiao Chu
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, SAR, Hong Kong
| | - Yang Qian
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, SAR, Hong Kong
| | - Michael W Henson
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.,Department of Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - V Celeste Lanclos
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Fang Qin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Shelby Barnes
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yanlin Zhao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, SAR, Hong Kong. .,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.
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18
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Rihtman B, Puxty RJ, Hapeshi A, Lee YJ, Zhan Y, Michniewski S, Waterfield NR, Chen F, Weigele P, Millard AD, Scanlan DJ, Chen Y. A new family of globally distributed lytic roseophages with unusual deoxythymidine to deoxyuridine substitution. Curr Biol 2021; 31:3199-3206.e4. [PMID: 34033748 PMCID: PMC8323127 DOI: 10.1016/j.cub.2021.05.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/19/2021] [Accepted: 05/10/2021] [Indexed: 01/27/2023]
Abstract
Marine bacterial viruses (bacteriophages) are abundant biological entities that are vital for shaping microbial diversity, impacting marine ecosystem function, and driving host evolution.1, 2, 3 The marine roseobacter clade (MRC) is a ubiquitous group of heterotrophic bacteria4,5 that are important in the elemental cycling of various nitrogen, sulfur, carbon, and phosphorus compounds.6, 7, 8, 9, 10 Bacteriophages infecting MRC (roseophages) have thus attracted much attention and more than 30 roseophages have been isolated,11, 12, 13 the majority of which belong to the N4-like group (Podoviridae family) or the Chi-like group (Siphoviridae family), although ssDNA-containing roseophages are also known.14 In our attempts to isolate lytic roseophages, we obtained two new phages (DSS3_VP1 and DSS3_PM1) infecting the model MRC strain Ruegeria pomeroyi DSS-3. Here, we show that not only do these phages have unusual substitution of deoxythymidine with deoxyuridine (dU) in their DNA, but they are also phylogenetically distinct from any currently known double-stranded DNA bacteriophages, supporting the establishment of a novel family (“Naomiviridae”). These dU-containing phages possess DNA that is resistant to the commonly used library preparation method for metagenome sequencing, which may have caused significant underestimation of their presence in the environment. Nevertheless, our analysis of Tara Ocean metagenome datasets suggests that these unusual bacteriophages are of global importance and more diverse than other well-known bacteriophages, e.g., the Podoviridae in the oceans, pointing to an overlooked role for these novel phages in the environment. Two new roseophages isolated from the marine environment They have an unusual deoxythymidine to deoxyuridine substitution in their genomes These dU genomes are resistant to a common method of metagenome library preparation These phages represent a new family and are globally distributed in the oceans
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Affiliation(s)
- Branko Rihtman
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
| | - Richard J Puxty
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Alexia Hapeshi
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Yan-Jiun Lee
- Research Department, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Yuanchao Zhan
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 E. Pratt Street, Baltimore, MD 21202, USA
| | - Slawomir Michniewski
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Nicholas R Waterfield
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 E. Pratt Street, Baltimore, MD 21202, USA
| | - Peter Weigele
- Research Department, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Andrew D Millard
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Yin Chen
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
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19
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Rahlff J, Stolle C, Giebel HA, Mustaffa NIH, Wurl O, P R Herlemann D. Sea foams are ephemeral hotspots for distinctive bacterial communities contrasting sea-surface microlayer and underlying surface water. FEMS Microbiol Ecol 2021; 97:6149170. [PMID: 33625484 PMCID: PMC8012113 DOI: 10.1093/femsec/fiab035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/22/2021] [Indexed: 12/17/2022] Open
Abstract
The occurrence of foams at oceans’ surfaces is patchy and generally short-lived, but a detailed understanding of bacterial communities inhabiting sea foams is lacking. Here, we investigated how marine foams differ from the sea-surface microlayer (SML), a <1-mm-thick layer at the air–sea interface, and underlying water from 1 m depth. Samples of sea foams, SML and underlying water collected from the North Sea and Timor Sea indicated that foams were often characterized by a high abundance of small eukaryotic phototrophic and prokaryotic cells as well as a high concentration of surface-active substances (SAS). Amplicon sequencing of 16S rRNA (gene) revealed distinctive foam bacterial communities compared with SML and underlying water, with high abundance of Gammaproteobacteria. Typical SML dwellers such as Pseudoalteromonas and Vibrio were highly abundant, active foam inhabitants and thus might enhance foam formation and stability by producing SAS. Despite a clear difference in the overall bacterial community composition between foam and SML, the presence of SML bacteria in foams supports the previous assumption that foam is strongly influenced by the SML. We conclude that active and abundant bacteria from interfacial habitats potentially contribute to foam formation and stability, carbon cycling and air–sea exchange processes in the ocean.
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Affiliation(s)
- Janina Rahlff
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Schleusenstraße 1, 26382 Wilhelmshaven, Germany
| | - Christian Stolle
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Schleusenstraße 1, 26382 Wilhelmshaven, Germany.,Leibniz Institute for Baltic Sea Research (IOW), Seestraße 15, 18119 Rostock, Germany
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
| | - Nur Ili Hamizah Mustaffa
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Schleusenstraße 1, 26382 Wilhelmshaven, Germany
| | - Oliver Wurl
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Schleusenstraße 1, 26382 Wilhelmshaven, Germany
| | - Daniel P R Herlemann
- Leibniz Institute for Baltic Sea Research (IOW), Seestraße 15, 18119 Rostock, Germany.,Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5, Tartu 51006, Estonia
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Han Y, Jiao N, Zhang Y, Zhang F, He C, Liang X, Cai R, Shi Q, Tang K. Opportunistic bacteria with reduced genomes are effective competitors for organic nitrogen compounds in coastal dinoflagellate blooms. MICROBIOME 2021; 9:71. [PMID: 33762013 PMCID: PMC7992965 DOI: 10.1186/s40168-021-01022-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/02/2021] [Indexed: 05/29/2023]
Abstract
BACKGROUND Phytoplankton blooms are frequent events in coastal areas and increase the production of organic matter that initially shapes the growth of opportunistic heterotrophic bacteria. However, it is unclear how these opportunists are involved in the transformation of dissolved organic matter (DOM) when blooms occur and the subsequent impacts on biogeochemical cycles. RESULTS We used a combination of genomic, proteomic, and metabolomic approaches to study bacterial diversity, genome traits, and metabolic responses to assess the source and lability of DOM in a spring coastal bloom of Akashiwo sanguinea. We identified molecules that significantly increased during bloom development, predominantly belonging to amino acids, dipeptides, lipids, nucleotides, and nucleosides. The opportunistic members of the bacterial genera Polaribacter, Lentibacter, and Litoricola represented a significant proportion of the free-living and particle-associated bacterial assemblages during the stationary phase of the bloom. Polaribacter marinivivus, Lentibacter algarum, and Litoricola marina were isolated and their genomes exhibited streamlining characterized by small genome size and low GC content and non-coding densities, as well as a smaller number of transporters and peptidases compared to closely related species. However, the core proteomes identified house-keeping functions, such as various substrate transporters, peptidases, motility, chemotaxis, and antioxidants, in response to bloom-derived DOM. We observed a unique metabolic signature for the three species in the utilization of multiple dissolved organic nitrogen compounds. The metabolomic data showed that amino acids and dipeptides (such as isoleucine and proline) were preferentially taken up by P. marinivivus and L. algarum, whereas nucleotides and nucleosides (such as adenosine and purine) were preferentially selected by L. marina. CONCLUSIONS The results suggest that the enriched DOM in stationary phase of phytoplankton bloom is a result of ammonium depletion. This environment drives genomic streamlining of opportunistic bacteria to exploit their preferred nitrogen-containing compounds and maintain nutrient cycling. Video abstract.
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Affiliation(s)
- Yu Han
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Fan Zhang
- Department of Molecular Virology & Microbiology, Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (Beijing), Beijing, 102249, People's Republic of China
| | - Xuejiao Liang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Ruanhong Cai
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (Beijing), Beijing, 102249, People's Republic of China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China.
