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Wang X, Xiao Y, Deng Y, Sang X, Deng QL, Wang L, Yang YW, Zhang BH, Zhang YQ. Sphingomonas lacusdianchii sp. nov., an attached bacterium inhibited by metabolites from its symbiotic cyanobacterium. Appl Microbiol Biotechnol 2024; 108:309. [PMID: 38661971 PMCID: PMC11045571 DOI: 10.1007/s00253-024-13081-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 02/12/2024] [Accepted: 02/20/2024] [Indexed: 04/26/2024]
Abstract
An alpha-proteobacterial strain JXJ CY 53 T was isolated from the cyanosphere of Microcystis sp. FACHB-905 (MF-905) collected from Lake Dianchi, China. JXJ CY 53 T was observed to be an aerobic, Gram-stain-negative, oval shaped, and mucus-secreting bacterium. It had C18:1ω7c and C16:0 as the major cellular fatty acids, Q-10 as the predominant ubiquinone, and sphingoglycolipid, diphosphatidylglycerol, phosphatidylcholine, and phosphatidylmethylethanolamine as the polar lipids. The G + C content of DNA was 65.85%. The bacterium had 16S rRNA gene sequence identities of 98.9% and 98.7% with Sphingomonas panni DSM 15761 T and Sphingomonas hankookensis KCTC 22579 T, respectively, while less than 97.4% identities with other members of the genus. Further taxonomic analysis indicated that JXJ CY 53 T represented a new member of Sphingomonas, and the species epithet was proposed as Sphingomonas lacusdianchii sp. nov. (type strain JXJ CY 53 T = KCTC 72813 T = CGMCC 1.17657 T). JXJ CY 53 T promoted the growth of MF-905 by providing bio-available phosphorus and nitrogen, plant hormones, vitamins, and carotenoids. It could modulate the relative abundances of nonculturable bacteria associated with MF-905 and influence the interactions of MF-905 and other bacteria isolated from the cyanobacterium, in addition to microcystin production characteristics. Meanwhile, MF-905 could provide JXJ CY 53 T dissolved organic carbon for growth, and control the growth of JXJ CY 53 T by secreting specific chemicals other than microcystins. Overall, these results suggest that the interactions between Microcystis and its attached bacteria are complex and dynamic, and may influence the growth characteristics of the cyanobacterium. This study provided new ideas to understand the interactions between Microcystis and its attached bacteria. KEY POINTS: • A novel bacterium (JXJCY 53 T) was isolated from the cyanosphere of Microcystis sp. FACHB-905 (MF-905) • JXJCY 53 T modulated the growth and microcystin production of MF-905 • MF-905 could control the attached bacteria by specific chemicals other than microcystins (MCs).
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Affiliation(s)
- Xin Wang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Yao Xiao
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Yang Deng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Xue Sang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Qing-Lin Deng
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Le Wang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Yi-Wen Yang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Bing-Huo Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China.
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
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Xiao Y, Du M, Deng Y, Deng Q, Wang X, Yang Y, Zhang B, Zhang YQ. Modulation of growth, microcystin production, and algal-bacterial interactions of the bloom-forming algae Microcystis aeruginosa by a novel bacterium recovered from its phycosphere. Front Microbiol 2024; 15:1295696. [PMID: 38495512 PMCID: PMC10940515 DOI: 10.3389/fmicb.2024.1295696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 02/21/2024] [Indexed: 03/19/2024] Open
Abstract
Harmful algal blooms (HABs) in natural waters are of escalating global concern due to their detrimental impact on environmental health. Emerging evidence indicates that algae-bacteria symbionts can affect HAB features, though much about this interplay remains largely unexplored. The current study isolated a new species of Mucilaginibacter (type strain JXJ CY 39T) from culture biomass of the bloom-causing Microcystis aeruginosa FACHB-905 (Maf) from Lake Dianchi, China. Strain JXJ CY 39T was an aerobic, Gram-stain-negative rod bacterium that grew at 5-38°C, pH 4.0-11.0, and 0-3.0% NaCl. Taxonomic evaluation proposed a new species, with Mucilaginibacter lacusdianchii sp. nov., as the species epithet. Experimental results revealed that strain JXJ CY 39T spurred the growth of Maf by supplying soluble phosphorus and nitrogen during cultivation, despite the unavailability of soluble phosphorus and nitrogen. Additionally, by producing the plant hormone indole-3-acetate, strain JXJ CY 39T possibly impacted Maf's functionality. Results from co-culture experiments with other strains from Maf biomass showed possible effects of strain JXJ CY 39T on the relationship between Maf and other cohabiting bacteria, as well as microcystin toxin production characteristics. Although Maf could foster the growth of strain JXJ CY 39T by supplying organic carbon, the strain's growth could be regulated via specific chemical compounds based on antibiotic assays. Community composition analysis disclosed that this Mucilaginibacter strain positively affected Maf's growth and modified densities and types of bacteria linked to Maf. Overall, these results suggest that the interactions between important HAB-causing organisms and their attached bacteria are complex, dynamic, and may influence the growth characteristics of algae.
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Affiliation(s)
- Yao Xiao
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Mijia Du
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Yang Deng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qinglin Deng
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Xin Wang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Yiwen Yang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Binghuo Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Wijewardene L, Schwenker JA, Friedrichsen M, Jensen A, Löbel F, Austen T, Ulrich U, Fohrer N, Bang C, Waschina S, Hölzel CS. Selection of aquatic microbiota exposed to the herbicides flufenacet and metazachlor. Environ Microbiol 2023; 25:2972-2987. [PMID: 37994199 DOI: 10.1111/1462-2920.16535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 10/24/2023] [Indexed: 11/24/2023]
Abstract
Herbicides are important, ubiquitous environmental contaminants, but little is known about their interaction with bacterial aquatic communities. Here, we sampled a protected natural freshwater habitat and characterised its microbiome in interaction with herbicides. We evolved the freshwater microbiomes in a microcosm assay of exposure (28 days) to flufenacet and metazachlor at environmental concentrations of 0.5, 5 and 50 μg L-1 . Inhibitory effects of herbicides were exemplarily assessed in cultured bacteria from the same pond (Pseudomonas alcaligenes, Paenibacillus amylolyticus and Microbacterium hominis). Findings were compared to long-term concentrations as provided by local authorities. Here, environmental concentrations reached up to 11 μg L-1 (flufenacet) and 76 μg L-1 (metazachlor). Bacteria were inhibited at minimum inhibitory concentrations far above these values; however, concentrations of 50 μg L-1 of flufenacet resulted in measurable growth impairment. While most herbicide-exposed microcosm assays did not differ from controls, Acidobacteria were selected at high environmental concentrations of herbicides. Alpha-diversity (e.g., taxonomic richness on phylum level) was reduced when aquatic microbiomes were exposed to 50 μg metazachlor or flufenacet. One environmental strain of P. alcaligenes showed resistance to high concentrations of flufenacet (50 g L-1 ). In total, this study reveals that ecologic imbalance due to herbicide use significantly impacts aquatic microbiomes.
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Affiliation(s)
- Lishani Wijewardene
- Faculty of Fisheries and Marine Sciences & Technology, Department of Limnology and Water Technology, University of Ruhuna, Matara, Sri Lanka
| | - Julia Anna Schwenker
- Institute of Animal Breeding and Husbandry, Department for Animal Hygiene, Animal Health and Food Hygiene, Kiel University, Kiel, Germany
| | - Meike Friedrichsen
- Institute of Animal Breeding and Husbandry, Department for Animal Hygiene, Animal Health and Food Hygiene, Kiel University, Kiel, Germany
| | - Ailina Jensen
- Institute of Animal Breeding and Husbandry, Department for Animal Hygiene, Animal Health and Food Hygiene, Kiel University, Kiel, Germany
| | - Franziska Löbel
- Institute of Animal Breeding and Husbandry, Department for Animal Hygiene, Animal Health and Food Hygiene, Kiel University, Kiel, Germany
| | - Tabea Austen
- Institute of Animal Breeding and Husbandry, Department for Animal Hygiene, Animal Health and Food Hygiene, Kiel University, Kiel, Germany
| | - Uta Ulrich
- Institute for Natural Resource Conservation, Department of Hydrology and Water Resources Management, Kiel University, Kiel, Germany
| | - Nicola Fohrer
- Institute for Natural Resource Conservation, Department of Hydrology and Water Resources Management, Kiel University, Kiel, Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Silvio Waschina
- Institute for Human Nutrition and Food Science, Department for Nutriinformatics, Kiel University, Kiel, Germany
| | - Christina Susanne Hölzel
- Institute of Animal Breeding and Husbandry, Department for Animal Hygiene, Animal Health and Food Hygiene, Kiel University, Kiel, Germany
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Hoshino Y, Nettersheim BJ, Gold DA, Hallmann C, Vinnichenko G, van Maldegem LM, Bishop C, Brocks JJ, Gaucher EA. Genetics re-establish the utility of 2-methylhopanes as cyanobacterial biomarkers before 750 million years ago. Nat Ecol Evol 2023; 7:2045-2054. [PMID: 37884688 PMCID: PMC10697835 DOI: 10.1038/s41559-023-02223-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 09/06/2023] [Indexed: 10/28/2023]
Abstract
Fossilized lipids offer a rare glimpse into ancient ecosystems. 2-Methylhopanes in sedimentary rocks were once used to infer the importance of cyanobacteria as primary producers throughout geological history. However, the discovery of hopanoid C-2 methyltransferase (HpnP) in Alphaproteobacteria led to the downfall of this molecular proxy. In the present study, we re-examined the distribution of HpnP in a new phylogenetic framework including recently proposed candidate phyla and re-interpreted a revised geological record of 2-methylhopanes based on contamination-free samples. We show that HpnP was probably present in the last common ancestor of cyanobacteria, while the gene appeared in Alphaproteobacteria only around 750 million years ago (Ma). A subsequent rise of sedimentary 2-methylhopanes around 600 Ma probably reflects the expansion of Alphaproteobacteria that coincided with the rise of eukaryotic algae-possibly connected by algal dependency on microbially produced vitamin B12. Our findings re-establish 2-methylhopanes as cyanobacterial biomarkers before 750 Ma and thus as a potential tool to measure the importance of oxygenic cyanobacteria as primary producers on early Earth. Our study illustrates how genetics can improve the diagnostic value of biomarkers and refine the reconstruction of early ecosystems.
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Affiliation(s)
- Yosuke Hoshino
- GFZ German Research Centre for Geosciences, Potsdam, Germany.
- Department of Biology, Georgia State University, Atlanta, GA, USA.
| | - Benjamin J Nettersheim
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany.
| | - David A Gold
- Department of Earth and Planetary Sciences, University of California Davis, Davis, CA, USA
| | | | - Galina Vinnichenko
- Research School of Earth Sciences, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Lennart M van Maldegem
- Research School of Earth Sciences, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Caleb Bishop
- Research School of Earth Sciences, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jochen J Brocks
- Research School of Earth Sciences, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Eric A Gaucher
- Department of Biology, Georgia State University, Atlanta, GA, USA
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5
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Hernanz-Torrijos M, Ortega MJ, Úbeda B, Bartual A. Polyunsaturated Aldehydes Profile in the Diatom Cyclotella cryptica Is Sensitive to Changes in Its Phycosphere Bacterial Assemblages. Mar Drugs 2023; 21:571. [PMID: 37999395 PMCID: PMC10672285 DOI: 10.3390/md21110571] [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: 09/13/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/25/2023] Open
Abstract
Diatoms are responsible for the fixation of ca. 20% of the global CO2 and live associated with bacteria that utilize the organic substances produced by them. Current research trends in marine microbial ecology show which diatom and bacteria interact mediated through the production and exchange of infochemicals. Polyunsaturated aldehydes (PUA) are organic molecules released by diatoms that are considered to have infochemical properties. In this work, we investigated the possible role of PUA as a mediator in diatom-bacteria interactions. To this end, we compare the PUA profile of a newly isolated oceanic PUA producer diatom, Cyclotella cryptica, co-cultured with and without associated bacteria at two phosphate availability conditions. We found that the PUA profile of C. cryptica cultured axenically was different than its profile when it was co-cultured with autochthonous (naturally associated) and non-autochthonous bacteria (unnaturally inoculated). We also observed that bacterial presence significantly enhanced diatom growth and that C. cryptica modulated the percentage of released PUA in response to the presence of bacteria, also depending on the consortium type. Based on our results, we propose that this diatom could use released PUA as a specific organic matter sign to attract beneficial bacteria for constructing its own phycosphere, for more beneficial growth.
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Affiliation(s)
- María Hernanz-Torrijos
- Instituto Universitario de Investigaciones Marinas (INMAR), Campus de Excelencia Internacional del Mar (CEI-MAR), Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain; (M.H.-T.); (B.Ú.)
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
| | - María J. Ortega
- Departamento de Química Orgánica, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain;
| | - Bárbara Úbeda
- Instituto Universitario de Investigaciones Marinas (INMAR), Campus de Excelencia Internacional del Mar (CEI-MAR), Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain; (M.H.-T.); (B.Ú.)
| | - Ana Bartual
- Instituto Universitario de Investigaciones Marinas (INMAR), Campus de Excelencia Internacional del Mar (CEI-MAR), Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain; (M.H.-T.); (B.Ú.)