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21
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Samylina OS, Rusanov II, Tarnovetskii IY, Yakushev EV, Grinko AA, Zakharova EE, Merkel AY, Kanapatskiy TA, Semiletov IP, Pimenov NV. On the Possibility of Aerobic Methane Production by Pelagic Microbial Communities of the Laptev Sea. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721020119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Abstract—
The taxonomic diversity and metabolic activity of microbial communities in the Laptev Sea water column above and outside the methane seep field were studied. The concentrations of dissolved methane in the water column at both stations were comparable until the depth of the pycnocline (25 m). At this depth, local methane maxima were recorded, with the highest concentration (116 nM CH4) found at the station outside the methane seep field. Results of the 16S rRNA gene sequencing and measurements of the rates of hydrogenotrophic methanogenesis indicated the absence of methanogenesis caused by the methanogenic archaea in the pycnocline and in other horizons of the water column. The 16S rRNA-based analysis of microbial phylogenetic diversity, as well as radiotracer analysis of the rates of primary production (PP), dark CO2 assimilation (DCA), and methane oxidation (MO), indicated the functioning of a diverse community of pelagic microorganisms capable of transforming a wide range of organic compounds under oligotrophic conditions of the Arctic basin. Hydrochemical prerequisites and possible microbial agents of aerobic methane production via demethylation of methylphosphonate and decomposition of dimethylsulfoniopropionate using dissolved organic matter synthesized in the PP, DCA, and MO processes are discussed.
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22
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Silvano E, Yang M, Wolterink M, Giebel HA, Simon M, Scanlan DJ, Zhao Y, Chen Y. Lipidomic Analysis of Roseobacters of the Pelagic RCA Cluster and Their Response to Phosphorus Limitation. Front Microbiol 2021; 11:552135. [PMID: 33408696 PMCID: PMC7779409 DOI: 10.3389/fmicb.2020.552135] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 11/25/2020] [Indexed: 01/15/2023] Open
Abstract
The marine roseobacter-clade affiliated cluster (RCA) represents one of the most abundant groups of bacterioplankton in the global oceans, particularly in temperate and sub-polar regions. They play a key role in the biogeochemical cycling of various elements and are important players in oceanic climate-active trace gas metabolism. In contrast to copiotrophic roseobacter counterparts such as Ruegeria pomeroyi DSS-3 and Phaeobacter sp. MED193, RCA bacteria are truly pelagic and have smaller genomes. We have previously shown that RCA bacteria do not appear to encode the PlcP-mediated lipid remodeling pathway, whereby marine heterotrophic bacteria remodel their membrane lipid composition in response to phosphorus (P) stress by substituting membrane glycerophospholipids with alternative glycolipids or betaine lipids. In this study, we report lipidomic analysis of six RCA isolates. In addition to the commonly found glycerophospholipids such as phosphatidylglycerol (PG) and phosphatidylethanolamine (PE), RCA bacteria synthesize a relatively uncommon phospholipid, acylphosphatidylglycerol, which is not found in copiotrophic roseobacters. Instead, like the abundant SAR11 clade, RCA bacteria upregulate ornithine lipid biosynthesis in response to P stress, suggesting a key role of this aminolipid in the adaptation of marine heterotrophs to oceanic nutrient limitation.
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Affiliation(s)
- Eleonora Silvano
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Mingyu Yang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mathias Wolterink
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Yanlin Zhao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
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23
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Liu Y, Blain S, Crispi O, Rembauville M, Obernosterer I. Seasonal dynamics of prokaryotes and their associations with diatoms in the Southern Ocean as revealed by an autonomous sampler. Environ Microbiol 2020; 22:3968-3984. [PMID: 32755055 DOI: 10.1111/1462-2920.15184] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/10/2020] [Accepted: 08/01/2020] [Indexed: 11/29/2022]
Abstract
The Southern Ocean remains one of the least explored marine environments. The investigation of temporal microbial dynamics has thus far been hampered by the limited access to this remote ocean. We present here high-resolution seasonal observations of the prokaryotic community composition during phytoplankton blooms induced by natural iron fertilization. A total of 18 seawater samples were collected by a moored remote autonomous sampler over 4 months at 5-11 day intervals in offshore surface waters (central Kerguelen Plateau). Illumina sequencing of the 16S rRNA gene revealed that among the most abundant amplicon sequence variants, SAR92 and Aurantivirga were the first bloom responders, Pseudomonadaceae, Nitrincolaceae and Polaribacter had successive peaks during the spring bloom decline, and Amylibacter increased in relative abundance later in the season. SAR11 and SUP05 were abundant prior to and after the blooms. Using network analysis, we identified two groups of diatoms representative of the spring and summer bloom that had opposite correlation patterns with prokaryotic taxa. Our study provides the first seasonal picture of microbial community dynamics in the open Southern Ocean and thereby offers biological insights to the cycling of carbon and iron, and to an important puzzling issue that is the modest nitrate decrease associated to iron fertilization.
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Affiliation(s)
- Yan Liu
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Banyuls-sur-Mer, France.,College of Marine Life Sciences, Ocean University of China, Qingdao, China.,School of Life Sciences, Ludong University, Yantai, China
| | - Stéphane Blain
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Banyuls-sur-Mer, France
| | - Olivier Crispi
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Banyuls-sur-Mer, France
| | - Mathieu Rembauville
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Banyuls-sur-Mer, France
| | - Ingrid Obernosterer
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Banyuls-sur-Mer, France
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24
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Podell S, Blanton JM, Oliver A, Schorn MA, Agarwal V, Biggs JS, Moore BS, Allen EE. A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes. MICROBIOME 2020; 8:97. [PMID: 32576248 PMCID: PMC7313196 DOI: 10.1186/s40168-020-00877-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 05/28/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND Marine sponges and their microbiomes contribute significantly to carbon and nutrient cycling in global reefs, processing and remineralizing dissolved and particulate organic matter. Lamellodysidea herbacea sponges obtain additional energy from abundant photosynthetic Hormoscilla cyanobacterial symbionts, which also produce polybrominated diphenyl ethers (PBDEs) chemically similar to anthropogenic pollutants of environmental concern. Potential contributions of non-Hormoscilla bacteria to Lamellodysidea microbiome metabolism and the synthesis and degradation of additional secondary metabolites are currently unknown. RESULTS This study has determined relative abundance, taxonomic novelty, metabolic capacities, and secondary metabolite potential in 21 previously uncharacterized, uncultured Lamellodysidea-associated microbial populations by reconstructing near-complete metagenome-assembled genomes (MAGs) to complement 16S rRNA gene amplicon studies. Microbial community compositions aligned with sponge host subgroup phylogeny in 16 samples from four host clades collected from multiple sites in Guam over a 3-year period, including representatives of Alphaproteobacteria, Gammaproteobacteria, Oligoflexia, and Bacteroidetes as well as Cyanobacteria (Hormoscilla). Unexpectedly, microbiomes from one host clade also included Cyanobacteria from the prolific secondary metabolite-producer genus Prochloron, a common tunicate symbiont. Two novel Alphaproteobacteria MAGs encoded pathways diagnostic for methylotrophic metabolism as well as type III secretion systems, and have been provisionally assigned to a new order, designated Candidatus Methylospongiales. MAGs from other taxonomic groups encoded light-driven energy production pathways using not only chlorophyll, but also bacteriochlorophyll and proteorhodopsin. Diverse heterotrophic capabilities favoring aerobic versus anaerobic conditions included pathways for degrading chitin, eukaryotic extracellular matrix polymers, phosphonates, dimethylsulfoniopropionate, trimethylamine, and benzoate. Genetic evidence identified an aerobic catabolic pathway for halogenated aromatics that may enable endogenous PBDEs to be used as a carbon and energy source. CONCLUSIONS The reconstruction of high-quality MAGs from all microbial taxa comprising greater than 0.1% of the sponge microbiome enabled species-specific assignment of unique metabolic features that could not have been predicted from taxonomic data alone. This information will promote more representative models of marine invertebrate microbiome contributions to host bioenergetics, the identification of potential new sponge parasites and pathogens based on conserved metabolic and physiological markers, and a better understanding of biosynthetic and degradative pathways for secondary metabolites and halogenated compounds in sponge-associated microbiota. Video Abstract.
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Affiliation(s)
- Sheila Podell
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Jessica M Blanton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Aaron Oliver
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Michelle A Schorn
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jason S Biggs
- University of Guam Marine Laboratory, UoG Station, Mangilao, GU, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Eric E Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
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25
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Lemonnier C, Perennou M, Eveillard D, Fernandez-Guerra A, Leynaert A, Marié L, Morrison HG, Memery L, Paillard C, Maignien L. Linking Spatial and Temporal Dynamic of Bacterioplankton Communities With Ecological Strategies Across a Coastal Frontal Area. FRONTIERS IN MARINE SCIENCE 2020. [DOI: 10.3389/fmars.2020.00376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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26
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Giebel HA, Wolterink M, Brinkhoff T, Simon M. Complementary energy acquisition via aerobic anoxygenic photosynthesis and carbon monoxide oxidation by Planktomarina temperata of the Roseobacter group. FEMS Microbiol Ecol 2020; 95:5437672. [PMID: 31055603 DOI: 10.1093/femsec/fiz050] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 04/05/2019] [Indexed: 02/06/2023] Open
Abstract
In marine pelagic ecosystems energy is often the limiting factor for growth of heterotrophic bacteria. Aerobic anoxygenic photosynthesis (AAP) and oxidation of carbon monoxide (CO) are modes to acquire complementary energy, but their significance in abundant and characteristic pelagic marine bacteria has not been well studied. In long-term batch culture experiments we found that Planktomarina temperata RCA23, representing the largest and most prominent subcluster of the Roseobacter group, maintains 2-3-fold higher cell numbers in the stationary and declining phase when grown in a light-dark cycle relative to dark conditions. Light enables P. temperata to continue to replicate its DNA during the stationary phase relative to a dark control such that when reinoculated into fresh medium growth resumed two days earlier than in control cultures. In cultures grown in the dark and supplemented with CO, cell numbers in the stationary phase remained significantly higher than in an unsupplemented control. Furthermore, repeated spiking with CO until day 372 resulted in significant CO consumption relative to an unsupplemented control. P. temperata represents a prominent marine pelagic bacterium for which AAP and CO consumption, to acquire complementary energy, have been documented.
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Affiliation(s)
- Helge-Ansgar Giebel
- Institute of Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Mathias Wolterink
- Institute of Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Thorsten Brinkhoff
- Institute of Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Meinhard Simon
- Institute of Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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27
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Alonso-Sáez L, Morán XAG, González JM. Transcriptional Patterns of Biogeochemically Relevant Marker Genes by Temperate Marine Bacteria. Front Microbiol 2020; 11:465. [PMID: 32265888 PMCID: PMC7098952 DOI: 10.3389/fmicb.2020.00465] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
Environmental microbial gene expression patterns remain largely unexplored, particularly at interannual time scales. We analyzed the variability in the expression of marker genes involved in ecologically relevant biogeochemical processes at a temperate Atlantic site over two consecutive years. Most of nifH transcripts, involved in nitrogen (N) fixation, were affiliated with the symbiotic cyanobacterium Candidatus Atelocyanobacterium thalassa, suggesting a key role as N providers in this system. The expression of nifH and amoA (i.e., marker for ammonia oxidation) showed consistent maxima in summer and autumn, respectively, suggesting a temporal succession of these important N cycling processes. The patterns of expression of genes related to the oxidation of carbon monoxide (coxL) and reduced sulfur (soxB) were different from that of amoA, indicating alternate timings for these energy conservation strategies. We detected expression of alkaline phosphatases, induced under phosphorus limitation, in agreement with the reported co-limitation by this nutrient at the study site. In contrast, low-affinity phosphate membrane transporters (pit) typically expressed under phosphorus luxury conditions, were mainly detected in post-bloom conditions. Rhodobacteraceae dominated the expression of soxB, coxL and ureases, while Pelagibacteraceae dominated the expression of proteorhodopsins. Bacteroidetes and Gammaproteobacteria were major contributors to the uptake of inorganic nutrients (pit and amt transporters). Yet, in autumn, Thauma- and Euryarchaeota unexpectedly contributed importantly to the uptake of ammonia and phosphate, respectively. We provide new hints on the active players and potential dynamics of ecologically relevant functions in situ, highlighting the potential of metatranscriptomics to provide significant input to future omics-driven marine ecosystem assessment.
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Affiliation(s)
- Laura Alonso-Sáez
- Marine Research Division, AZTI, Sukarrieta, Spain.,Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía (IEO), Gijón/Xixón, Spain
| | - Xosé Anxelu G Morán
- Biological and Environmental Sciences and Engineering Division, Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - José M González
- Department of Microbiology, University of La Laguna, La Laguna, Spain
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A Collection of 13 Archaeal and 46 Bacterial Genomes Reconstructed from Marine Metagenomes Derived from the North Sea. DATA 2020. [DOI: 10.3390/data5010015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Marine bacteria are key drivers of ocean biogeochemistry. Despite the increasing number of studies, the complex interaction of marine bacterioplankton communities with their environment is still not fully understood. Additionally, our knowledge about prominent marine lineages is mostly based on genomic information retrieved from single isolates, which do not necessarily represent these groups. Consequently, deciphering the ecological contributions of single bacterioplankton community members is one major challenge in marine microbiology. In the present study, we reconstructed 13 archaeal and 46 bacterial metagenome-assembled genomes (MAGs) from four metagenomic data sets derived from the North Sea. Archaeal MAGs were affiliated to Marine Group II within the Euryarchaeota. Bacterial MAGs mainly belonged to marine groups within the Bacteroidetes as well as alpha- and gammaproteobacteria. In addition, two bacterial MAGs were classified as members of the Actinobacteria and Verrucomicrobiota, respectively. The reconstructed genomes contribute to our understanding of important marine lineages and may serve as a basis for further research on functional traits of these groups.
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29
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Metagenomic Analysis of the Effect of Enteromorpha prolifera Bloom on Microbial Community and Function in Aquaculture Environment. Curr Microbiol 2020; 77:816-825. [PMID: 31927597 DOI: 10.1007/s00284-019-01862-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/27/2019] [Indexed: 10/25/2022]
Abstract
Enteromorpha prolifera blooms considerably affected coastal environments in recent years. However, the effects of E. prolifera on microbial ecology and function remained unknown. In this study, metagenomic sequencing was used to investigate the effect of E. prolifera bloom on the microbial communities and functional genes in an aquaculture environment. Results showed that E. prolifera bloom could significantly alter the microbial composition and abundance, and heterotrophic bacteria comprised the major groups in the E. prolifera bloom pond, which was dominated by Actinomycetales and Flavobacteriales. The study indicated that viruses played an important role in shaping the microbial community and diversity during E. prolifera bloom. These viruses affected various dominant microbial taxa (such as Rhodobacteraceae, Synechococcus, and Prochlorococcus), which produced an obvious impact on potential nutrient transformation. Functional annotation analysis indicated that E. prolifera bloom would considerably shift the metabolism function by altering the structure and abundance of the microbial community. E. prolifera bloom pond had the low ability of potential metabolic capabilities of nitrogen, sulfur, and phosphate, whereas promoted gene abundance of genetic information processing. These changes in the microbial community and function could produce serious effect on aquaculture ecosystem.