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
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6
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Xia C, Zhao Y, Zhang L, Li X, Cheng Y, Wang D, Xu C, Qi M, Wang J, Guo X, Ye X, Huang Y, Shen D, Dou D, Cao H, Li Z, Cui Z. Myxobacteria restrain Phytophthora invasion by scavenging thiamine in soybean rhizosphere via outer membrane vesicle-secreted thiaminase I. Nat Commun 2023; 14:5646. [PMID: 37704617 PMCID: PMC10499793 DOI: 10.1038/s41467-023-41247-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 08/29/2023] [Indexed: 09/15/2023] Open
Abstract
Public metabolites such as vitamins play critical roles in maintaining the ecological functions of microbial community. However, the biochemical and physiological bases for fine-tuning of public metabolites in the microbiome remain poorly understood. Here, we examine the interactions between myxobacteria and Phytophthora sojae, an oomycete pathogen of soybean. We find that host plant and soil microbes complement P. sojae's auxotrophy for thiamine. Whereas, myxobacteria inhibits Phytophthora growth by a thiaminase I CcThi1 secreted into extracellular environment via outer membrane vesicles (OMVs). CcThi1 scavenges the required thiamine and thus arrests the thiamine sharing behavior of P. sojae from the supplier, which interferes with amino acid metabolism and expression of pathogenic effectors, probably leading to impairment of P. sojae growth and pathogenicity. Moreover, myxobacteria and CcThi1 are highly effective in regulating the thiamine levels in soil, which is correlated with the incidence of soybean Phytophthora root rot. Our findings unravel a novel ecological tactic employed by myxobacteria to maintain the interspecific equilibrium in soil microbial community.
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Affiliation(s)
- Chengyao Xia
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuqiang Zhao
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Lei Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xu Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Cheng
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Nanjing Agriculture University, Nanjing, 210095, China
| | - Dongming Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Changsheng Xu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mengyi Qi
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jihong Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiangrui Guo
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Danyu Shen
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Nanjing Agriculture University, Nanjing, 210095, China
| | - Daolong Dou
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Nanjing Agriculture University, Nanjing, 210095, China
- Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hui Cao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhoukun Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
- Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China.
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7
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Mayali X, Samo TJ, Kimbrel JA, Morris MM, Rolison K, Swink C, Ramon C, Kim YM, Munoz-Munoz N, Nicora C, Purvine S, Lipton M, Stuart RK, Weber PK. Single-cell isotope tracing reveals functional guilds of bacteria associated with the diatom Phaeodactylum tricornutum. Nat Commun 2023; 14:5642. [PMID: 37704622 PMCID: PMC10499878 DOI: 10.1038/s41467-023-41179-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/24/2023] [Indexed: 09/15/2023] Open
Abstract
Bacterial remineralization of algal organic matter fuels algal growth but is rarely quantified. Consequently, we cannot currently predict whether some bacterial taxa may provide more remineralized nutrients to algae than others. Here, we quantified bacterial incorporation of algal-derived complex dissolved organic carbon and nitrogen and algal incorporation of remineralized carbon and nitrogen in fifteen bacterial co-cultures growing with the diatom Phaeodactylum tricornutum at the single-cell level using isotope tracing and nanoSIMS. We found unexpected strain-to-strain and cell-to-cell variability in net carbon and nitrogen incorporation, including non-ubiquitous complex organic nitrogen utilization and remineralization. We used these data to identify three distinct functional guilds of metabolic interactions, which we termed macromolecule remineralizers, macromolecule users, and small-molecule users, the latter exhibiting efficient growth under low carbon availability. The functional guilds were not linked to phylogeny and could not be elucidated strictly from metabolic capacity as predicted by comparative genomics, highlighting the need for direct activity-based measurements in ecological studies of microbial metabolic interactions.
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Affiliation(s)
- Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - Ty J Samo
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jeff A Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Megan M Morris
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kristina Rolison
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Courtney Swink
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Christina Ramon
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Nathalie Munoz-Munoz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Carrie Nicora
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Sam Purvine
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Mary Lipton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Rhona K Stuart
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
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8
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Xue X, Su X, Zhou L, Ji J, Qin Z, Liu J, Li K, Wang H, Wang Z. Antibiotic-Induced Recruitment of Specific Algae-Associated Microbiome Enhances the Adaptability of Chlorella vulgaris to Antibiotic Stress and Incidence of Antibiotic Resistance. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:13336-13345. [PMID: 37642958 DOI: 10.1021/acs.est.3c02801] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Insights into the symbiotic relation between eukaryotic hosts and their microbiome lift the curtain on the crucial roles of microbes in host fitness, behavior, and ecology. However, it remains unclear whether and how abiotic stress shapes the microbiome and further affects host adaptability. This study first investigated the effect of antibiotic exposure on behavior across varying algae taxa at the community level. Chlorophyta, in particular Chlorella vulgaris, exhibited remarkable adaptability to antibiotic stress, leading to their dominance in phytoplankton communities. Accordingly, we isolated C. vulgaris strains and compared the growth of axenic and nonaxenic ones under antibiotic conditions. The positive roles of antibiotics in algal growth were apparent only in the presence of bacteria. Results of 16S rRNA sequencing further revealed that antibiotic challenges resulted in the recruitment of specific bacterial consortia in the phycosphere, whose functions were tightly linked to the host growth promotion and adaptability enhancement. In addition, the algal phycosphere was characterized with 47-fold higher enrichment capability of antibiotic resistance genes (ARGs) than the surrounding water. Under antibiotic stress, specific ARG profiles were recruited in C. vulgaris phycosphere, presumably driven by the specific assembly of bacterial consortia and mobile genetic elements induced by antibiotics. Moreover, the antibiotics even enhanced the dissemination potential of the bacteria carrying ARGs from the algal phycosphere to broader environmental niches. Overall, this study provides an in-depth understanding into the potential functional significance of antibiotic-mediated recruitment of specific algae-associated bacteria for algae adaptability and ARG proliferation in antibiotic-polluted waters.
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Affiliation(s)
- Xue Xue
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoyue Su
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Linjun Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiaqi Ji
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ziwei Qin
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jialin Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kaiqi Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - He Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
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9
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Huang D, Yuan MM, Chen J, Zheng X, Wong D, Alvarez PJJ, Yu P. The association of prokaryotic antiviral systems and symbiotic phage communities in drinking water microbiomes. ISME COMMUNICATIONS 2023; 3:46. [PMID: 37142716 PMCID: PMC10160068 DOI: 10.1038/s43705-023-00249-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/11/2023] [Accepted: 04/18/2023] [Indexed: 05/06/2023]
Abstract
Prokaryotic antiviral systems are important mediators for prokaryote-phage interactions, which have significant implications for the survival of prokaryotic community. However, the prokaryotic antiviral systems under environmental stress are poorly understood, limiting the understanding of microbial adaptability. Here, we systematically investigated the profile of the prokaryotic antiviral systems at the community level and prokaryote-phage interactions in the drinking water microbiome. Chlorine disinfectant was revealed as the main ecological driver for the difference in prokaryotic antiviral systems and prokaryote-phage interactions. Specifically, the prokaryotic antiviral systems in the microbiome exhibited a higher abundance, broader antiviral spectrum, and lower metabolic burden under disinfectant stress. Moreover, significant positive correlations were observed between phage lysogenicity and enrichment of antiviral systems (e.g., Type IIG and IV restriction-modification (RM) systems, and Type II CRISPR-Cas system) in the presence of disinfection, indicating these antiviral systems might be more compatible with lysogenic phages and prophages. Accordingly, there was a stronger prokaryote-phage symbiosis in disinfected microbiome, and the symbiotic phages carried more auxiliary metabolic genes (AMGs) related to prokaryotic adaptability as well as antiviral systems, which might further enhance prokaryote survival in drinking water distribution systems. Overall, this study demonstrates that the prokaryotic antiviral systems had a close association with their symbiotic phages, which provides novel insights into prokaryote-phage interactions and microbial environmental adaptation.
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Affiliation(s)
- Dan Huang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Mengting Maggie Yuan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Xiaoxuan Zheng
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Dongsheng Wong
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, USA
| | - Pingfeng Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
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10
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Holderman NR, Ferrer-González FX, Glushka J, Moran MA, Edison AS. Dissolved organic metabolite extraction from high-salt media. NMR IN BIOMEDICINE 2023; 36:e4797. [PMID: 35799308 DOI: 10.1002/nbm.4797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 06/13/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
We describe considerations and strategies for developing a nuclear magnetic resonance (NMR) sample preparation method to extract low molecular weight metabolites from high-salt spent media in a model coculture system of phytoplankton and marine bacteria. Phytoplankton perform half the carbon fixation and oxygen generation on Earth. A substantial fraction of fixed carbon becomes part of a metabolite pool of small molecules known as dissolved organic matter (DOM), which are taken up by marine bacteria proximate to phytoplankton. There is an urgent need to elucidate these metabolic exchanges due to widespread anthropogenic transformations on the chemical, phenotypic, and species composition of seawater. These changes are increasing water temperature and the amount of CO2 absorbed by the ocean at energetic costs to marine microorganisms. Little is known about the metabolite-mediated, structured interactions occurring between phytoplankton and associated marine bacteria, in part because of challenges in studying high-salt solutions on various analytical platforms. NMR analysis is problematic due to the high-salt content of both natural seawater and culture media for marine microbes. High-salt concentration degrades the performance of the radio frequency coil, reduces the efficiency of some pulse sequences, limits signal-to-noise, and prolongs experimental time. The method described herein can reproducibly extract low molecular weight DOM from small-volume, high-salt cultures. It is a promising tool for elucidating metabolic flux between marine microorganisms and facilitates genetic screens of mutant microorganisms.
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Affiliation(s)
- Nicole R Holderman
- Department of Biochemistry and Molecular Biology and Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | | | - John Glushka
- Department of Biochemistry and Molecular Biology and Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, Georgia, USA
| | - Arthur S Edison
- Department of Biochemistry and Molecular Biology and Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
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11
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Romano PS, Akematsu T, Besteiro S, Bindschedler A, Carruthers VB, Chahine Z, Coppens I, Descoteaux A, Alberto Duque TL, He CY, Heussler V, Le Roch KG, Li FJ, de Menezes JPB, Menna-Barreto RFS, Mottram JC, Schmuckli-Maurer J, Turk B, Tavares Veras PS, Salassa BN, Vanrell MC. Autophagy in protists and their hosts: When, how and why? AUTOPHAGY REPORTS 2023; 2:2149211. [PMID: 37064813 PMCID: PMC10104450 DOI: 10.1080/27694127.2022.2149211] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 11/15/2022] [Indexed: 03/12/2023]
Abstract
Pathogenic protists are a group of organisms responsible for causing a variety of human diseases including malaria, sleeping sickness, Chagas disease, leishmaniasis, and toxoplasmosis, among others. These diseases, which affect more than one billion people globally, mainly the poorest populations, are characterized by severe chronic stages and the lack of effective antiparasitic treatment. Parasitic protists display complex life-cycles and go through different cellular transformations in order to adapt to the different hosts they live in. Autophagy, a highly conserved cellular degradation process, has emerged as a key mechanism required for these differentiation processes, as well as other functions that are crucial to parasite fitness. In contrast to yeasts and mammals, protist autophagy is characterized by a modest number of conserved autophagy-related proteins (ATGs) that, even though, can drive the autophagosome formation and degradation. In addition, during their intracellular cycle, the interaction of these pathogens with the host autophagy system plays a crucial role resulting in a beneficial or harmful effect that is important for the outcome of the infection. In this review, we summarize the current state of knowledge on autophagy and other related mechanisms in pathogenic protists and their hosts. We sought to emphasize when, how, and why this process takes place, and the effects it may have on the parasitic cycle. A better understanding of the significance of autophagy for the protist life-cycle will potentially be helpful to design novel anti-parasitic strategies.