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Zhang Z, Chen F, Chu X, Zhang H, Luo H, Qin F, Zhai Z, Yang M, Sun J, Zhao Y. Diverse, Abundant, and Novel Viruses Infecting the Marine Roseobacter RCA Lineage. mSystems 2019; 4:e00494-19. [PMID: 31848303 PMCID: PMC6918029 DOI: 10.1128/msystems.00494-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 11/21/2019] [Indexed: 02/05/2023] Open
Abstract
Many major marine bacterial lineages such as SAR11, Prochlorococcus, SAR116, and several Roseobacter lineages have members that are abundant, relatively slow-growing, and genome streamlined. The isolation of phages that infect SAR11 and SAR116 have demonstrated the dominance of these phages in the marine virosphere. However, no phages have been isolated from bacteria in the Roseobacter RCA lineage, another abundant group of marine bacteria. In this study, seven RCA phages that infect three different RCA strains were isolated and characterized. All seven RCA phages belong to the Podoviridae family and have genome sizes ranging from 39.6 to 58.1 kb. Interestingly, three RCA phages (CRP-1, CRP-2, and CRP-3) show similar genomic content and architecture as SAR116 phage HMO-2011, which represents one of the most abundant known viral groups in the ocean. The high degree of homology among CRP-1, CRP-2, CRP-3, and HMO-2011 resulted in the contribution of RCA phages to the dominance of the HMO-2011-type group. CRP-4 and CRP-5 are similar to the Cobavirus group roseophages in terms of gene content and organization. The remaining two RCA phages, CRP-6 and CRP-7, show limited genomic similarity with known phages and represent two new phage groups. Metagenomic fragment recruitment analyses reveal that these RCA phage groups are much more abundant in the ocean than most existing marine roseophage groups. The characterization of these RCA phages has greatly expanded our understanding of the genomic diversity and evolution of marine roseophages and suggests the critical need for isolating phages from the abundant but "unculturable" bacteria.IMPORTANCE The RCA lineage of the marine Roseobacter group represents one of the slow-growing but dominant components of marine microbial communities. Although dozens of roseophages have been characterized, no phages infecting RCA strains have been reported. In this study, we reported on the first RCA phage genomes and investigated their distribution pattern and relative abundance in comparison with other important marine phage groups. Two of the four RCA phage groups were found closely related to previously reported SAR116 phage HMO-2011 and Cobavirus group roseophages, respectively. The remaining two groups are novel in the genome contents. Our study also revealed that RCA phages are widely distributed and exhibit high abundance in marine viromic data sets. Altogether, our findings have greatly broadened our understanding of RCA phages and emphasize the ecological and evolutionary importance of RCA phages in the marine virosphere.
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Affiliation(s)
- Zefeng Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Xiao Chu
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hao Zhang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Fang Qin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhiqiang Zhai
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Mingyu Yang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jing Sun
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
| | - Yanlin Zhao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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Effects of Vertical Water Mass Segregation on Bacterial Community Structure in the Beaufort Sea. Microorganisms 2019; 7:microorganisms7100385. [PMID: 31554216 PMCID: PMC6843845 DOI: 10.3390/microorganisms7100385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/13/2019] [Accepted: 09/18/2019] [Indexed: 11/16/2022] Open
Abstract
The Arctic Ocean is one of the least well-studied marine microbial ecosystems. Its low-temperature and low-salinity conditions are expected to result in distinct bacterial communities, in comparison to lower latitude oceans. However, this is an ocean currently in flux, with climate change exerting pronounced effects on sea-ice coverage and freshwater inputs. How such changes will affect this ecosystem are poorly constrained. In this study, we characterized the bacterial community compositions at different depths in both coastal, freshwater-influenced, and pelagic, sea-ice-covered locations in the Beaufort Sea in the western Canadian Arctic Ocean. The environmental factors controlling the bacterial community composition and diversity were investigated. Alphaproteobacteria dominated the bacterial communities in samples from all depths and stations. The Pelagibacterales and Rhodobacterales groups were the predominant taxonomic representatives within the Alphaproteobacteria. Bacterial communities in coastal and offshore samples differed significantly, and vertical water mass segregation was the controlling factor of community composition among the offshore samples, regardless of the taxonomic level considered. These data provide an important baseline view of the bacterial community in this ocean system that will be of value for future studies investigating possible changes in the Arctic Ocean in response to global change and/or anthropogenic disturbance.
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32
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Distinct relationships between fluorescence in situ hybridization and 16S rRNA gene- and amplicon-based sequencing data of bacterioplankton lineages. Syst Appl Microbiol 2019; 42:126000. [DOI: 10.1016/j.syapm.2019.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 06/21/2019] [Accepted: 06/28/2019] [Indexed: 11/22/2022]
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Kim SJ, Kim JG, Lee SH, Park SJ, Gwak JH, Jung MY, Chung WH, Yang EJ, Park J, Jung J, Hahn Y, Cho JC, Madsen EL, Rodriguez-Valera F, Hyun JH, Rhee SK. Genomic and metatranscriptomic analyses of carbon remineralization in an Antarctic polynya. MICROBIOME 2019; 7:29. [PMID: 30786927 PMCID: PMC6383258 DOI: 10.1186/s40168-019-0643-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 02/01/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Polynyas in the Southern Ocean are regions of intense primary production, mainly by Phaeocystis antarctica. Carbon fixed by phytoplankton in the water column is transferred to higher trophic levels, and finally, to the deep ocean. However, in the Amundsen Sea, most of this organic carbon does not reach the sediment but is degraded in the water column due to high bacterial heterotrophic activity. RESULTS We reconstructed 12 key bacterial genomes from different phases of bloom and analyzed the expression of genes involved in organic carbon remineralization. A high correlation of gene expression between the peak and decline phases was observed in an individual genome bin-based pairwise comparison of gene expression. Polaribacter belonging to Bacteroidetes was found to be dominant in the peak phase, and its transcriptional activity was high (48.9% of the total mRNA reads). Two dominant Polaribacter bins had the potential to utilize major polymers in P. antarctica, chrysolaminarin and xylan, with a distinct set of glycosyl hydrolases. In the decline phase, Gammaproteobacteria (Ant4D3, SUP05, and SAR92), with the potential to utilize low molecular weight-dissolved organic matter (LMW-DOM) including compatible solutes, was increased. The versatility of Gammaproteobacteria may contribute to their abundance in organic carbon-rich polynya waters, while the SAR11 clade was found to be predominant in the sea ice-covered oligotrophic ocean. SAR92 clade showed transcriptional activity for utilization of both polysaccharides and LMW-DOM; this may account for their abundance both in the peak and decline phases. Ant4D3 clade was dominant in all phases of the polynya bloom, implicating the crucial roles of this clade in LMW-DOM remineralization in the Antarctic polynyas. CONCLUSIONS Genomic reconstruction and in situ gene expression analyses revealed the unique metabolic potential of dominant bacteria of the Antarctic polynya at a finer taxonomic level. The information can be used to predict temporal community succession linked to the availability of substrates derived from the P. antarctica bloom. Global warming has resulted in compositional changes in phytoplankton from P. antarctica to diatoms, and thus, repeated parallel studies in various polynyas are required to predict global warming-related changes in carbon remineralization.
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Affiliation(s)
- So-Jeong Kim
- Geologic Environment Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, 34132, Republic of Korea
| | - Jong-Geol Kim
- Department of Microbiology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Sang-Hoon Lee
- Division of Polar Ocean Environment, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Soo-Je Park
- Department of Biology, Jeju National University, Jeju, 63243, Republic of Korea
| | - Joo-Han Gwak
- Department of Microbiology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Man-Young Jung
- Department of Microbial Ecology, University of Vienna, 1090, Vienna, Austria
| | - Won-Hyung Chung
- Research Group of Gut Microbiome, Korea Food Research Institute, Sungnam, 13539, Republic of Korea
| | - Eun-Jin Yang
- Division of Polar Ocean Environment, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Jisoo Park
- Division of Polar Ocean Environment, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Jinyoung Jung
- Division of Polar Ocean Environment, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Yoonsoo Hahn
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Eugene L Madsen
- Department of Microbiology, Cornell University, Ithaca, NY, 14853-8101, USA
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan de Alicante, 03550, Alicante, Spain
| | - Jung-Ho Hyun
- Department of Marine Science and Convergence Engineering, Hanyang University ERICA Campus, Ansan, 15588, Republic of Korea
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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Duarte LN, Coelho FJRC, Oliveira V, Cleary DFR, Martins P, Gomes NCM. Characterization of bacterioplankton communities from a hatchery recirculating aquaculture system (RAS) for juvenile sole (Solea senegalensis) production. PLoS One 2019; 14:e0211209. [PMID: 30682196 PMCID: PMC6347143 DOI: 10.1371/journal.pone.0211209] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 01/09/2019] [Indexed: 12/18/2022] Open
Abstract
There is a growing consensus that future technological developments of aquaculture systems should account for the structure and function of microbial communities in the whole system and not only in fish guts. In this study, we aimed to investigate the composition of bacterioplankton communities of a hatchery recirculating aquaculture system (RAS) used for the production of Senegalese sole (Solea senegalensis) juveniles. To this end, we used a 16S rRNA gene based denaturing gradient gel electrophoresis (DGGE) and pyrosequencing analyses to characterize the bacterioplankton communities of the RAS and its water supply. Overall, the most abundant orders were Alteromonadales, Rhodobacterales, Oceanospirillales, Vibrionales, Flavobacteriales, Lactobacillales, Thiotrichales, Burkholderiales and Bdellovibrionales. Although we found a clear distinction between the RAS and the water supply bacterioplankton communities, most of the abundant OTUs (≥50 sequences) in the hatchery RAS were also present in the water supply. These included OTUs related to Pseudoalteromonas genus and the Roseobacter clade, which are known to comprise bacterial members with activity against Vibrio fish pathogens. Overall, in contrast to previous findings for sole grow-out RAS, our results suggest that the water supply may influence the bacterioplankton community structure of sole hatchery RAS. Further studies are needed to investigate the effect of aquaculture practices on RAS bacterioplankton communities and identification of the key drivers of their structure and diversity.
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Affiliation(s)
- Letícia N. Duarte
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | | | - Vanessa Oliveira
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | | | - Patrícia Martins
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - Newton C. M. Gomes
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
- * E-mail:
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35
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Zhan Y, Chen F. Bacteriophages that infect marine roseobacters: genomics and ecology. Environ Microbiol 2019; 21:1885-1895. [DOI: 10.1111/1462-2920.14504] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 12/01/2018] [Accepted: 12/11/2018] [Indexed: 01/05/2023]
Affiliation(s)
- Yuanchao Zhan
- Institute of Marine and Environmental TechnologyUniversity of Maryland Center for Environmental Science Baltimore MD USA
| | - Feng Chen
- Institute of Marine and Environmental TechnologyUniversity of Maryland Center for Environmental Science Baltimore MD USA
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36
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Bartling P, Vollmers J, Petersen J. The first world swimming championships of roseobacters—Phylogenomic insights into an exceptional motility phenotype. Syst Appl Microbiol 2018; 41:544-554. [DOI: 10.1016/j.syapm.2018.08.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/13/2018] [Accepted: 08/25/2018] [Indexed: 11/29/2022]
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37
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Sieradzki ET, Fuhrman JA, Rivero-Calle S, Gómez-Consarnau L. Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities. PeerJ 2018; 6:e5798. [PMID: 30370186 PMCID: PMC6202958 DOI: 10.7717/peerj.5798] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/20/2018] [Indexed: 12/13/2022] Open
Abstract
The most abundant and ubiquitous microbes in the surface ocean use light as an energy source, capturing it via complex chlorophyll-based photosystems or simple retinal-based rhodopsins. Studies in various ocean regimes compared the abundance of these mechanisms, but few investigated their expression. Here we present the first full seasonal study of abundance and expression of light-harvesting mechanisms (proteorhodopsin, PR; aerobic anoxygenic photosynthesis, AAnP; and oxygenic photosynthesis, PSI) from deep-sequenced metagenomes and metatranscriptomes of marine picoplankton (<1 µm) at three coastal stations of the San Pedro Channel in the Pacific Ocean. We show that, regardless of season or sampling location, the most common phototrophic mechanism in metagenomes of this dynamic region was PR (present in 65–104% of the genomes as estimated by single-copy recA), followed by PSI (5–104%) and AAnP (5–32%). Furthermore, the normalized expression (RNA to DNA ratio) of PR genes was higher than that of oxygenic photosynthesis (average ± standard deviation 26.2 ± 8.4 vs. 11 ± 9.7), and the expression of the AAnP marker gene was significantly lower than both mechanisms (0.013 ± 0.02). We demonstrate that PR expression was dominated by the SAR11-cluster year-round, followed by other Alphaproteobacteria, unknown-environmental clusters and Gammaproteobacteria. This highly dynamic system further allowed us to identify a trend for PR spectral tuning, in which blue-absorbing PR genes dominate in areas with low chlorophyll-a concentrations (<0.25 µgL−1). This suggests that PR phototrophy is not an accessory function but instead a central mechanism that can regulate photoheterotrophic population dynamics.
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Affiliation(s)
- Ella T Sieradzki
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States of America
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States of America
| | - Sara Rivero-Calle
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States of America
| | - Laura Gómez-Consarnau
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States of America
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38
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Bakenhus I, Dlugosch L, Giebel HA, Beardsley C, Simon M, Wietz M. Distinct biogeographic patterns of bacterioplankton composition and single-cell activity between the subtropics and Antarctica. Environ Microbiol 2018; 20:3100-3108. [PMID: 30109757 DOI: 10.1111/1462-2920.14383] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/26/2018] [Indexed: 11/26/2022]
Abstract
Bacterial biogeography and activity in the Southern Ocean are poorly understood to date. Here, we applied CARD-FISH to quantify bacterial community structure from the subtropics to Antarctica between 10°W and 10°E, covering four biogeographic provinces with distinct environmental properties. In addition, incorporation of radiolabeled glucose, amino acids and leucine via MAR-FISH served to quantify the contribution to substrate turnover by selected bacterial groups. SAR11, Bacteroidetes, Gammaproteobacteria and the Roseobacter group accounted for the majority of the bacterial community (52%-88% of DAPI-stained cells) but showed little distributional variation between provinces. In contrast, taxonomic subclades Polaribacter, NS5, NS2b (Bacteroidetes) as well as RCA (Roseobacter group) featured marked geographic variation, illustrated by NMDS and coefficients of variation. Roseobacter (specifically RCA) and Gammaproteobacteria constituted considerable fractions of cells incorporating glucose and amino acids respectively. Bacteroidetes had generally lower activities, but Polaribacter accounted for a major fraction of biomass production at one station near the Antarctic ice shelf. In conclusion, distributional patterns at finer taxonomic level and highest substrate turnover by less abundant taxa highlight the importance of taxonomic subclades in marine carbon fluxes, contributing to the understanding of functional bacterial biogeography in the Southern Ocean.
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Affiliation(s)
- Insa Bakenhus
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Leon Dlugosch
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Christine Beardsley
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
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39
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Daniel R, Simon M, Wemheuer B. Editorial: Molecular Ecology and Genetic Diversity of the Roseobacter Clade. Front Microbiol 2018; 9:1185. [PMID: 29910792 PMCID: PMC5992283 DOI: 10.3389/fmicb.2018.01185] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/16/2018] [Indexed: 12/26/2022] Open
Affiliation(s)
- Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Meinhard Simon
- Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany.,Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia.,School of Biological Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
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40
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Taxonomic profiles in metagenomic analyses of free-living microbial communities in the Ofunato Bay. Gene 2018; 665:192-200. [PMID: 29705124 DOI: 10.1016/j.gene.2018.04.075] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 04/25/2018] [Indexed: 12/21/2022]
Abstract
The Ofunato Bay in Iwate Prefecture, Japan is a deep coastal bay located at the center of the Sanriku Rias Coast and considered an economically and environmentally important asset. Here, we describe the first whole genome sequencing (WGS) study on the microbial community of the bay, where surface water samples were collected from three stations along its length to cover the entire bay; we preliminarily sequenced a 0.2 μm filter fraction among sequentially size-fractionated samples of 20.0, 5.0, 0.8 and 0.2 μm filters, targeting the free-living fraction only. From the 0.27-0.34 Gb WGS library, 0.9 × 106-1.2 × 106 reads from three sampling stations revealed 29 bacterial phyla (~80% of assigned reads), 3 archaeal phyla (~4%) and 59 eukaryotic phyla (~15%). Microbial diversity obtained from the WGS approach was compared with 16S rRNA gene results by mining WGS metagenomes, and we found similar estimates. The most frequently recovered bacterial sequences were Proteobacteria, predominantly comprised of 18.0-19.6% Planktomarina (Family Rhodobacteraceae) and 13.7-17.5% Candidatus Pelagibacter (Family Pelagibacterales). Other dominant bacterial genera, including Polaribacter (3.5-6.1%), Flavobacterium (1.8-2.6%), Sphingobacterium (1.4-1.6%) and Cellulophaga (1.4-2.0%), were members of Bacteroidetes and likely associated with the degradation and turnover of organic matter. The Marine Group I Archaea Nitrosopumilus was also detected. Remarkably, eukaryotic green alga Bathycoccus, Ostreococcus and Micromonas accounted for 8.8-15.2%, 3.6-4.9% and 2.1-3.1% of total read counts, respectively, highlighting their potential roles in the phytoplankton bloom after winter mixing.