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Affiliation(s)
- Patricia Silvia Romano
- Laboratorio de Biología de Trypanosoma cruzi y de la célula hospedadora. Instituto de Histología y Embriología de Mendoza. Universidad Nacional de Cuyo. (IHEM-CONICET-UNCUYO). Facultad de Ciencias Médicas. Universidad Nacional de Cuyo. Av. Libertador 80 (5500), Mendoza, Argentina
| | - Takahiko Akematsu
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Tokyo, Japan
| | | | | | - Vern B Carruthers
- Department of Microbiology and Immunology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Zeinab Chahine
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Isabelle Coppens
- Department of Molecular Microbiology and Immunology. Department of Molecular Microbiology and Immunology. Johns Hopkins Malaria Research Institute. Johns Hopkins University Bloomberg School of Public Health. Baltimore 21205, MD, USA
| | - Albert Descoteaux
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, QC
| | - Thabata Lopes Alberto Duque
- Autophagy Inflammation and Metabolism Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Cynthia Y He
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Volker Heussler
- Institute of Cell Biology.University of Bern. Baltzerstr. 4 3012 Bern
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Feng-Jun Li
- Department of Biological Sciences, National University of Singapore, Singapore
| | | | | | - Jeremy C Mottram
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | | | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
| | - Patricia Sampaio Tavares Veras
- Laboratory of Host-Parasite Interaction and Epidemiology, Gonçalo Moniz Institute, Fiocruz-Bahia
- National Institute of Science and Technology of Tropical Diseases - National Council for Scientific Research and Development (CNPq)
| | - Betiana Nebai Salassa
- Laboratorio de Biología de Trypanosoma cruzi y de la célula hospedadora. Instituto de Histología y Embriología de Mendoza. Universidad Nacional de Cuyo. (IHEM-CONICET-UNCUYO). Facultad de Ciencias Médicas. Universidad Nacional de Cuyo. Av. Libertador 80 (5500), Mendoza, Argentina
| | - María Cristina Vanrell
- Laboratorio de Biología de Trypanosoma cruzi y de la célula hospedadora. Instituto de Histología y Embriología de Mendoza. Universidad Nacional de Cuyo. (IHEM-CONICET-UNCUYO). Facultad de Ciencias Médicas. Universidad Nacional de Cuyo. Av. Libertador 80 (5500), Mendoza, Argentina
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12
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Algicidal process and mechanisms of Enterobacter hormaechei F2 revealed by an integrated transcriptomic and metabolomic approach. Genomics 2023; 115:110586. [PMID: 36796656 DOI: 10.1016/j.ygeno.2023.110586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/27/2023] [Accepted: 02/11/2023] [Indexed: 02/16/2023]
Abstract
Controlling eutrophication with algicidal bacteria is widely recognized as an effective solution. Here, an integrated transcriptomic and metabolomic approach was used to elucidate the algicidal process of Enterobacter hormaechei F2, which exhibits substantial algicidal activity. At the transcriptome level, RNA sequencing (RNA-seq) identified 1104 differentially expressed genes in the algicidal process of the strain, thus indicating that amino acids, energy metabolism, and signaling-related genes were significantly activated during the algicidal process according to the Kyoto Encyclopedia of Genes and Genomes enrichment analysis. By analyzing the enriched amino acid and energy metabolism pathways using metabolomics, we identified 38 upregulated and 255 downregulated significantly changed metabolites in the algicidal process and an accumulation of B vitamins, peptides, and energy substances. The integrated analysis demonstrated that energy and amino acid metabolism, co-enzymes and vitamins, and bacterial chemotaxis are the most important pathways for the algicidal process of this strain, and metabolites from these pathways, such as thiomethyladenosine, isopentenyl diphosphate, hypoxanthine, xanthine, nicotinamide, and thiamine, all exhibited algicidal activity.
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13
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Diwan A, Harke SN, Panche AN. Host-microbiome interaction in fish and shellfish: An overview. FISH AND SHELLFISH IMMUNOLOGY REPORTS 2023; 4:100091. [PMID: 37091066 PMCID: PMC10113762 DOI: 10.1016/j.fsirep.2023.100091] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/28/2023] [Accepted: 03/30/2023] [Indexed: 04/03/2023] Open
Abstract
The importance of the gut microbiome in the management of various physiological activities including healthy growth and performance of fish and shellfish is now widely considered and being studied in detail for potential applications in aquaculture farming and the future growth of the fish industry. The gut microbiome in all animals including fish is associated with a number of beneficial functions for the host, such as stimulating optimal gastrointestinal development, producing and supplying vitamins to the host, and improving the host's nutrient uptake by providing additional enzymatic activities. Besides nutrient uptake, the gut microbiome is involved in strengthening the immune system and maintaining mucosal tolerance, enhancing the host's resilience against infectious diseases, and the production of anticarcinogenic and anti-inflammatory compounds. Because of its significant role, the gut microbiome is very often considered an "extra organ," as it plays a key role in intestinal development and regulation of other physiological functions. Recent studies suggest that the gut microbiome is involved in energy homeostasis by regulating feeding, digestive and metabolic processes, as well as the immune response. Consequently, deciphering gut microbiome dynamics in cultured fish and shellfish species will play an indispensable role in promoting animal health and aquaculture productivity. It is mentioned that the microbiome community available in the gut tract, particularly in the intestine acts as an innovative source of natural product discovery. The microbial communities that are associated with several marine organisms are the source of natural products with a diverse array of biological activities and as of today, more than 1000 new compounds have been reported from such microbial species. Exploration of such new ingredients from microbial species would create more opportunities for the development of the bio-pharma/aquaculture industries. Considering the important role of the microbiome in the whole life span of fish and shellfish, it is necessary to understand the interaction process between the host and microbial community. However, information pertaining to host-microbiome interaction, particularly at the cellular level, gene expression, metabolic pathways, and immunomodulation mechanisms, the available literature is scanty. It has been reported that there are three ways of interaction involving the host-microbe-environment operates to maintain homeostasis in the fish and shellfish gut i.e. host intrinsic factors, the environment that shapes the gut microbiome composition, and the core microbial community present in the gut system itself has equal influence on the host biology. In the present review, efforts have been made to collect comprehensive information on various aspects of host-microbiome interaction, particularly on the immune system and health maintenance, management of diseases, nutrient uptake, digestion and absorption, gene expression, and metabolism in fish and shellfish.
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Affiliation(s)
- A.D. Diwan
- Institute of Biosciences and Technology, Mahatma Gandhi Mission (MGM) University, Aurangabad, 431003, Maharashtra, India
- Corresponding author at: MGM Institute of Biosciences and Technology, MGM University, N-6, CIDCO, Aurangabad 431003, Maharashtra, India.
| | - Sanjay N Harke
- Institute of Biosciences and Technology, Mahatma Gandhi Mission (MGM) University, Aurangabad, 431003, Maharashtra, India
| | - Archana N Panche
- Novo Nordisk Centre for Biosustainability, Technical University of Denmark, B220 Kemitorvet, 2800 Kgs, Lyngby, Denmark
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14
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From the Sunlit to the Aphotic Zone: Assembly Mechanisms and Co-Occurrence Patterns of Protistan-Bacterial Microbiotas in the Western Pacific Ocean. mSystems 2023; 8:e0001323. [PMID: 36847533 PMCID: PMC10134807 DOI: 10.1128/msystems.00013-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
We know little about the assembly processes and association patterns of microbial communities below the photic zone. In marine pelagic systems, there are insufficient observational data regarding why and how the microbial assemblies and associations vary from photic to aphotic zones. In this study, we investigated size-fractionated oceanic microbiotas, specifically free-living (FL; 0.22 to 3 μm) and particle-associated (PA; >3 μm) bacteria and protists (0.22 to 200 μm) collected from the surface to 2,000 m in the western Pacific Ocean, to see how assembly mechanisms and association patterns changed from photic to aphotic zones. Taxonomic analysis revealed a distinct community composition between photic and aphotic zones that was largely driven by biotic associations rather than abiotic factors. Aphotic community co-occurrence was less widespread and robust than its photic counterparts, and biotic associations were crucial in microbial co-occurrence, having a higher influence on photic than aphotic co-occurrences. The decrease in biotic associations and the increase in dispersal limitation from the photic to the aphotic zone affect the deterministic-stochastic balance, leading to a more stochastic-process-driven community assembly for all three microbial groups in the aphotic zone. Our findings significantly contribute to our understanding of how and why microbial assembly and co-occurrence vary from photic to aphotic zones, offering insight into the dynamics of the protistan-bacterial microbiota in the western Pacific's photic and aphotic zones. IMPORTANCE We know little about the assembly processes and association patterns of microbial communities below the photic zone in marine pelagic systems. We discovered that community assembly processes differed between photic and aphotic zones, with all three microbial groups studied (protists and FL and PA bacteria) being more influenced by stochastic processes than in the photic zone. The decrease in organismic associations and the increase in dispersal limitation from the photic to the aphotic zone both have an impact on the deterministic-stochastic balance, resulting in a more stochastic process-driven community assembly for all three microbial groups in the aphotic zone. Our findings significantly contribute to the understanding of how and why microbial assembly and co-occurrence change between photic and aphotic zones, offering insight into the dynamics of the protist-bacteria microbiota in the western Pacific oceans.
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15
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Calatrava V, Tejada-Jimenez M, Sanz-Luque E, Fernandez E, Galvan A, Llamas A. Chlamydomonas reinhardtii, a Reference Organism to Study Algal-Microbial Interactions: Why Can't They Be Friends? PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12040788. [PMID: 36840135 PMCID: PMC9965935 DOI: 10.3390/plants12040788] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 05/13/2023]
Abstract
The stability and harmony of ecological niches rely on intricate interactions between their members. During evolution, organisms have developed the ability to thrive in different environments, taking advantage of each other. Among these organisms, microalgae are a highly diverse and widely distributed group of major primary producers whose interactions with other organisms play essential roles in their habitats. Understanding the basis of these interactions is crucial to control and exploit these communities for ecological and biotechnological applications. The green microalga Chlamydomonas reinhardtii, a well-established model, is emerging as a model organism for studying a wide variety of microbial interactions with ecological and economic significance. In this review, we unite and discuss current knowledge that points to C. reinhardtii as a model organism for studying microbial interactions.
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Affiliation(s)
- Victoria Calatrava
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama St., Stanford, CA 94305, USA
| | - Manuel Tejada-Jimenez
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
| | - Emanuel Sanz-Luque
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
| | - Emilio Fernandez
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
| | - Aurora Galvan
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
| | - Angel Llamas
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
- Correspondence: ; Tel.: +34-957-218352
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16
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Rawat D, Sharma U, Poria P, Finlan A, Parker B, Sharma RS, Mishra V. Iron-dependent mutualism between Chlorella sorokiniana and Ralstonia pickettii forms the basis for a sustainable bioremediation system. ISME COMMUNICATIONS 2022; 2:83. [PMID: 36407791 PMCID: PMC9476460 DOI: 10.1038/s43705-022-00161-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 06/15/2022] [Accepted: 07/14/2022] [Indexed: 01/11/2023]
Abstract
Phototrophic communities of autotrophic microalgae and heterotrophic bacteria perform complex tasks of nutrient acquisition and tackling environmental stress but remain underexplored as a basis for the bioremediation of emerging pollutants. In industrial monoculture designs, poor iron uptake by microalgae limits their productivity and biotechnological efficacy. Iron supplementation is expensive and ineffective because iron remains insoluble in an aqueous medium and is biologically unavailable. However, microalgae develop complex interkingdom associations with siderophore-producing bacteria that help solubilize iron and increase its bioavailability. Using dye degradation as a model, we combined environmental isolations and synthetic ecology as a workflow to design a simplified microbial community based on iron and carbon exchange. We established a mutualism between the previously non-associated alga Chlorella sorokiniana and siderophore-producing bacterium Ralstonia pickettii. Siderophore-mediated increase in iron bioavailability alleviated Fe stress for algae and increased the reductive iron uptake mechanism and bioremediation potential. In exchange, C. sorokiniana produced galactose, glucose, and mannose as major extracellular monosaccharides, supporting bacterial growth. We propose that extracellular iron reduction by ferrireductase is crucial for azoreductase-mediated dye degradation in microalgae. These results demonstrate that iron bioavailability, often overlooked in cultivation, governs microalgal growth, enzymatic processes, and bioremediation potential. Our results suggest that phototrophic communities with an active association for iron and carbon exchange have the potential to overcome challenges associated with micronutrient availability, while scaling up bioremediation designs.
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Affiliation(s)
- Deepak Rawat
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi, 110007 India
- Department of Biochemical Engineering, Bernard Katz Building, University College London, Gower Street, London, WC1E 6BT UK
- Department of Environmental Studies, Janki Devi Memorial College, University of Delhi, Delhi, 110060 India
| | - Udita Sharma
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi, 110007 India
| | - Pankaj Poria
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi, 110007 India
| | - Arran Finlan
- Department of Biochemical Engineering, Bernard Katz Building, University College London, Gower Street, London, WC1E 6BT UK
| | - Brenda Parker
- Department of Biochemical Engineering, Bernard Katz Building, University College London, Gower Street, London, WC1E 6BT UK
| | - Radhey Shyam Sharma
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi, 110007 India
- Delhi School of Climate Change & Sustainability, Institute of Eminence, University of Delhi, Delhi, 110007 India
| | - Vandana Mishra
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi, 110007 India
- Centre for Interdisciplinary Studies on Mountain & Hill Environment, University of Delhi, Delhi, 110007 India
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Xiao Y, Chen J, Chen M, Deng SJ, Xiong ZQ, Tian BY, Zhang BH. Mycolicibacterium lacusdiani sp. nov., an Attached Bacterium of Microcystis aeruginosa. Front Microbiol 2022; 13:861291. [PMID: 35633692 PMCID: PMC9134240 DOI: 10.3389/fmicb.2022.861291] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/11/2022] [Indexed: 11/24/2022] Open
Abstract
In eutrophic water, attached bacteria of Microcystis play an important role in the formation, development, and degradation of Microcystis blooms. A novel actinobacterium, designated as JXJ CY 35T, was isolated from the culture mass of Microcystis aeruginosa FACHB-905 (Maf) collected from Lake Dianchi, Yunnan Province, China. Strain JXJ CY 35T was gram-positive, acid-fast staining, aerobic, with short rod-shaped cells, positive for catalase, and negative for oxidase. The isolate was able to grow at 10.0–36.0°C, pH 4.0–10.0, and tolerate up to 5.0% (w/v) NaCl, with optimal growth at 28°C, pH 7.0–8.0, and 0% (w/v) NaCl. Cell-wall peptidoglycan contains aspartic acid, glutamic acid, glycine, and alanine, with mannose, ribose, galactose, and arabinose as whole-cell sugars. Polar lipids consist of diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), glycolipid (GL1-3), phosphoglycolipid (PGL), phosphatidylinositol (PI), and unidentified lipid (L1). The predominant menaquinone was MK-9. Major fatty acids (>10%) were C17:1ω7c (37.0%) and C18:1ω9c (18.9%). The complete genome sequence of strain JXJ CY 35T was 6,138,096 bp in size with a DNA G + C content of 68.3%. Based on 16S rRNA gene sequences, it has 98.2% similarity to Mycolicibacterium arabiense JCM 18538T. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain JXJ CY 35T and the closest five type strains M. arabiense JCM 18538T, M. goodii ATCC 700504T, M. mageritense DSM 44476T, M. austroafricanum DSM 44191T, and Mycobacterium neglectum CECT 8778T were 52.1, 20.3, 20.3, 20.6, and 19.8%, and 92.7, 75.5, 75.6, 76.0, and 75.2%, respectively. On the basis of the above taxonomic data and differences in physiological characteristics from the closely related type strain, strain JXJ CY 35T was determined to represent a novel species of genus Mycolicibacterium, for which the name Mycolicibacterium lacusdiani sp. nov., is proposed. The type strain is JXJ CY 35T (=KCTC 49379T = CGMCC 1.17501T). Different inoculation dosages of the type strain JXJ CY 35T could exhibit different effects on the growth of Maf and its toxin synthesis and release. Strain JXJ CY 35T could promote the growth of Maf by providing it with available phosphorus, nitrogen, probably vitamins, and plant growth hormones.