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41
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Kudo T, Kobiyama A, Rashid J, Reza MS, Yamada Y, Ikeda Y, Ikeda D, Mizusawa N, Ikeo K, Sato S, Ogata T, Jimbo M, Kaga S, Watanabe S, Naiki K, Kaga Y, Segawa S, Mineta K, Bajic V, Gojobori T, Watabe S. Seasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis. Gene 2018; 665:174-184. [PMID: 29705130 DOI: 10.1016/j.gene.2018.04.072] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 04/25/2018] [Indexed: 11/18/2022]
Abstract
Ofunato Bay is located in the northeastern Pacific Ocean area of Japan, and it has the highest biodiversity of marine organisms in the world, primarily due to tidal influences from the cold Oyashio and warm Kuroshio Currents. Our previous results from performing shotgun metagenomics indicated that Candidatus Pelagibacter ubique and Planktomarina temperata were the dominant bacteria (Reza et al., 2018a, 2018b). These bacteria are reportedly able to catabolize dimethylsulfoniopropionate (DMSP) produced from phytoplankton into dimethyl sulfide (DMS) or methanethiol (MeSH). This study was focused on seasonal changes in the abundances of bacterial genes (dddP, dmdA) related to DMSP catabolism in the seawater of Ofunato Bay by BLAST+ analysis using shotgun metagenomic datasets. We found seasonal changes among the Candidatus Pelagibacter ubique strains, including those of the HTCC1062 type and the Red Sea type. A good correlation was observed between the chlorophyll a concentrations and the abundances of the catabolic genes, suggesting that the bacteria directly interact with phytoplankton in the marine material cycle system and play important roles in producing DMS and MeSH from DMSP as signaling molecules for the possible formation of the scent of the tidewater or as fish attractants.
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Affiliation(s)
- Toshiaki Kudo
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Atsushi Kobiyama
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Jonaira Rashid
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Md Shaheed Reza
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Yuichiro Yamada
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Yuri Ikeda
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Daisuke Ikeda
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Nanami Mizusawa
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Kazuho Ikeo
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Shigeru Sato
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Takehiko Ogata
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Mitsuru Jimbo
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Shinnosuke Kaga
- Iwate Fisheries Technology Center, Kamaishi, Iwate 026-0001, Japan
| | - Shiho Watanabe
- Iwate Fisheries Technology Center, Kamaishi, Iwate 026-0001, Japan
| | - Kimiaki Naiki
- Iwate Fisheries Technology Center, Kamaishi, Iwate 026-0001, Japan
| | - Yoshimasa Kaga
- Iwate Fisheries Technology Center, Kamaishi, Iwate 026-0001, Japan
| | - Satoshi Segawa
- Iwate Fisheries Technology Center, Kamaishi, Iwate 026-0001, Japan
| | - Katsuhiko Mineta
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia
| | - Vladimir Bajic
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia
| | - Takashi Gojobori
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia.
| | - Shugo Watabe
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan.
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42
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Bakenhus I, Voget S, Poehlein A, Brinkhoff T, Daniel R, Simon M. Genome sequence of Planktotalea frisia type strain (SH6-1 T), a representative of the Roseobacter group isolated from the North Sea during a phytoplankton bloom. Stand Genomic Sci 2018; 13:7. [PMID: 29682168 PMCID: PMC5896138 DOI: 10.1186/s40793-018-0311-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 03/21/2018] [Indexed: 12/15/2022] Open
Abstract
Planktotalea frisia SH6-1T Hahnke et al. (Int J Syst Evol Microbiol 62:1619-24, 2012) is a planktonic marine bacterium isolated during a phytoplankton bloom from the southern North Sea. It belongs to the Roseobacter group within the alphaproteobacterial family Rhodobacteraceae. Here we describe the draft genome sequence and annotation of the type strain SH6-1T. The genome comprises 4,106,736 bp and contains 4128 protein-coding and 38 RNA genes. The draft genome sequence provides evidence for at least three extrachromosomal elements, encodes genes for DMSP utilization, quorum sensing, photoheterotrophy and a type IV secretion system. This indicates not only adaptation to a free-living lifestyle of P. frisia but points also to interactions with prokaryotic or eukaryotic organisms.
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Affiliation(s)
- Insa Bakenhus
- 1Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Sonja Voget
- 2Institute of Microbiology and Genetics, Genomic and Applied Microbiology and Göttingen Genomics Laboratory, University of Göttingen, Göttingen, Germany
| | - Anja Poehlein
- 2Institute of Microbiology and Genetics, Genomic and Applied Microbiology and Göttingen Genomics Laboratory, University of Göttingen, Göttingen, Germany
| | - Thorsten Brinkhoff
- 1Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Rolf Daniel
- 2Institute of Microbiology and Genetics, Genomic and Applied Microbiology and Göttingen Genomics Laboratory, University of Göttingen, Göttingen, Germany
| | - Meinhard Simon
- 1Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
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Shin H, Lee E, Shin J, Ko SR, Oh HS, Ahn CY, Oh HM, Cho BK, Cho S. Elucidation of the bacterial communities associated with the harmful microalgae Alexandrium tamarense and Cochlodinium polykrikoides using nanopore sequencing. Sci Rep 2018; 8:5323. [PMID: 29593350 PMCID: PMC5871755 DOI: 10.1038/s41598-018-23634-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 03/14/2018] [Indexed: 01/04/2023] Open
Abstract
Interactions between microalgae and bacteria are often obligatory for harmful algal blooms (HABs). Here, we investigated the specific bacterial communities associated with Alexandrium tamarense and Cochlodinium polykrikoides, which cause ecological and economic damage during their blooms. To this end, the bacterial metagenome was selectively isolated from the two dinoflagellates and subsequently used for 16S rRNA analysis via the Nanopore MinION and Illumina sequencing platforms. Although the full-length 16S rRNA reads from the MinION platform showed high correlation in higher taxonomic ranks to the partial-length 16S rRNA reads from the Illumina platform, there was less correlation at the genus and species levels. MinION reads that are similar in the V3-V4 hypervariable regions with Illumina reads are classified to different taxonomies due to the extra information encoded in the full-length 16S rRNA reads. This indicates that bias arising from the short length Illumina reads can be supplemented by MinION reads. Furthermore, integrated analysis of the Illumina and MinION data showed that A. tamarense was predominantly enriched in the Roseobacter clade and C. polykrikoides was enriched in Gammaproteobacteria and Alphaproteobacteria. These results suggest that the association of different bacterial communities with A. tamarense and C. polykrikoides may be required for HABs.