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Affiliation(s)
- Yao Xiao
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Jian Chen
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Min Chen
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Shao-Ji Deng
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Zhi-Qian Xiong
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Bao-Yu Tian
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Bing-Huo Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
- *Correspondence: Bing-Huo Zhang
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18
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Moran MA, Kujawinski EB, Schroer WF, Amin SA, Bates NR, Bertrand EM, Braakman R, Brown CT, Covert MW, Doney SC, Dyhrman ST, Edison AS, Eren AM, Levine NM, Li L, Ross AC, Saito MA, Santoro AE, Segrè D, Shade A, Sullivan MB, Vardi A. Microbial metabolites in the marine carbon cycle. Nat Microbiol 2022; 7:508-523. [PMID: 35365785 DOI: 10.1038/s41564-022-01090-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/23/2022] [Indexed: 01/08/2023]
Abstract
One-quarter of photosynthesis-derived carbon on Earth rapidly cycles through a set of short-lived seawater metabolites that are generated from the activities of marine phytoplankton, bacteria, grazers and viruses. Here we discuss the sources of microbial metabolites in the surface ocean, their roles in ecology and biogeochemistry, and approaches that can be used to analyse them from chemistry, biology, modelling and data science. Although microbial-derived metabolites account for only a minor fraction of the total reservoir of marine dissolved organic carbon, their flux and fate underpins the central role of the ocean in sustaining life on Earth.
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Affiliation(s)
- Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, USA.
| | - Elizabeth B Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - William F Schroer
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Shady A Amin
- Division of Science, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Nicholas R Bates
- Bermuda Institute of Ocean Sciences, St George's, Bermuda.,School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - Erin M Bertrand
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Rogier Braakman
- Departments of Earth, Atmospheric and Planetary Sciences, and Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - C Titus Brown
- Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Scott C Doney
- Department of Environmental Sciences, University of Virginia, Charlottesville, VA, USA
| | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, USA.,Department of Earth and Environmental Science, Columbia University, Palisades, NY, USA
| | - Arthur S Edison
- Departments of Biochemistry and Genetics, Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - A Murat Eren
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA.,Helmholtz-Institute for Functional Marine Biodiversity (HIFMB), University of Oldenburg, Oldenburg, Germany
| | - Naomi M Levine
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada
| | - Mak A Saito
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Alyson E Santoro
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Daniel Segrè
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA, USA
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, and Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
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19
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Exchange of Vitamin B 1 and Its Biosynthesis Intermediates Shapes the Composition of Synthetic Microbial Cocultures and Reveals Complexities of Nutrient Sharing. J Bacteriol 2022; 204:e0050321. [PMID: 35357164 DOI: 10.1128/jb.00503-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Microbial communities occupy diverse niches in nature, and community members routinely exchange a variety of nutrients among themselves. While large-scale metagenomic and metabolomic studies shed some light on these exchanges, the contribution of individual species and the molecular details of specific interactions are difficult to track. In this study, we follow the exchange of vitamin B1 (thiamin) and its intermediates between microbes within synthetic cocultures of Escherichia coli and Vibrio anguillarum. Thiamin contains two moieties, 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) and 4-methyl-5-(2-hydroxyethyl)thiazole (THZ), which are synthesized by distinct pathways using enzymes ThiC and ThiG, respectively, and then coupled by ThiE to form thiamin. Even though E. coli ΔthiC, ΔthiE, and ΔthiG mutants are thiamin auxotrophs, we observed that cocultures of ΔthiC-ΔthiE and ΔthiC-ΔthiG mutants are able to grow in a thiamin-deficient medium, whereas the ΔthiE-ΔthiG coculture does not. Further, the exchange of thiamin and its intermediates in V. anguillarum cocultures and in mixed cocultures of V. anguillarum and E. coli revealed that there exist specific patterns for thiamin metabolism and exchange among these microbes. Our findings show that HMP is shared more frequently than THZ, concurrent with previous observations that free HMP and HMP auxotrophy is commonly found in various environments. Furthermore, we observe that the availability of exogenous thiamin in the media affects whether these strains interact with each other or grow independently. These findings collectively underscore the importance of the exchange of essential metabolites as a defining factor in building and modulating synthetic or natural microbial communities. IMPORTANCE Vitamin B1 (thiamin) is an essential nutrient for cellular metabolism. Microorganisms that are unable to synthesize thiamin either fully or in part exogenously obtain it from their environment or via exchanges with other microbial members in their community. In this study, we created synthetic microbial cocultures that rely on sharing thiamin and its biosynthesis intermediates and observed that some of them are preferentially exchanged. We also observed that the coculture composition is dictated by the production and/or availability of thiamin and its intermediates. Our studies with synthetic cocultures provide the molecular basis for understanding thiamin sharing among microorganisms and lay out broad guidelines for setting up synthetic microbial cocultures by using the exchange of an essential metabolite as their foundation.
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20
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Gobler CJ, Jankowiak JG. Dynamic Responses of Endosymbiotic Microbial Communities Within Microcystis Colonies in North American Lakes to Altered Nitrogen, Phosphorus, and Temperature Levels. Front Microbiol 2022; 12:781500. [PMID: 35222297 PMCID: PMC8867038 DOI: 10.3389/fmicb.2021.781500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/23/2021] [Indexed: 11/29/2022] Open
Abstract
The toxic cyanobacterium, Microcystis, is a pervasive cyanobacterial harmful algal bloom (CHAB) - forming genus that naturally occurs in colonies that harbor diverse microbiomes of heterotrophic bacteria. While the effects of nutrient loading and climatic warming on CHABs are well-known, little is known regarding how these environmental drivers alter the structural and functional potential of the microbial assemblages associated with blooms that, in turn, may impact cyanobacterial growth. Here, we used next-generation sequencing of 16S ribosomal rRNA genes to characterize the dynamics of the bacterial assemblages within Microcystis colonies in two temperate North American lakes: Lake Erie and Lake Agawam (NY, United States) and quantified their responses to experimentally increased levels of nitrogen (N), phosphorus (P) and temperature. Across experiments, Microcystis populations were consistently and significantly promoted by N and, to a lesser extent, elevated temperature (p < 0.05). In contrast, bacterial assemblages within Microcystis colonies were more resilient to environmental perturbations, with the relative abundance of 7–16% of amplicon sequence variants changing and several individual taxa displaying significant (p < 0.05) increases and decreases in relative abundance, primarily in response to elevated temperature and to a lesser extent, N. In contrast to individual taxa, community diversity was not significantly altered by individual treatments during experiments but rather was inversely correlated with the intensity of Microcystis blooms (p < 0.001). While predicted metabolic function was even less impacted by environmental drivers than microbial diversity, the predicted abundance of nitrogenase (nifH), alkaline phosphatase (phoX), and urease (ure) genes significantly increased in response to N but decreased in response to increased temperature (p < 0.05). Collectively, the resilience of microbial community structure and function within colonies suggests they may support the ability of Microcystis to persist through short-term fluctuations in environmental conditions by supplying essential nutrients.
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21
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Jin X, Yang Y, Cao H, Gao B, Zhao Z. Eco-phylogenetic analyses reveal divergent evolution of vitamin B 12 metabolism in the marine bacterial family 'Psychromonadaceae'. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:147-163. [PMID: 34921716 DOI: 10.1111/1758-2229.13036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Cobalamin (vitamin B12 ) is an essential micronutrient required by both prokaryotes and eukaryotes. Nevertheless, with high genetic and metabolic cost, de novo cobalamin biosynthesis is exclusive to a subset of prokaryotic taxa. Many Cyanobacterial and Archaeal taxa have been implicated in de novo cobalamin biosynthesis in epi- and mesopelagic ocean respectively. However, the contributions of Gammaproteobacteria particularly the family 'Psychromonadaceae' is largely unknown. Through phylo-pangenomic analyses using concatenated single-copy proteins and homologous gene clusters respectively, the phylogenies within 'Psychromonadaceae' recapitulate both their taxonomic delineations and environmental distributions. Moreover, uneven distribution of cobalamin de novo biosynthetic operon and cobalamin-dependent light-responsive regulon were observed, and of which the linkages to the environmental conditions where cobalamin availability and light regime can be varied respectively were discussed, suggesting the impacts of ecological divergence in shaping their disparate cobalamin-related metabolisms. Functional analysis demonstrated a varying degree of cobalamin dependency for both central metabolic processes and cobalamin-mediated light-responsive regulation, and underlying sequence characteristics of cis- and trans-regulatory elements were revealed. Our findings emphasized the potential roles of cobalamin in shaping the ecological distributions and driving the metabolic evolution in the marine bacterial family 'Psychromonadaceae', and have further implications for an improved understanding of nutritional interdependencies and community metabolism modulated by cobalamin.
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Affiliation(s)
- Xingkun Jin
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yaofang Yang
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Haihang Cao
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Beile Gao
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Zhe Zhao
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
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22
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OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6585976. [DOI: 10.1093/femsre/fuac020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
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23
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Martin K, Schmidt K, Toseland A, Boulton CA, Barry K, Beszteri B, Brussaard CPD, Clum A, Daum CG, Eloe-Fadrosh E, Fong A, Foster B, Foster B, Ginzburg M, Huntemann M, Ivanova NN, Kyrpides NC, Lindquist E, Mukherjee S, Palaniappan K, Reddy TBK, Rizkallah MR, Roux S, Timmermans K, Tringe SG, van de Poll WH, Varghese N, Valentin KU, Lenton TM, Grigoriev IV, Leggett RM, Moulton V, Mock T. The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole. Nat Commun 2021; 12:5483. [PMID: 34531387 PMCID: PMC8446083 DOI: 10.1038/s41467-021-25646-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 08/12/2021] [Indexed: 02/08/2023] Open
Abstract
Eukaryotic phytoplankton are responsible for at least 20% of annual global carbon fixation. Their diversity and activity are shaped by interactions with prokaryotes as part of complex microbiomes. Although differences in their local species diversity have been estimated, we still have a limited understanding of environmental conditions responsible for compositional differences between local species communities on a large scale from pole to pole. Here, we show, based on pole-to-pole phytoplankton metatranscriptomes and microbial rDNA sequencing, that environmental differences between polar and non-polar upper oceans most strongly impact the large-scale spatial pattern of biodiversity and gene activity in algal microbiomes. The geographic differentiation of co-occurring microbes in algal microbiomes can be well explained by the latitudinal temperature gradient and associated break points in their beta diversity, with an average breakpoint at 14 °C ± 4.3, separating cold and warm upper oceans. As global warming impacts upper ocean temperatures, we project that break points of beta diversity move markedly pole-wards. Hence, abrupt regime shifts in algal microbiomes could be caused by anthropogenic climate change.
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Affiliation(s)
- Kara Martin
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Katrin Schmidt
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrew Toseland
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bánk Beszteri
- Department of Biology, University of Duisburg-Essen, Essen, Essen, Germany
| | | | - Alicia Clum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris G Daum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Emiley Eloe-Fadrosh
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Allison Fong
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | - Brian Foster
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bryce Foster
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael Ginzburg
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | - Marcel Huntemann
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Natalia N Ivanova
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nikos C Kyrpides
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Erika Lindquist
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Supratim Mukherjee
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Krishnaveni Palaniappan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - T B K Reddy
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mariam R Rizkallah
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | - Simon Roux
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Klaas Timmermans
- Royal Netherlands Institute for Sea Research, Texel, The Netherlands
| | - Susannah G Tringe
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Willem H van de Poll
- Centre for Isotope Research - Oceans, Energy and Sustainability Research Institute Groningen, Faculty of Science and Engineering, University of Groningen, AG Groningen, The Netherlands
| | - Neha Varghese
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Klaus U Valentin
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | | | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Plant and Microbial Biology Department, University of California, Berkeley, CA, USA
| | | | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
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24
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Xue X, Wang L, Xing H, Zhao Y, Li X, Wang G, Wang Z. Characteristics of phytoplankton-zooplankton communities and the roles in the transmission of antibiotic resistance genes under the pressure of river contamination. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 780:146452. [PMID: 33770605 DOI: 10.1016/j.scitotenv.2021.146452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Insight into the distribution of antibiotic resistance genes (ARGs) in phytoplankton-zooplankton communities (PZCs) is essential for the management and control of antibiotic resistance in aquatic ecosystems. This study characterized the profiles of PZCs and their carried ARGs in a typical urban river and ranked the factors (water physicochemical parameters, PZCs, bacterial abundance, and mobile genetic elements) influencing the dynamic of ARG profiles by the partial least squares path modeling. Results showed Cyanobacteria, Bacillariophyta and Chlorophyta were dominant phyla of phytoplankton, and Rotifera was with the highest abundance in zooplankton. River contamination markedly altered the structure of PZCs, increasing the abundance of phytoplankton and zooplankton, decreasing the diversity of phytoplankton while elevating in zooplankton. PZCs harbored large amounts of ARGs with average relative abundance of 2.35 × 10-2/copies nearly an order magnitude higher than the living water and most ARGs exhibited significant accumulation in PZCs with the aggravated environmental pollution. The partial least squares path modeling predicted the water parameters as the most important factor mainly playing indirect effects on ARGs via PZCs and bacterial communities, followed by mobile genetic elements as the most essential direct factor for ARGs profiles. Besides, PZCs were also important drivers for the carried ARGs via direct effects on the ARGs' composition and indirect effects on host bacterial communities of ARGs and their mobile genetic elements. The present study fills the gaps in knowledge about the distribution of ARGs in PZCs and provided a new perspective to decipher the key roles of PZCs in the maintenance and dissemination of ARGs in urban river ecosystems.
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Affiliation(s)
- Xue Xue
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lihong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Haoran Xing
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiangju Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gaoxue Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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25
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Abstract
Nutrient acquisition is a challenge that often favors small individual phytoplanktors because they are superior competitors at low nutrient levels. An alternative to these individual solutions is the union of different species into consortia that rely upon division of labor for competitive advantage. Although planktonic epibionts are well documented, the advantages of consortia for the larger host cells have remained unclear. Here, we demonstrate that attached ciliates dramatically increase the flux of dissolved nutrients to host phytoplankton cells, providing the necessary conditions for large diatoms to thrive in oligotrophic ecosystems. This demonstrates that unions between different species can substantially increase rates of nutrient flow to host cells and provides an alternative to sinking for protists living in low-nutrient conditions. Nutrient acquisition is crucial for oceanic microbes, and competitive solutions to solve this challenge have evolved among a range of unicellular protists. However, solitary solutions are not the only approach found in natural populations. A diverse array of oceanic protists form temporary or even long-lasting attachments to other protists and marine aggregates. Do these planktonic consortia provide benefits to their members? Here, we use empirical and modeling approaches to evaluate whether the relationship between a large centric diatom, Coscinodiscus wailesii, and a ciliate epibiont, Pseudovorticella coscinodisci, provides nutrient flux benefits to the host diatom. We find that fluid flows generated by ciliary beating can increase nutrient flux to a diatom cell surface four to 10 times that of a still cell without ciliate epibionts. This cosmopolitan species of diatom does not form consortia in all environments but frequently joins such consortia in nutrient-depleted waters. Our results demonstrate that symbiotic consortia provide a cooperative alternative of comparable or greater magnitude to sinking for enhancement of nutrient acquisition in challenging environments.
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26
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Ma R, Lai J, Chen X, Wang L, Yang Y, Wei S, Jiao N, Zhang R. A Novel Phage Infecting Alteromonas Represents a Distinct Group of Siphophages Infecting Diverse Aquatic Copiotrophs. mSphere 2021; 6:e0045421. [PMID: 34106770 PMCID: PMC8265664 DOI: 10.1128/msphere.00454-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 12/14/2022] Open
Abstract
Bacteriophages play critical roles in impacting microbial community succession both ecologically and evolutionarily. Although the majority of phage genetic diversity has been increasingly unveiled, phages infecting members of the ecologically important genus Alteromonas remain poorly understood. Here, we present a comprehensive analysis of a newly isolated alterophage, vB_AcoS-R7M (R7M), to characterize its life cycle traits, genomic features, and putative evolutionary origin. R7M harbors abundant genes identified as host-like auxiliary metabolic genes facilitating viral propagation. Genomic analysis suggested that R7M is distinct from currently known alterophages. Interestingly, R7M was found to share a set of similar characteristics with a number of siphophages infecting diverse aquatic opportunistic copiotrophs. We therefore proposed the creation of one new subfamily (Queuovirinae) to group with these evolutionarily related phages. Notably, tail genes were less likely to be shared among them, and baseplate-related genes varied the most. In-depth analyses indicated that R7M has replaced its distal tail with a Rhodobacter capsulatus gene transfer agent (RcGTA)-like baseplate and further acquired a putative receptor interaction site targeting Alteromonas. These findings suggest that horizontal exchanges of viral tail adsorption apparatuses are widespread and vital for phages to hunt new hosts and to adapt to new niches. IMPORTANCE The evolution and ecology of phages infecting members of Alteromonas, a marine opportunistic genus that is widely distributed and of great ecological significance, remain poorly understood. The present study integrates physiological and genomic evidence to characterize the properties and putative phage-host interactions of a newly isolated Alteromonas phage, vB_AcoS-R7M (R7M). A taxonomic study reveals close evolutionary relationships among R7M and a number of siphophages infecting various aquatic copiotrophs. Their similar head morphology and overall genetic framework suggest their putative common ancestry and the grouping of a new viral subfamily. However, their major difference lies in the viral tail adsorption apparatuses and the horizontal exchanges of which possibly account for variations in host specificity. These findings outline an evolutionary scenario for the emergence of diverse viral lineages of a shared genetic pool and give insights into the genetics and ecology of viral host jumps.
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Affiliation(s)
- Ruijie Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Jiayong Lai
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Long Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Yahui Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Shuzhen Wei
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
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27
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Dow L. How Do Quorum-Sensing Signals Mediate Algae-Bacteria Interactions? Microorganisms 2021; 9:microorganisms9071391. [PMID: 34199114 PMCID: PMC8307130 DOI: 10.3390/microorganisms9071391] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/11/2021] [Accepted: 06/15/2021] [Indexed: 11/16/2022] Open
Abstract
Quorum sensing (QS) describes a process by which bacteria can sense the local cell density of their own species, thus enabling them to coordinate gene expression and physiological processes on a community-wide scale. Small molecules called autoinducers or QS signals, which act as intraspecies signals, mediate quorum sensing. As our knowledge of QS has progressed, so too has our understanding of the structural diversity of QS signals, along with the diversity of bacteria conducting QS and the range of ecosystems in which QS takes place. It is now also clear that QS signals are more than just intraspecies signals. QS signals mediate interactions between species of prokaryotes, and between prokaryotes and eukaryotes. In recent years, our understanding of QS signals as mediators of algae-bacteria interactions has advanced such that we are beginning to develop a mechanistic understanding of their effects. This review will summarize the recent efforts to understand how different classes of QS signals contribute to the interactions between planktonic microalgae and bacteria in our oceans, primarily N-acyl-homoserine lactones, their degradation products of tetramic acids, and 2-alkyl-4-quinolones. In particular, this review will discuss the ways in which QS signals alter microalgae growth and metabolism, namely as direct effectors of photosynthesis, regulators of the cell cycle, and as modulators of other algicidal mechanisms. Furthermore, the contribution of QS signals to nutrient acquisition is discussed, and finally, how microalgae can modulate these small molecules to dampen their effects.
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Affiliation(s)
- Lachlan Dow
- Root Microbe Interactions Laboratory, Australian National University, Canberra 0200, Australia
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28
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Combining SIMS and mechanistic modelling to reveal nutrient kinetics in an algal-bacterial mutualism. PLoS One 2021; 16:e0251643. [PMID: 34014955 PMCID: PMC8136852 DOI: 10.1371/journal.pone.0251643] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/29/2021] [Indexed: 11/21/2022] Open
Abstract
Microbial communities are of considerable significance for biogeochemical processes, for the health of both animals and plants, and for biotechnological purposes. A key feature of microbial interactions is the exchange of nutrients between cells. Isotope labelling followed by analysis with secondary ion mass spectrometry (SIMS) can identify nutrient fluxes and heterogeneity of substrate utilisation on a single cell level. Here we present a novel approach that combines SIMS experiments with mechanistic modelling to reveal otherwise inaccessible nutrient kinetics. The method is applied to study the onset of a synthetic mutualistic partnership between a vitamin B12-dependent mutant of the alga Chlamydomonas reinhardtii and the B12-producing, heterotrophic bacterium Mesorhizobium japonicum, which is supported by algal photosynthesis. Results suggest that an initial pool of fixed carbon delays the onset of mutualistic cross-feeding; significantly, our approach allows the first quantification of this expected delay. Our method is widely applicable to other microbial systems, and will contribute to furthering a mechanistic understanding of microbial interactions.
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29
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Wang M, Liu X, Nie Y, Wu XL. Selfishness driving reductive evolution shapes interdependent patterns in spatially structured microbial communities. THE ISME JOURNAL 2021; 15:1387-1401. [PMID: 33343001 PMCID: PMC8115099 DOI: 10.1038/s41396-020-00858-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 11/14/2020] [Accepted: 11/24/2020] [Indexed: 12/28/2022]
Abstract
Microbes release a wide variety of metabolites to the environment that benefit the whole population, called public goods. Public goods sharing drives adaptive function loss, and allows the rise of metabolic cross-feeding. However, how public goods sharing governs the succession of communities over evolutionary time scales remains unclear. To resolve this issue, we constructed an individual-based model, where an autonomous population that possessed functions to produce three essential public goods, was allowed to randomly lose functions. Simulations revealed that function loss genotypes could evolve from the autonomous ancestor, driven by the selfish public production trade-off at the individual level. These genotypes could then automatically develop to three possible types of interdependent patterns: complete functional division, one-way dependency, and asymmetric functional complementation, which were influenced by function cost and function redundancy. In addition, we found random evolutionary events, i.e., the priority and the relative spatial positioning of genotype emergence, are also important in governing community assembly. Moreover, communities occupied by interdependent patterns exhibited better resistance to environmental perturbation, suggesting such patterns are selectively favored. Our work integrates ecological interactions with evolution dynamics, providing a new perspective to explain how reductive evolution shapes microbial interdependencies and governs the succession of communities.
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Affiliation(s)
- Miaoxiao Wang
- College of Engineering, Peking University, 100871, Beijing, China
| | - Xiaonan Liu
- College of Engineering, Peking University, 100871, Beijing, China
| | - Yong Nie
- College of Engineering, Peking University, 100871, Beijing, China.
| | - Xiao-Lei Wu
- College of Engineering, Peking University, 100871, Beijing, China.
- Institute of Ocean Research, Peking University, 100871, Beijing, China.
- Institute of Ecology, Peking University, 100871, Beijing, China.
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30
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Toward the Enhancement of Microalgal Metabolite Production through Microalgae-Bacteria Consortia. BIOLOGY 2021; 10:biology10040282. [PMID: 33915681 PMCID: PMC8065533 DOI: 10.3390/biology10040282] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/19/2021] [Accepted: 03/25/2021] [Indexed: 12/13/2022]
Abstract
Engineered mutualistic consortia of microalgae and bacteria may be a means of assembling a novel combination of metabolic capabilities with potential biotechnological advantages. Microalgae are promising organisms for the sustainable production of metabolites of commercial interest, such as lipids, carbohydrates, pigments, and proteins. Several studies reveal that microalgae growth and cellular storage of these metabolites can be enhanced significantly by co-cultivation with growth-promoting bacteria. This review summarizes the state of the art of microalgae-bacteria consortia for the production of microalgal metabolites. We discuss the current knowledge on microalgae-bacteria mutualism and the mechanisms of bacteria to enhance microalgae metabolism. Furthermore, the potential routes for a microalgae-bacteria biorefinery are outlined in an attempt to overcome the economic failures and negative energy balances of the existing production processes.
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31
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Dittami SM, Arboleda E, Auguet JC, Bigalke A, Briand E, Cárdenas P, Cardini U, Decelle J, Engelen AH, Eveillard D, Gachon CMM, Griffiths SM, Harder T, Kayal E, Kazamia E, Lallier FH, Medina M, Marzinelli EM, Morganti TM, Núñez Pons L, Prado S, Pintado J, Saha M, Selosse MA, Skillings D, Stock W, Sunagawa S, Toulza E, Vorobev A, Leblanc C, Not F. A community perspective on the concept of marine holobionts: current status, challenges, and future directions. PeerJ 2021; 9:e10911. [PMID: 33665032 PMCID: PMC7916533 DOI: 10.7717/peerj.10911] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/16/2021] [Indexed: 12/19/2022] Open
Abstract
Host-microbe interactions play crucial roles in marine ecosystems. However, we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help to describe and understand these complex systems. It posits that a host and its associated microbiota with which it interacts, form a holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences. Given the connectivity and the unexplored biodiversity specific to marine ecosystems, a deeper understanding of such complex systems requires further technological and conceptual advances, e.g., the development of controlled experimental model systems for holobionts from all major lineages and the modeling of (info)chemical-mediated interactions between organisms. Here we propose that one significant challenge is to bridge cross-disciplinary research on tractable model systems in order to address key ecological and evolutionary questions. This first step is crucial to decipher the main drivers of the dynamics and evolution of holobionts and to account for the holobiont concept in applied areas, such as the conservation, management, and exploitation of marine ecosystems and resources, where practical solutions to predict and mitigate the impact of human activities are more important than ever.