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Affiliation(s)
- HyeonSeok Shin
- Department of Biological Sciences, Korea advanced institute of Science and Technology, Daejeon, Republic of Korea.,KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Eunju Lee
- Department of Biological Sciences, Korea advanced institute of Science and Technology, Daejeon, Republic of Korea.,KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Jongoh Shin
- Department of Biological Sciences, Korea advanced institute of Science and Technology, Daejeon, Republic of Korea.,KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - So-Ra Ko
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Hyung-Seok Oh
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Chi-Yong Ahn
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Hee-Mock Oh
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea advanced institute of Science and Technology, Daejeon, Republic of Korea. .,KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea. .,Intelligent Synthetic Biology Center, Daejeon, 34141, Republic of Korea.
| | - Suhyung Cho
- Department of Biological Sciences, Korea advanced institute of Science and Technology, Daejeon, Republic of Korea. .,KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
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44
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Wallace JC, Youngblood JE, Port JA, Cullen AC, Smith MN, Workman T, Faustman EM. Variability in metagenomic samples from the Puget Sound: Relationship to temporal and anthropogenic impacts. PLoS One 2018; 13:e0192412. [PMID: 29438385 PMCID: PMC5811002 DOI: 10.1371/journal.pone.0192412] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/23/2018] [Indexed: 11/18/2022] Open
Abstract
Whole-metagenome sequencing (WMS) has emerged as a powerful tool to assess potential public health risks in marine environments by measuring changes in microbial community structure and function in uncultured bacteria. In addition to monitoring public health risks such as antibiotic resistance determinants, it is essential to measure predictors of microbial variation in order to identify natural versus anthropogenic factors as well as to evaluate reproducibility of metagenomic measurements.This study expands our previous metagenomic characterization of Puget Sound by sampling new nearshore environments including the Duwamish River, an EPA superfund site, and the Hood Canal, an area characterized by highly variable oxygen levels. We also resampled a wastewater treatment plant, nearshore and open ocean sites introducing a longitudinal component measuring seasonal and locational variations and establishing metagenomics sampling reproducibility. Microbial composition from samples collected in the open sound were highly similar within the same season and location across different years, while nearshore samples revealed multi-fold seasonal variation in microbial composition and diversity. Comparisons with recently sequenced predominant marine bacterial genomes helped provide much greater species level taxonomic detail compared to our previous study. Antibiotic resistance determinants and pollution and detoxification indicators largely grouped by location showing minor seasonal differences. Metal resistance, oxidative stress and detoxification systems showed no increase in samples proximal to an EPA superfund site indicating a lack of ecosystem adaptation to anthropogenic impacts. Taxonomic analysis of common sewage influent families showed a surprising similarity between wastewater treatment plant and open sound samples suggesting a low-level but pervasive sewage influent signature in Puget Sound surface waters. Our study shows reproducibility of metagenomic data sampling in multiple Puget Sound locations while establishing baseline measurements of antibiotic resistance determinants, pollution and detoxification systems. Combining seasonal and longitudinal data across these locations provides a foundation for evaluating variation in future studies.
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Affiliation(s)
- James C. Wallace
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Jessica E. Youngblood
- Environmental Toxicology, Amec Foster Wheeler, Lynnwood, Washington, United States of America
| | - Jesse A. Port
- Center for Ocean Solutions, Stanford University, Monterey, California, United States of America
| | - Alison C. Cullen
- Daniel J. Evans School of Public Affairs, University of Washington, Seattle, Washington, United States of America
| | - Marissa N. Smith
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Tomomi Workman
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Elaine M. Faustman
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail: ,
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45
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Wemheuer B, Wemheuer F, Meier D, Billerbeck S, Giebel HA, Simon M, Scherber C, Daniel R. Linking Compositional and Functional Predictions to Decipher the Biogeochemical Significance in DFAA Turnover of Abundant Bacterioplankton Lineages in the North Sea. Microorganisms 2017; 5:microorganisms5040068. [PMID: 29113091 PMCID: PMC5748577 DOI: 10.3390/microorganisms5040068] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 11/01/2017] [Accepted: 11/02/2017] [Indexed: 11/16/2022] Open
Abstract
Deciphering the ecological traits of abundant marine bacteria is a major challenge in marine microbial ecology. In the current study, we linked compositional and functional predictions to elucidate such traits for abundant bacterioplankton lineages in the North Sea. For this purpose, we investigated entire and active bacterioplankton composition along a transect ranging from the German Bight to the northern North Sea by pyrotag sequencing of bacterial 16S rRNA genes and transcripts. Functional profiles were inferred from 16S rRNA data using Tax4Fun. Bacterioplankton communities were dominated by well-known marine lineages including clusters/genera that are affiliated with the Roseobacter group and the Flavobacteria. Variations in community composition and function were significantly explained by measured environmental and microbial properties. Turnover of dissolved free amino acids (DFAA) showed the strongest correlation to community composition and function. We applied multinomial models, which enabled us to identify bacterial lineages involved in DFAA turnover. For instance, the genus Planktomarina was more abundant at higher DFAA turnover rates, suggesting its vital role in amino acid degradation. Functional predictions further indicated that Planktomarina is involved in leucine and isoleucine degradation. Overall, our results provide novel insights into the biogeochemical significance of abundant bacterioplankton lineages in the North Sea.
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Affiliation(s)
- Bernd Wemheuer
- Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany.
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia.
| | - Franziska Wemheuer
- Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany.
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia.
| | - Dimitri Meier
- Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany.
| | - Sara Billerbeck
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, D-26111 Oldenburg, Germany.
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, D-26111 Oldenburg, Germany.
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, D-26111 Oldenburg, Germany.
| | - Christoph Scherber
- Institute of Landscape Ecology, University of Muenster, Heisenbergstr. 2, D-48149 Muenster, Germany.
| | - Rolf Daniel
- Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany.
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46
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Luria CM, Amaral-Zettler LA, Ducklow HW, Repeta DJ, Rhyne AL, Rich JJ. Seasonal Shifts in Bacterial Community Responses to Phytoplankton-Derived Dissolved Organic Matter in the Western Antarctic Peninsula. Front Microbiol 2017; 8:2117. [PMID: 29163409 PMCID: PMC5675858 DOI: 10.3389/fmicb.2017.02117] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/17/2017] [Indexed: 11/13/2022] Open
Abstract
Bacterial consumption of dissolved organic matter (DOM) drives much of the movement of carbon through the oceanic food web and the global carbon cycle. Understanding complex interactions between bacteria and marine DOM remains an important challenge. We tested the hypothesis that bacterial growth and community succession would respond differently to DOM additions due to seasonal changes in phytoplankton abundance in the environment. Four mesocosm experiments were conducted that spanned the spring transitional period (August-December 2013) in surface waters of the Western Antarctic Peninsula (WAP). Each mesocosm consisted of nearshore surface seawater (50 L) incubated in the laboratory for 10 days. The addition of DOM, in the form of cell-free exudates extracted from Thalassiosira weissflogii diatom cultures led to changes in bacterial abundance, production, and community composition. The timing of each mesocosm experiment (i.e., late winter vs. late spring) influenced the magnitude and direction of bacterial changes. For example, the same DOM treatment applied at different times during the season resulted in different levels of bacterial production and different bacterial community composition. There was a mid-season shift from Collwelliaceae to Polaribacter having the greatest relative abundance after incubation. This shift corresponded to a modest but significant increase in the initial relative abundance of Polaribacter in the nearshore seawater used to set up experiments. This finding supports a new hypothesis that starting community composition, through priority effects, influenced the trajectory of community succession in response to DOM addition. As strong inter-annual variability and long-term climate change may shift the timing of WAP phytoplankton blooms, and the corresponding production of DOM exudates, this study suggests a mechanism by which different seasonal successional patterns in bacterial communities could occur.
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Affiliation(s)
- Catherine M. Luria
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, United States
| | - Linda A. Amaral-Zettler
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, MA, United States
- Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, RI, United States
- NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Hugh W. Ducklow
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States
| | - Daniel J. Repeta
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Andrew L. Rhyne
- Department of Biology, Marine Biology, and Environmental Science, Roger Williams University, Bristol, RI, United States
| | - Jeremy J. Rich
- School of Marine Sciences, Darling Marine Center, University of Maine, Walpole, ME, United States
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47
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Chafee M, Fernàndez-Guerra A, Buttigieg PL, Gerdts G, Eren AM, Teeling H, Amann RI. Recurrent patterns of microdiversity in a temperate coastal marine environment. ISME JOURNAL 2017; 12:237-252. [PMID: 29064479 PMCID: PMC5739018 DOI: 10.1038/ismej.2017.165] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 08/18/2017] [Accepted: 09/04/2017] [Indexed: 12/25/2022]
Abstract
Temperate coastal marine environments are replete with complex biotic and abiotic interactions that are amplified during spring and summer phytoplankton blooms. During these events, heterotrophic bacterioplankton respond to successional releases of dissolved organic matter as algal cells are lysed. Annual seasonal shifts in the community composition of free-living bacterioplankton follow broadly predictable patterns, but whether similar communities respond each year to bloom disturbance events remains unknown owing to a lack of data sets, employing high-frequency sampling over multiple years. We capture the fine-scale microdiversity of these events with weekly sampling using a high-resolution method to discriminate 16S ribosomal RNA gene amplicons that are >99% identical. Furthermore, we used 2 complete years of data to facilitate identification of recurrent sub-networks of co-varying microbes. We demonstrate that despite inter-annual variation in phytoplankton blooms and despite the dynamism of a coastal–oceanic transition zone, patterns of microdiversity are recurrent during both bloom and non-bloom conditions. Sub-networks of co-occurring microbes identified reveal that correlation structures between community members appear quite stable in a seasonally driven response to oligotrophic and eutrophic conditions.