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Affiliation(s)
- Simon M Dittami
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Enrique Arboleda
- FR2424, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | | | - Arite Bigalke
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Enora Briand
- Laboratoire Phycotoxines, Ifremer, Nantes, France
| | - Paco Cárdenas
- Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Ulisse Cardini
- Integrative Marine Ecology Dept, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Johan Decelle
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRA, Grenoble, France
| | | | - Damien Eveillard
- Laboratoire des Sciences Numériques de Nantes (LS2N), Université de Nantes, CNRS, Nantes, France
| | - Claire M M Gachon
- Scottish Marine Institute, Scottish Association for Marine Science, Oban, United Kingdom
| | - Sarah M Griffiths
- School of Science and the Environment, Manchester Metropolitan University, Manchester, United Kingdom
| | | | - Ehsan Kayal
- FR2424, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | | | - François H Lallier
- Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, University Park, United States of America
| | - Ezequiel M Marzinelli
- Ecology and Environment Research Centre, The University of Sydney, Sydney, Australia.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Sydney Institute of Marine Science, Mosman, Australia
| | | | - Laura Núñez Pons
- Section Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Soizic Prado
- Molecules of Communication and Adaptation of Microorganisms (UMR 7245), National Museum of Natural History, CNRS, Paris, France
| | - José Pintado
- Instituto de Investigaciones Marinas, CSIC, Vigo, Spain
| | - Mahasweta Saha
- Benthic Ecology, Helmholtz Center for Ocean Research, Kiel, Germany.,Marine Ecology and Biodiversity, Plymouth Marine Laboratory, Plymouth, United Kingdom
| | - Marc-André Selosse
- National Museum of Natural History, Département Systématique et Evolution, Paris, France.,Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Derek Skillings
- Philosophy Department, University of Pennsylvania, Philadelphia, United States of America
| | - Willem Stock
- Laboratory of Protistology & Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Shinichi Sunagawa
- Dept. of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH, Zürich, Switzerland
| | - Eve Toulza
- IHPE, Univ. de Montpellier, CNRS, IFREMER, UPDV, Perpignan, France
| | - Alexey Vorobev
- CEA - Institut de Biologie François Jacob, Genoscope, Evry, France
| | - Catherine Leblanc
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Fabrice Not
- Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
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32
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Extracellular Metabolism Sets the Table for Microbial Cross-Feeding. Microbiol Mol Biol Rev 2021; 85:85/1/e00135-20. [PMID: 33441489 DOI: 10.1128/mmbr.00135-20] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The transfer of nutrients between cells, or cross-feeding, is a ubiquitous feature of microbial communities with emergent properties that influence our health and orchestrate global biogeochemical cycles. Cross-feeding inevitably involves the externalization of molecules. Some of these molecules directly serve as cross-fed nutrients, while others can facilitate cross-feeding. Altogether, externalized molecules that promote cross-feeding are diverse in structure, ranging from small molecules to macromolecules. The functions of these molecules are equally diverse, encompassing waste products, enzymes, toxins, signaling molecules, biofilm components, and nutrients of high value to most microbes, including the producer cell. As diverse as the externalized and transferred molecules are the cross-feeding relationships that can be derived from them. Many cross-feeding relationships can be summarized as cooperative but are also subject to exploitation. Even those relationships that appear to be cooperative exhibit some level of competition between partners. In this review, we summarize the major types of actively secreted, passively excreted, and directly transferred molecules that either form the basis of cross-feeding relationships or facilitate them. Drawing on examples from both natural and synthetic communities, we explore how the interplay between microbial physiology, environmental parameters, and the diverse functional attributes of extracellular molecules can influence cross-feeding dynamics. Though microbial cross-feeding interactions represent a burgeoning field of interest, we may have only begun to scratch the surface.
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33
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Käse L, Metfies K, Neuhaus S, Boersma M, Wiltshire KH, Kraberg AC. Host-parasitoid associations in marine planktonic time series: Can metabarcoding help reveal them? PLoS One 2021; 16:e0244817. [PMID: 33411833 PMCID: PMC7790432 DOI: 10.1371/journal.pone.0244817] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 12/16/2020] [Indexed: 11/26/2022] Open
Abstract
In this study, we created a dataset of a continuous three-year 18S metabarcoding survey to identify eukaryotic parasitoids, and potential connections to hosts at the Long-Term Ecological Research station Helgoland Roads. The importance of parasites and parasitoids for food web dynamics has previously been recognized mostly in terrestrial and freshwater systems, while marine planktonic parasitoids have been understudied in comparison to those. Therefore, the occurrence and role of parasites and parasitoids remains mostly unconsidered in the marine environment. We observed high abundances and diversity of parasitoid operational taxonomic units in our dataset all year round. While some parasitoid groups were present throughout the year and merely fluctuated in abundances, we also detected a succession of parasitoid groups with peaks of individual species only during certain seasons. Using co-occurrence and patterns of seasonal occurrence, we were able to identify known host-parasitoid dynamics, however identification of new potential host-parasitoid interactions was not possible due to their high dynamics and variability in the dataset.
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Affiliation(s)
- Laura Käse
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Schleswig-Holstein, Germany
| | - Katja Metfies
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Bremen, Germany
- Helmholtz-Institut für Funktionelle Marine Biodiversität, Oldenburg, Germany
| | - Stefan Neuhaus
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Bremen, Germany
| | - Maarten Boersma
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Schleswig-Holstein, Germany
- University of Bremen, Bremen, Bremen, Germany
| | - Karen Helen Wiltshire
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Schleswig-Holstein, Germany
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Wadden Sea Station, List auf Sylt, Schleswig-Holstein, Germany
| | - Alexandra Claudia Kraberg
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Bremen, Germany
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34
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Zakem EJ, Polz MF, Follows MJ. Redox-informed models of global biogeochemical cycles. Nat Commun 2020; 11:5680. [PMID: 33173062 PMCID: PMC7656242 DOI: 10.1038/s41467-020-19454-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/15/2020] [Indexed: 12/13/2022] Open
Abstract
Microbial activity mediates the fluxes of greenhouse gases. However, in the global models of the marine and terrestrial biospheres used for climate change projections, typically only photosynthetic microbial activity is resolved mechanistically. To move forward, we argue that global biogeochemical models need a theoretically grounded framework with which to constrain parameterizations of diverse microbial metabolisms. Here, we explain how the key redox chemistry underlying metabolisms provides a path towards this goal. Using this first-principles approach, the presence or absence of metabolic functional types emerges dynamically from ecological interactions, expanding model applicability to unobserved environments. “Nothing is less real than realism. It is only by selection, by elimination, by emphasis, that we get at the real meaning of things.” –Georgia O’Keefe Marine microbial activities fuel biogeochemical cycles that impact the climate, but global models do not account for the myriad physiological processes that microbes perform. Here the authors argue for a model framework that reinterprets the ocean as physics coupled to biologically-driven redox chemistry.
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Affiliation(s)
- Emily J Zakem
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Microbial Ecology, Center for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Michael J Follows
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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35
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Zachar I, Boza G. Endosymbiosis before eukaryotes: mitochondrial establishment in protoeukaryotes. Cell Mol Life Sci 2020; 77:3503-3523. [PMID: 32008087 PMCID: PMC7452879 DOI: 10.1007/s00018-020-03462-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 12/25/2019] [Accepted: 01/14/2020] [Indexed: 02/07/2023]
Abstract
Endosymbiosis and organellogenesis are virtually unknown among prokaryotes. The single presumed example is the endosymbiogenetic origin of mitochondria, which is hidden behind the event horizon of the last eukaryotic common ancestor. While eukaryotes are monophyletic, it is unlikely that during billions of years, there were no other prokaryote-prokaryote endosymbioses as symbiosis is extremely common among prokaryotes, e.g., in biofilms. Therefore, it is even more precarious to draw conclusions about potentially existing (or once existing) prokaryotic endosymbioses based on a single example. It is yet unknown if the bacterial endosymbiont was captured by a prokaryote or by a (proto-)eukaryote, and if the process of internalization was parasitic infection, slow engulfment, or phagocytosis. In this review, we accordingly explore multiple mechanisms and processes that could drive the evolution of unicellular microbial symbioses with a special attention to prokaryote-prokaryote interactions and to the mitochondrion, possibly the single prokaryotic endosymbiosis that turned out to be a major evolutionary transition. We investigate the ecology and evolutionary stability of inter-species microbial interactions based on dependence, physical proximity, cost-benefit budget, and the types of benefits, investments, and controls. We identify challenges that had to be conquered for the mitochondrial host to establish a stable eukaryotic lineage. Any assumption about the initial interaction of the mitochondrial ancestor and its contemporary host based solely on their modern relationship is rather perilous. As a result, we warn against assuming an initial mutually beneficial interaction based on modern mitochondria-host cooperation. This assumption is twice fallacious: (i) endosymbioses are known to evolve from exploitative interactions and (ii) cooperativity does not necessarily lead to stable mutualism. We point out that the lack of evidence so far on the evolution of endosymbiosis from mutual syntrophy supports the idea that mitochondria emerged from an exploitative (parasitic or phagotrophic) interaction rather than from syntrophy.
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Affiliation(s)
- István Zachar
- Evolutionary Systems Research Group, Institute of Evolution, Centre for Ecological Research, Klebelsberg Kunó str. 3., Tihany, 8237, Hungary.
- MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Department of Plant Taxonomy and Ecology, Eötvös Loránd University, Pázmány Péter sétány 1/c, Budapest, 1117, Hungary.
- Center for the Conceptual Foundations of Science, Parmenides Foundation, Kirchplatz 1, 82049, Munich, Germany.
| | - Gergely Boza
- Evolutionary Systems Research Group, Institute of Evolution, Centre for Ecological Research, Klebelsberg Kunó str. 3., Tihany, 8237, Hungary
- Evolution and Ecology Program, International Institute for Applied Systems Analysis (IIASA), Schlossplatz 1, 2361, Laxenburg, Austria
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36
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Patin NV, Brown E, Chebli G, Garfield C, Kubanek J, Stewart FJ. Microbial and chemical dynamics of a toxic dinoflagellate bloom. PeerJ 2020; 8:e9493. [PMID: 33240577 PMCID: PMC7676380 DOI: 10.7717/peerj.9493] [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: 03/27/2020] [Accepted: 06/17/2020] [Indexed: 01/10/2023] Open
Abstract
Harmful Algal Blooms (HABs) exert considerable ecological and economic damage and are becoming increasingly frequent worldwide. However, the biological factors underlying HABs remain uncertain. Relationships between algae and bacteria may contribute to bloom formation, strength, and duration. We investigated the microbial communities and metabolomes associated with a HAB of the toxic dinoflagellate Karenia brevis off the west coast of Florida in June 2018. Microbial communities and intracellular metabolite pools differed based on both bacterial lifestyle and bloom level, suggesting a complex role for blooms in reshaping microbial processes. Network analysis identified K. brevis as an ecological hub in the planktonic ecosystem, with significant connections to diverse microbial taxa. These included four flavobacteria and one sequence variant unidentified past the domain level, suggesting uncharacterized diversity in phytoplankton-associated microbial communities. Additionally, intracellular metabolomic analyses associated high K. brevis levels with higher levels of aromatic compounds and lipids. These findings reveal water column microbial and chemical characteristics with potentially important implications for understanding HAB onset and duration.
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Affiliation(s)
- Nastassia V Patin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America.,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Emily Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Gabriella Chebli
- Department of Chemistry, Agnes Scott College, Decatur, GA, United States of America
| | - Claire Garfield
- School of Arts and Sciences, State University of New York at Stony Brook, Stony Brook, NY, United States of America
| | - Julia Kubanek
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America.,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, United States of America.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America.,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, United States of America.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States of America
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37
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Stock W, Blommaert L, De Troch M, Mangelinckx S, Willems A, Vyverman W, Sabbe K. Host specificity in diatom-bacteria interactions alleviates antagonistic effects. FEMS Microbiol Ecol 2020; 95:5606784. [PMID: 31647551 DOI: 10.1093/femsec/fiz171] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/23/2019] [Indexed: 11/13/2022] Open
Abstract
While different microalgae tend to be associated with different bacteria, it remains unclear whether such specific associations are beneficial for the microalgae. We assessed the impact of bacterial isolates, derived from various marine benthic diatoms, on the growth of several strains belonging to the Cylindrotheca closterium diatom species complex. We first tested the effect of 35 different bacterial isolates on the growth of a single C. closterium strain, and then evaluated the impact of 8 of these isolates on the growth of 6 C. closterium strains and 1 Cylindrotheca fusiformis strain. Surprisingly, most interactions were neutral to antagonistic. The interactions were highly specific, with diatom growth in the presence of specific bacteria differing between Cylindrotheca strains and species, and closely related bacteria eliciting contrasting diatom growth responses. These differences could be related to the origin of the bacterial isolates, as only isolates from foreign diatom hosts significantly reduced diatom growth, implying coadaptation between different Cylindrotheca strains and their associated bacteria. Interestingly, the antagonistic effect of a Marinobacter strain was alleviated by the presence of a microbial inoculum that was native to the diatom host, suggesting that coadapted bacteria might also benefit their host indirectly by preventing the establishment of harmful bacteria.
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Affiliation(s)
- Willem Stock
- Laboratory of Protistology and Aquatic Ecology, Biology Department, Ghent University, Krijgslaan 281-S8, 9000 Ghent, Belgium
| | - Lander Blommaert
- Laboratory of Protistology and Aquatic Ecology, Biology Department, Ghent University, Krijgslaan 281-S8, 9000 Ghent, Belgium
| | - Marleen De Troch
- Marine Biology, Biology Department, Ghent University, Krijgslaan 281-S8, 9000 Ghent, Belgium
| | - Sven Mangelinckx
- SynBioC, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Anne Willems
- Laboratory of Microbiology, Biology Department, Ghent University, Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Biology Department, Ghent University, Krijgslaan 281-S8, 9000 Ghent, Belgium
| | - Koen Sabbe
- Laboratory of Protistology and Aquatic Ecology, Biology Department, Ghent University, Krijgslaan 281-S8, 9000 Ghent, Belgium
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38
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Bunbury F, Helliwell KE, Mehrshahi P, Davey MP, Salmon DL, Holzer A, Smirnoff N, Smith AG. Responses of a Newly Evolved Auxotroph of Chlamydomonas to B 12 Deprivation. PLANT PHYSIOLOGY 2020; 183:167-178. [PMID: 32079734 PMCID: PMC7210614 DOI: 10.1104/pp.19.01375] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/04/2020] [Indexed: 05/10/2023]
Abstract
The corrinoid B12 is synthesized only by prokaryotes yet is widely required by eukaryotes as an enzyme cofactor. Microalgae have evolved B12 dependence on multiple occasions, and we previously demonstrated that experimental evolution of the non-B12-requiring alga Chlamydomonas reinhardtii in media supplemented with B12 generated a B12-dependent mutant (hereafter metE7). This clone provides a unique opportunity to study the physiology of a nascent B12 auxotroph. Our analyses demonstrate that B12 deprivation of metE7 disrupts C1 metabolism, causes an accumulation of starch and triacylglycerides, and leads to a decrease in photosynthetic pigments, proteins, and free amino acids. B12 deprivation also caused a substantial increase in reactive oxygen species, which preceded rapid cell death. Survival could be improved without compromising growth by simultaneously depriving the cells of nitrogen, suggesting a type of cross protection. Significantly, we found further improvements in survival under B12 limitation and an increase in B12 use efficiency after metE7 underwent a further period of experimental evolution, this time in coculture with a B12-producing bacterium. Therefore, although an early B12-dependent alga would likely be poorly adapted to coping with B12 deprivation, association with B12-producers can ensure long-term survival whilst also providing a suitable environment for evolving mechanisms to tolerate B12 limitation better.
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Affiliation(s)
- Freddy Bunbury
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Katherine E Helliwell
- Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth EX4 4PY, United Kingdom
- School of Biosciences, University of Exeter, Exeter, PL1 2PB, United Kingdom
| | - Payam Mehrshahi
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Matthew P Davey
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Deborah L Salmon
- School of Biosciences, University of Exeter, Exeter, PL1 2PB, United Kingdom
| | - Andre Holzer
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Nicholas Smirnoff
- School of Biosciences, University of Exeter, Exeter, PL1 2PB, United Kingdom
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
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39
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Wang H, Zhu R, Zhang X, Li Y, Ni L, Xie P, Shen H. Abiotic environmental factors override phytoplankton succession in shaping both free-living and attached bacterial communities in a highland lake. AMB Express 2019; 9:170. [PMID: 31673822 PMCID: PMC6823470 DOI: 10.1186/s13568-019-0889-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 09/30/2019] [Indexed: 11/10/2022] Open
Abstract
Bacterial communities are an important part of biological diversity and biogeochemical cycling in aquatic ecosystems. In this study, the relationship amongst the phytoplankton species composition and abiotic environmental factors on seasonal changes in the community composition of free-living and attached bacteria in Lake Erhai were studied. Using Illumina high-throughput sequencing, we found that the impact of environmental factors on both the free-living and attached bacterial community composition was greater than that of the phytoplankton community, amongst which total phosphorus, Secchi disk, water temperature, dissolved oxygen and conductivity strongly influenced bacterial community composition. Microcystis blooms associated with subdominant Psephonema occurred during the summer and autumn, and Fragilaria, Melosira and Mougeotia were found at high densities in the other seasons. Only small numbers of algal species-specific bacteria, including Xanthomonadaceae (Proteobacteria) and Alcaligenaceae (Betaproteobacteria), were tightly coupled to Microcystis and Psephonema during Microcystis blooms. Redundancy analysis showed that although the composition of the bacterial communities was controlled by species composition mediated by changes in phytoplankton communities and abiotic environmental factors, the impact of the abiotic environment on both free-living and attached bacterial community compositions were greater than the impact of the phytoplankton community. These results suggest that the species composition of both free-living and attached bacterial communities are affected by abiotic environmental factors, even when under strong control by biotic factors, particularly dominant genera of Microcystis and Psephonema during algal blooms.
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Cirri E, Pohnert G. Algae-bacteria interactions that balance the planktonic microbiome. THE NEW PHYTOLOGIST 2019; 223:100-106. [PMID: 30825329 DOI: 10.1111/nph.15765] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/19/2019] [Indexed: 05/10/2023]
Abstract
Phytoplankton communities within the photic zones of the oceans and lakes are characterised by highly complex assemblages of unicellular microalgae and associated bacteria. The interconnected evolutionary history of algae and bacteria allowed the formation of a wide spectrum of associations defined by orchestrated nutrient exchange, mutual support with growth factors, quorum sensing mediation, and episodic killing of the partners to obtain more resources. In this review, we discuss how these cross-kingdom interactions shape plankton communities that undergo annual, seasonal switching between alternative states with balanced multispecies consortia. We illustrate how these microscopic interactions can have consequences that scale up to influence global element cycling.
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Affiliation(s)
- Emilio Cirri
- Friedrich Schiller University Jena, Institute of Inorganic and Analytical Chemistry, Lessingstr. 8, D-07743, Jena, Germany
| | - Georg Pohnert
- Friedrich Schiller University Jena, Institute of Inorganic and Analytical Chemistry, Lessingstr. 8, D-07743, Jena, Germany
- Microverse Cluster Friedrich Schiller University Jena, Neugasse 23, 07743, Jena, Germany
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Cross-exchange of B-vitamins underpins a mutualistic interaction between Ostreococcus tauri and Dinoroseobacter shibae. ISME JOURNAL 2018; 13:334-345. [PMID: 30228381 DOI: 10.1038/s41396-018-0274-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/30/2018] [Accepted: 07/27/2018] [Indexed: 11/09/2022]
Abstract
Ostreococcus tauri, a picoeukaryotic alga that contributes significantly to primary production in oligotrophic waters, has a highly streamlined genome, lacking the genetic capacity to grow without the vitamins thiamine (B1) and cobalamin (B12). Here we demonstrate that the B12 and B1 auxotrophy of O. tauri can be alleviated by co-culturing with a heterotrophic bacterial partner Dinoroseobacter shibae, a member of the Rhodobacteraceae family of alpha-proteobacteria, genera of which are frequently found associated with marine algae. D. shibae lacks the complete pathway to synthesise three other B-vitamins: niacin (B3), biotin (B7), and p-aminobenzoic acid (a precursor for folate, B9), and the alga is in turn able to satisfy the reciprocal vitamin requirements of its bacterial partner in a stable long-term co-culture. Bioinformatics searches of 197 representative marine bacteria with sequenced genomes identified just nine species that had a similar combination of traits (ability to make vitamin B12, but missing one or more genes for niacin and biotin biosynthesis enzymes), all of which were from the Rhodobacteraceae. Further analysis of 70 species from this family revealed the majority encoded the B12 pathway, but only half were able to make niacin, and fewer than 13% biotin. These characteristics may have either contributed to or resulted from the tendency of members of this lineage to adopt lifestyles in close association with algae. This study provides a nuanced view of bacterial-phytoplankton interactions, emphasising the complexity of the sources, sinks and dynamic cycling between marine microbes of these important organic micronutrients.
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Role of Chemical Mediators in Aquatic Interactions across the Prokaryote-Eukaryote Boundary. J Chem Ecol 2018; 44:1008-1021. [PMID: 30105643 DOI: 10.1007/s10886-018-1004-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 07/24/2018] [Accepted: 07/30/2018] [Indexed: 10/28/2022]
Abstract
There is worldwide growing interest in the occurrence and diversity of metabolites used as chemical mediators in cross-kingdom interactions within aquatic systems. Bacteria produce metabolites to protect and influence the growth and life cycle of their eukaryotic hosts. In turn, the host provides a nutrient-enriched environment for the bacteria. Here, we discuss the role of waterborne chemical mediators that are responsible for such interactions in aquatic multi-partner systems, including algae or invertebrates and their associated bacteria. In particular, this review highlights recent advances in the chemical ecology of aquatic systems that support the overall ecological significance of signaling molecules across the prokaryote-eukaryote boundary (cross-kingdom interactions) for growth, development and morphogenesis of the host. We emphasize the value of establishing well-characterized model systems that provide the basis for the development of ecological principles that represent the natural lifestyle and dynamics of aquatic microbial communities and enable a better understanding of the consequences of environmental change and the most effective means of managing community interactions.
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Guidi F, Pezzolesi L, Vanucci S. Microbial dynamics during harmful dinoflagellate Ostreopsis cf. ovata growth: Bacterial succession and viral abundance pattern. Microbiologyopen 2018; 7:e00584. [PMID: 29484854 PMCID: PMC6079179 DOI: 10.1002/mbo3.584] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 12/13/2017] [Accepted: 12/19/2017] [Indexed: 12/13/2022] Open
Abstract
Algal-bacterial interactions play a major role in shaping diversity of algal associated bacterial communities. Temporal variation in bacterial phylogenetic composition reflects changes of these complex interactions which occur during the algal growth cycle as well as throughout the lifetime of algal blooms. Viruses are also known to cause shifts in bacterial community diversity which could affect algal bloom phases. This study investigated on changes of bacterial and viral abundances, bacterial physiological status, and on bacterial successional pattern associated with the harmful benthic dinoflagellate Ostreopsis cf. ovata in batch cultures over the algal growth cycle. Bacterial community phylogenetic structure was assessed by 16S rRNA gene ION torrent sequencing. A comparison between bacterial community retrieved in cultures and that one co-occurring in situ during the development of the O. cf. ovata bloom from where the algal strain was isolated was also reported. Bacterial community growth was characterized by a biphasic pattern with the highest contributions (~60%) of highly active bacteria found at the two bacterial exponential growth steps. An alphaproteobacterial consortium composed by the Rhodobacteraceae Dinoroseobacter (22.2%-35.4%) and Roseovarius (5.7%-18.3%), together with Oceanicaulis (14.2-40.3%), was strongly associated with O. cf. ovata over the algal growth. The Rhodobacteraceae members encompassed phylotypes with an assessed mutualistic-pathogenic bimodal behavior. Fabibacter (0.7%-25.2%), Labrenzia (5.6%-24.3%), and Dietzia (0.04%-1.7%) were relevant at the stationary phase. Overall, the successional pattern and the metabolic and functional traits of the bacterial community retrieved in culture mirror those ones underpinning O. cf. ovata bloom dynamics in field. Viral abundances increased synoptically with bacterial abundances during the first bacterial exponential growth step while being stationary during the second step. Microbial trends also suggest that viruses induced some shifts in bacterial community composition.
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Affiliation(s)
- Flavio Guidi
- Department of Biological, Geological and Environmental Sciences (BiGeA)University of BolognaRavennaItaly
| | - Laura Pezzolesi
- Department of Biological, Geological and Environmental Sciences (BiGeA)University of BolognaRavennaItaly
| | - Silvana Vanucci
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm)University of MessinaMessinaItaly
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Boyd PW, Collins S, Dupont S, Fabricius K, Gattuso JP, Havenhand J, Hutchins DA, Riebesell U, Rintoul MS, Vichi M, Biswas H, Ciotti A, Gao K, Gehlen M, Hurd CL, Kurihara H, McGraw CM, Navarro JM, Nilsson GE, Passow U, Pörtner HO. Experimental strategies to assess the biological ramifications of multiple drivers of global ocean change-A review. GLOBAL CHANGE BIOLOGY 2018; 24:2239-2261. [PMID: 29476630 DOI: 10.1111/gcb.14102] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/11/2017] [Accepted: 01/02/2018] [Indexed: 05/19/2023]
Abstract
Marine life is controlled by multiple physical and chemical drivers and by diverse ecological processes. Many of these oceanic properties are being altered by climate change and other anthropogenic pressures. Hence, identifying the influences of multifaceted ocean change, from local to global scales, is a complex task. To guide policy-making and make projections of the future of the marine biosphere, it is essential to understand biological responses at physiological, evolutionary and ecological levels. Here, we contrast and compare different approaches to multiple driver experiments that aim to elucidate biological responses to a complex matrix of ocean global change. We present the benefits and the challenges of each approach with a focus on marine research, and guidelines to navigate through these different categories to help identify strategies that might best address research questions in fundamental physiology, experimental evolutionary biology and community ecology. Our review reveals that the field of multiple driver research is being pulled in complementary directions: the need for reductionist approaches to obtain process-oriented, mechanistic understanding and a requirement to quantify responses to projected future scenarios of ocean change. We conclude the review with recommendations on how best to align different experimental approaches to contribute fundamental information needed for science-based policy formulation.