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Affiliation(s)
- Meghan Chafee
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Antonio Fernàndez-Guerra
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Jacobs University Bremen gGmbH, Bremen, Germany.,University of Oxford, Oxford e-Research Centre, Oxford, UK
| | - Pier Luigi Buttigieg
- HGF-MPG Bridge-Group for Deep Sea Ecology and Technology, Alfred-Wegener Institute, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Gunnar Gerdts
- Alfred-Wegener Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany
| | - A Murat Eren
- University of Chicago, Department of Medicine, Knapp Center for Biomedical Discovery, Chicago, IL, USA.,Marine Biological Laboratory, Woods Hole, MA, USA
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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48
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Bakenhus I, Dlugosch L, Billerbeck S, Giebel HA, Milke F, Simon M. Composition of Total and Cell-Proliferating Bacterioplankton Community in Early Summer in the North Sea - Roseobacters Are the Most Active Component. Front Microbiol 2017; 8:1771. [PMID: 28959250 PMCID: PMC5604061 DOI: 10.3389/fmicb.2017.01771] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/31/2017] [Indexed: 11/13/2022] Open
Abstract
Heterotrophic bacterioplankton communities play an important role in organic matter processing in the oceans worldwide. In order to investigate the significance of distinct phylogenetic bacterial groups it is not only important to assess their quantitative abundance but also their growth dynamics in relation to the entire bacterioplankton. Therefore bacterial abundance, biomass production and the composition of the entire and cell-proliferating bacterioplankton community were assessed in North Sea surface waters between the German Bight and 58°N in early summer by applying catalyzed reporter deposition (CARD-FISH) and bromodeoxyuridine fluorescence in situ hybridization (BrdU-FISH). Bacteroidetes and the Roseobacter group dominated the cell-proliferating fraction with 10-55 and 8-31% of total BrdU-positive cells, respectively. While Bacteroidetes also showed high abundances in the total bacterial fraction, roseobacters constituted only 1-9% of all cells. Despite abundances of up to 55% of total bacterial cells, the SAR11 clade constituted <6% of BrdU-positive cells. Gammaproteobacteria accounted for 2-16% of the total and 2-13% of the cell-proliferating cells. Within the two most active groups, BrdU-positive cells made up 28% of Bacteroidetes as an overall mean and 36% of roseobacters. Estimated mean growth rates of Bacteroidetes and the Roseobacter group were 1.2 and 1.5 day-1, respectively, and much higher than bulk growth rates of the bacterioplankton whereas those of the SAR11 clade and Gammaproteobacteria were 0.04 and 0.21 day-1, respectively, and much lower than bulk growth rates. Only numbers of total and cell-proliferating roseobacters but not those of Bacteroidetes and the other groups were significantly correlated to chlorophyll fluorescence and bacterioplankton biomass production. The Roseobacter group, besides Bacteroidetes, appeared to be a major player in processing phytoplankton derived organic matter despite its low partitioning in the total bacterioplankton community.
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Affiliation(s)
- Insa Bakenhus
- Institute for Chemistry and Biology of the Marine Environment, University of OldenburgOldenburg, Germany
| | - Leon Dlugosch
- Institute for Chemistry and Biology of the Marine Environment, University of OldenburgOldenburg, Germany
| | - Sara Billerbeck
- Institute for Chemistry and Biology of the Marine Environment, University of OldenburgOldenburg, Germany
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment, University of OldenburgOldenburg, Germany
| | - Felix Milke
- Institute for Chemistry and Biology of the Marine Environment, University of OldenburgOldenburg, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of OldenburgOldenburg, Germany
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49
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Dogs M, Wemheuer B, Wolter L, Bergen N, Daniel R, Simon M, Brinkhoff T. Rhodobacteraceae on the marine brown alga Fucus spiralis are abundant and show physiological adaptation to an epiphytic lifestyle. Syst Appl Microbiol 2017; 40:370-382. [PMID: 28641923 DOI: 10.1016/j.syapm.2017.05.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/05/2017] [Accepted: 05/12/2017] [Indexed: 12/01/2022]
Abstract
Macroalgae harbour specific microbial communities on their surface that have functions related to host health and defence. In this study, the bacterial biofilm of the marine brown alga Fucus spiralis was investigated using 16S rRNA gene amplicon-based analysis and isolation of bacteria. Rhodobacteraceae (Alphaproteobacteria) were the predominant family constituting 23% of the epibacterial community. At the genus level, Sulfitobacter, Loktanella, Octadecabacter and a previously undescribed cluster were most abundant, and together they comprised 89% of the Rhodobacteraceae. Supported by a specific PCR approach, 23 different Rhodobacteraceae-affiliated strains were isolated from the surface of F. spiralis, which belonged to 12 established and three new genera. For seven strains, closely related sequences were detected in the 16S rRNA gene dataset. Growth experiments with substrates known to be produced by Fucus spp. showed that all of them were consumed by at least three strains, and vitamin B12 was produced by 70% of the isolates. Since growth of F. spiralis depends on B12 supplementation, bacteria may provide the alga with this vitamin. Most strains produced siderophores, which can enhance algal growth under iron-deficient conditions. Inhibiting properties against other bacteria were only observed when F. spiralis material was present in the medium. Thus, the physiological properties of the isolates indicated adaption to an epiphytic lifestyle.
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Affiliation(s)
- Marco Dogs
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Bernd Wemheuer
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Laura Wolter
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Nils Bergen
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
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50
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Lin G, Sun F, Wang C, Zhang L, Zhang X. Assessment of the effect of Enteromorpha prolifera on bacterial community structures in aquaculture environment. PLoS One 2017; 12:e0179792. [PMID: 28742878 PMCID: PMC5526538 DOI: 10.1371/journal.pone.0179792] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 06/05/2017] [Indexed: 11/18/2022] Open
Abstract
In recent years, Enteromorpha prolifera blooms had serious impacts on costal environments and fisheries in China. Nevertheless, the effects of E. prolifera on microbial ecology remain unknown. In this study, for the first time, an Illumina sequencing analysis was used to investigate bacterial communities in source water, aquaculture ponds with E. prolifera, and an aquaculture pond in which E. prolifera -free. Principal coordinate and phylogenic analyses revealed obvious differences among the bacterial communities in the pond water with and without E. prolifera. Abundant bacterial taxa in the E. prolifera-containing pond were generally absent from the pond without E. prolifera. Interestingly, pond water with E. prolifera was dominated by Actinomycetales (> 50%), as well as by anaerobic bacteria in the underlying sediment (Desulfobacterales and Desulfuromonadales (> 20%). Pond water in which E. prolifera-free was dominated by Rhodobacterales (58.19%), as well as aerobic and facultative anaerobic bacteria in the sediment. In addition, the ecological functions of other dominant bacteria, such as Candidatus Aquiluna, Microcella spp., and Marivita spp., should be studied in depth. Overall, massive growth of E. prolifera will have serious effects on bacterial communities, and, thus, it will have an important impact on the environment. The novel findings in this study will be valuable for understanding green tides.
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Affiliation(s)
- Guorong Lin
- College of Environmental and Biological Engineering, Fujian Provincial Key Laboratory of Ecology-toxicological Effects & Control for Emerging Contaminants, Putian University, Putian, China
| | - Fulin Sun
- State Key Laboratory of Tropical Oceanography, Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- * E-mail:
| | - Chunzhong Wang
- Putian Institute of Aquaculture Science of Fujian Province, Putian, China
| | - Li Zhang
- Putian Oceanic and Fishery Enviormental Monitoring Station, Putian, China
| | - Xinzhong Zhang
- School of Life Sciences, Nantong University, Nantong, China
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