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Affiliation(s)
- Philip W Boyd
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tas., Australia
- Antarctic Climate and Ecosystems Cooperative Research Centre, University of Tasmania, Hobart, Tas., Australia
| | - Sinead Collins
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Sam Dupont
- Department of Biological & Environmental Sciences - Kristineberg, University of Gothenburg, Gothenburg, Sweden
| | | | - Jean-Pierre Gattuso
- Observatoire Océanologique, Laboratoire d'Océanographie, CNRS-UPMC, Villefranche-Sur-Mer, France
| | - Jonathan Havenhand
- Department of Marine Sciences - Tjärnö, University of Gothenburg, Gothenburg, Sweden
| | | | - Ulf Riebesell
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Max S Rintoul
- Antarctic Climate and Ecosystems Cooperative Research Centre, University of Tasmania, Hobart, Tas., Australia
| | - Marcello Vichi
- Marine Research Institute and Department of Oceanography, University of Cape Town, Cape Town, South Africa
| | | | - Aurea Ciotti
- Centro de Biologia Marinha, Universidade de São Paulo, Sao Sebastiao, São Paulo, Brazil
| | - Kunshan Gao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
| | - Marion Gehlen
- Laboratoire des Sciences du Climat et de l'Environnement, Gif-Sur-Yvette, France
| | - Catriona L Hurd
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tas., Australia
| | | | - Christina M McGraw
- Department of Chemistry, NIWA/University of Otago Research Centre for Oceanography, University of Otago, Dunedin, New Zealand
| | - Jorge M Navarro
- Instituto de Ciencias Marinas y Limnológicas, Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile
| | | | - Uta Passow
- Marine Science Institute, UC Santa Barbara, Santa Barbara, CA, USA
| | - Hans-Otto Pörtner
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Bremerhaven, Germany
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Behringer G, Ochsenkühn MA, Fei C, Fanning J, Koester JA, Amin SA. Bacterial Communities of Diatoms Display Strong Conservation Across Strains and Time. Front Microbiol 2018; 9:659. [PMID: 29681892 PMCID: PMC5897529 DOI: 10.3389/fmicb.2018.00659] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 03/21/2018] [Indexed: 11/13/2022] Open
Abstract
Interactions between phytoplankton and bacteria play important roles in shaping the microenvironment surrounding these organisms and in turn influence global biogeochemical cycles. This microenvironment, known as the phycosphere, is presumed to shape the bacterial diversity around phytoplankton and thus stimulate a diverse array of interactions between both groups. Although many studies have attempted to characterize bacterial communities that associate and interact with phytoplankton, bias in bacterial cultivation and consistency and persistence of bacterial communities across phytoplankton isolates likely impede the understanding of these microbial associations. Here, we isolate four strains of the diatom Asterionellopsis glacialis and three strains of the diatom Nitzschia longissima and show through metabarcoding of the bacterial 16S rDNA gene that though each species possesses a unique bacterial community, the bacterial composition across strains from the same species are highly conserved at the genus level. Cultivation of all seven strains in the laboratory for longer than 1 year resulted in only small changes to the bacterial composition, suggesting that despite strong pressures from laboratory culturing conditions associations between these diatoms and their bacterial communities are robust. Specific operational taxonomic units (OTUs) belonging to the Roseobacter-clade appear to be conserved across all strains and time, suggesting their importance to diatoms. In addition, we isolate a range of cultivable bacteria from one of these cultures, A. glacialis strain A3, including several strains of Shimia marina and Nautella sp. that appear closely related to OTUs conserved across all strains and times. Coculturing of A3 with some of its cultivable bacteria as well as other diatom-associated bacteria shows a wide range of responses that include enhancing diatom growth. Cumulatively, these findings suggest that phytoplankton possess unique microbiomes that are consistent across strains and temporal scales.
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Affiliation(s)
- Gregory Behringer
- Marine Microbial Ecology Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Michael A. Ochsenkühn
- Marine Microbial Ecology Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Cong Fei
- Marine Microbial Ecology Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- College of Resources and Environmental Science, Nanjing Agriculture University, Nanjing, China
| | - Jhamal Fanning
- Marine Microbial Ecology Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Julie A. Koester
- Department of Biology and Marine Biology, University of North Carolina at Wilmington, Wilmington, NC, United States
| | - Shady A. Amin
- Marine Microbial Ecology Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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46
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Peaudecerf FJ, Bunbury F, Bhardwaj V, Bees MA, Smith AG, Goldstein RE, Croze OA. Microbial mutualism at a distance: The role of geometry in diffusive exchanges. Phys Rev E 2018; 97:022411. [PMID: 29548216 DOI: 10.1103/physreve.97.022411] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Indexed: 05/27/2023]
Abstract
The exchange of diffusive metabolites is known to control the spatial patterns formed by microbial populations, as revealed by recent studies in the laboratory. However, the matrices used, such as agarose pads, lack the structured geometry of many natural microbial habitats, including in the soil or on the surfaces of plants or animals. Here we address the important question of how such geometry may control diffusive exchanges and microbial interaction. We model mathematically mutualistic interactions within a minimal unit of structure: two growing reservoirs linked by a diffusive channel through which metabolites are exchanged. The model is applied to study a synthetic mutualism, experimentally parametrized on a model algal-bacterial co-culture. Analytical and numerical solutions of the model predict conditions for the successful establishment of remote mutualisms, and how this depends, often counterintuitively, on diffusion geometry. We connect our findings to understanding complex behavior in synthetic and naturally occurring microbial communities.
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Affiliation(s)
- François J Peaudecerf
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
| | - Freddy Bunbury
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, United Kingdom
| | - Vaibhav Bhardwaj
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, United Kingdom
| | - Martin A Bees
- Department of Mathematics, University of York, Heslington, York Y010 5DD, United Kingdom
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, United Kingdom
| | - Raymond E Goldstein
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
| | - Ottavio A Croze
- Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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Yang W, Zheng Z, Zheng C, Lu K, Ding D, Zhu J. Temporal variations in a phytoplankton community in a subtropical reservoir: An interplay of extrinsic and intrinsic community effects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 612:720-727. [PMID: 28866399 DOI: 10.1016/j.scitotenv.2017.08.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 08/04/2017] [Accepted: 08/04/2017] [Indexed: 06/07/2023]
Abstract
The phytoplankton community structure is potentially influenced by both extrinsic effects originating from the surrounding environment and intrinsic effects relying on interspecific interactions between two species. However, few studies have simultaneously considered both types of effects and assessed the relative importance of these factors. In this study, we used data collected over nine months (August 2012-May 2013) from a typical subtropical reservoir in southeast China to analyze the temporal variation of its phytoplankton community structure and develop a quantitative understanding of the extrinsic and intrinsic effects on phytoplankton community dynamics. Significant temporal variations were observed in environmental variables as well as the phytoplankton and zooplankton communities, whereas their variational trajectories and directions were entirely different. Variance partitioning analysis showed that extrinsic factors significantly explained only 31% of the variation in the phytoplankton community, thus suggesting that these factors were incomplete predictors of the community structure. Random forest-based models showed that 48% of qualified responsible phytoplankton species were more accurately predicted by phytoplankton-only models, which revealed clear effects of interspecific species-to-species interactions. Furthermore, we used association networks to model the interactions among phytoplankton, zooplankton and the environment. Network comparisons indicated that interspecific interactions were widely present in the phytoplankton community and dominated the network rather than those between phytoplankton and extrinsic factors. These findings expand the current understanding of the underlying mechanisms that govern phytoplankton community dynamics.
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Affiliation(s)
- Wen Yang
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Zhongming Zheng
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Cheng Zheng
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Kaihong Lu
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Dewen Ding
- The First Institute of Oceanography, State Oceanic Administration (SOA), Qingdao 266061, China
| | - Jinyong Zhu
- School of Marine Science, Ningbo University, Ningbo 315211, China.
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48
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Helliwell KE, Pandhal J, Cooper MB, Longworth J, Kudahl UJ, Russo DA, Tomsett EV, Bunbury F, Salmon DL, Smirnoff N, Wright PC, Smith AG. Quantitative proteomics of a B 12 -dependent alga grown in coculture with bacteria reveals metabolic tradeoffs required for mutualism. THE NEW PHYTOLOGIST 2018; 217:599-612. [PMID: 29034959 PMCID: PMC5765456 DOI: 10.1111/nph.14832] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/31/2017] [Indexed: 05/02/2023]
Abstract
The unicellular green alga Lobomonas rostrata requires an external supply of vitamin B12 (cobalamin) for growth, which it can obtain in stable laboratory cultures from the soil bacterium Mesorhizobium loti in exchange for photosynthate. We investigated changes in protein expression in the alga that allow it to engage in this mutualism. We used quantitative isobaric tagging (iTRAQ) proteomics to determine the L. rostrata proteome grown axenically with B12 supplementation or in coculture with M. loti. Data are available via ProteomeXchange (PXD005046). Using the related Chlamydomonas reinhardtii as a reference genome, 588 algal proteins could be identified. Enzymes of amino acid biosynthesis were higher in coculture than in axenic culture, and this was reflected in increased amounts of total cellular protein and several free amino acids. A number of heat shock proteins were also elevated. Conversely, photosynthetic proteins and those of chloroplast protein synthesis were significantly lower in L. rostrata cells in coculture. These observations were confirmed by measurement of electron transfer rates in cells grown under the two conditions. The results indicate that, despite the stability of the mutualism, L. rostrata experiences stress in coculture with M. loti, and must adjust its metabolism accordingly.
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Affiliation(s)
| | - Jagroop Pandhal
- Department of Chemical and Biological EngineeringUniversity of SheffieldMappin StreetSheffieldS1 3JDUK
| | - Matthew B. Cooper
- Department of Plant SciencesUniversity of CambridgeCambridgeCB2 3EAUK
| | - Joseph Longworth
- Department of Chemical and Biological EngineeringUniversity of SheffieldMappin StreetSheffieldS1 3JDUK
| | | | - David A. Russo
- Department of Chemical and Biological EngineeringUniversity of SheffieldMappin StreetSheffieldS1 3JDUK
| | | | - Freddy Bunbury
- Department of Plant SciencesUniversity of CambridgeCambridgeCB2 3EAUK
| | - Deborah L. Salmon
- BiosciencesCollege of Life and Environmental SciencesUniversity of ExeterExeterEX4 4QDUK
| | - Nicholas Smirnoff
- BiosciencesCollege of Life and Environmental SciencesUniversity of ExeterExeterEX4 4QDUK
| | - Phillip C. Wright
- Department of Chemical and Biological EngineeringUniversity of SheffieldMappin StreetSheffieldS1 3JDUK
| | - Alison G. Smith
- Department of Plant SciencesUniversity of CambridgeCambridgeCB2 3EAUK
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49
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Hillesland KL. Evolution on the bright side of life: microorganisms and the evolution of mutualism. Ann N Y Acad Sci 2017; 1422:88-103. [PMID: 29194650 DOI: 10.1111/nyas.13515] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/05/2017] [Accepted: 09/11/2017] [Indexed: 01/15/2023]
Abstract
Mutualistic interactions, where two interacting species have a net beneficial effect on each other's fitness, play a crucial role in the survival and evolution of many species. Despite substantial empirical and theoretical work in past decades, the impact of these interactions on natural selection is not fully understood. In addition, mutualisms between microorganisms have been largely ignored, even though they are ecologically important and can be used as tools to bridge the gap between theory and empirical work. Here, I describe two problems with our current understanding of natural selection in mutualism and highlight the properties of microbial mutualisms that could help solve them. One problem is that bias and methodological problems have limited our understanding of the variety of mechanisms by which species may adapt to mutualism. Another problem is that it is rare for experiments testing coevolution in mutualism to address whether each species has adapted to evolutionary changes in its partner. These problems can be addressed with genome resequencing and time-shift experiments, techniques that are easier to perform in microorganisms. In addition, microbial mutualisms may inspire novel insights and hypotheses about natural selection in mutualism.
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50
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Helliwell KE. The roles of B vitamins in phytoplankton nutrition: new perspectives and prospects. THE NEW PHYTOLOGIST 2017; 216:62-68. [PMID: 28656633 DOI: 10.1111/nph.14669] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/05/2017] [Indexed: 06/07/2023]
Abstract
Contents 62 I. 62 II. 63 III. 63 IV. 66 V. 66 VI. 67 67 References 67 SUMMARY: B vitamins play essential roles in central metabolism. These organic water-soluble molecules act as, or as part of, coenzymes within the cell. Unlike land plants, many eukaryotic algae are auxotrophic for certain B vitamins. Recent progress in algal genetic resources and environmental chemistry have promoted a renewal of interest in the role of vitamins in governing phytoplankton dynamics, and illuminated amazing versatility in phytoplankton vitamin metabolism. Accumulating evidence demonstrates metabolic complexity in the production and bioavailability of different vitamin forms, coupled with specialized acquisition strategies to salvage and remodel vitamin precursors. Here, I describe recent advances and discuss how they redefine our view of the way in which vitamins are cycled in aquatic ecosystems and their importance in structuring phytoplankton communities.
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Affiliation(s)
- Katherine E Helliwell
- The Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
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