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Uptake of Phytoplankton-Derived Carbon and Cobalamins by Novel Acidobacteria Genera in Microcystis Blooms Inferred from Metagenomic and Metatranscriptomic Evidence. Appl Environ Microbiol 2022; 88:e0180321. [PMID: 35862730 PMCID: PMC9317899 DOI: 10.1128/aem.01803-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Interactions between bacteria and phytoplankton can influence primary production, community composition, and algal bloom development. However, these interactions are poorly described for many consortia, particularly for freshwater bloom-forming cyanobacteria. Here, we assessed the gene content and expression of two uncultivated Acidobacteria from Lake Erie Microcystis blooms. These organisms were targeted because they were previously identified as important catalase producers in Microcystis blooms, suggesting that they protect Microcystis from H2O2. Metatranscriptomics revealed that both Acidobacteria transcribed genes for uptake of organic compounds that are known cyanobacterial products and exudates, including lactate, glycolate, amino acids, peptides, and cobalamins. Expressed genes for amino acid metabolism and peptide transport and degradation suggest that use of amino acids and peptides by Acidobacteria may regenerate nitrogen for cyanobacteria and other organisms. The Acidobacteria genomes lacked genes for biosynthesis of cobalamins but expressed genes for its transport and remodeling. This indicates that the Acidobacteria obtained cobalamins externally, potentially from Microcystis, which has a complete gene repertoire for pseudocobalamin biosynthesis; expressed them in field samples; and produced pseudocobalamin in axenic culture. Both Acidobacteria were detected in Microcystis blooms worldwide. Together, the data support the hypotheses that uncultured and previously unidentified Acidobacteria taxa exchange metabolites with phytoplankton during harmful cyanobacterial blooms and influence nitrogen available to phytoplankton. Thus, novel Acidobacteria may play a role in cyanobacterial physiology and bloom development. IMPORTANCE Interactions between heterotrophic bacteria and phytoplankton influence competition and successions between phytoplankton taxa, thereby influencing ecosystem-wide processes such as carbon cycling and algal bloom development. The cyanobacterium Microcystis forms harmful blooms in freshwaters worldwide and grows in buoyant colonies that harbor other bacteria in their phycospheres. Bacteria in the phycosphere and in the surrounding community likely influence Microcystis physiology and ecology and thus the development of freshwater harmful cyanobacterial blooms. However, the impacts and mechanisms of interaction between bacteria and Microcystis are not fully understood. This study explores the mechanisms of interaction between Microcystis and uncultured members of its phycosphere in situ with population genome resolution to investigate the cooccurrence of Microcystis and freshwater Acidobacteria in blooms worldwide.
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Smith DJ, Tan JY, Powers MA, Lin XN, Davis TW, Dick GJ. Individual Microcystis colonies harbour distinct bacterial communities that differ by Microcystis oligotype and with time. Environ Microbiol 2021; 23:3020-3036. [PMID: 33830633 DOI: 10.1111/1462-2920.15514] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 03/11/2021] [Accepted: 04/06/2021] [Indexed: 12/31/2022]
Abstract
Interactions between bacteria and phytoplankton in the phycosphere have impacts at the scale of whole ecosystems, including the development of harmful algal blooms. The cyanobacterium Microcystis causes toxic blooms that threaten freshwater ecosystems and human health globally. Microcystis grows in colonies that harbour dense assemblages of other bacteria, yet the taxonomic composition of these phycosphere communities and the nature of their interactions with Microcystis are not well characterized. To identify the taxa and compositional variance within Microcystis phycosphere communities, we performed 16S rRNA V4 region amplicon sequencing on individual Microcystis colonies collected biweekly via high-throughput droplet encapsulation during a western Lake Erie cyanobacterial bloom. The Microcystis phycosphere communities were distinct from microbial communities in whole water and bulk phytoplankton seston in western Lake Erie but lacked 'core' taxa found across all colonies. However, dissimilarity in phycosphere community composition correlated with sampling date and the Microcystis 16S rRNA oligotype. Several taxa in the phycosphere were specific to and conserved with Microcystis of a single oligotype or sampling date. Together, this suggests that physiological differences between Microcystis strains, temporal changes in strain phenotypes, and the composition of seeding communities may impact community composition of the Microcystis phycosphere.
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Affiliation(s)
- Derek J Smith
- Department of Earth & Environmental Science, The University of Michigan, 1100 N. University Building, 1100 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - James Y Tan
- Department of Chemical Engineering, The University of Michigan, NCRC, 2800 Plymouth Rd., Ann Abor, MI, 48109, USA
| | - McKenzie A Powers
- Department of Earth & Environmental Science, The University of Michigan, 1100 N. University Building, 1100 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Xiaoxia N Lin
- Department of Chemical Engineering, The University of Michigan, NCRC, 2800 Plymouth Rd., Ann Abor, MI, 48109, USA
| | - Timothy W Davis
- Department of Biological Sciences, Bowling Green State University, Life Sciences Building, Corner of N. College Dr and E. Merry Avenue, Bowling Green, OH, 43403, USA
| | - Gregory J Dick
- Department of Earth & Environmental Science, The University of Michigan, 1100 N. University Building, 1100 N. University Avenue, Ann Arbor, MI, 48109, USA
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Xie G, Tang X, Gong Y, Shao K, Gao G. How do Planktonic Particle Collection Methods Affect Bacterial Diversity Estimates and Community Composition in Oligo-, Meso- and Eutrophic Lakes? Front Microbiol 2020; 11:593589. [PMID: 33343534 PMCID: PMC7746777 DOI: 10.3389/fmicb.2020.593589] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/17/2020] [Indexed: 12/26/2022] Open
Abstract
Particles are hotspots of bacterial growth and nutrient recycling in aquatic ecosystems. In the study of particle-attached (PA) and/or free-living (FL) microbial assemblages, the first step is to separate particles from their surrounding water columns. Widely used collection techniques are filtration using different pore size filters, and centrifugation; however, it is unclear how the bacterial diversity, bacterial community structure (BCS) and taxonomic composition of PA assemblages are affected by different particle collection methods. To address this knowledge gap, we collected planktonic particles from eutrophic Lake Taihu, mesotrophic Lake Tianmu, and oligotrophic Lake Fuxian in China, using filtration with five pore size of filters (20, 10, 8.0, 5.0, and 3.0 μm), and centrifugation. Bacterial communities were then analyzed using Illumina MiSeq sequencing of the 16S rRNA gene. We found that PA collection method affected BCS significantly in all lakes. Centrifugation yielded the highest species diversity and lowest mean percentage of photoautotrophic Cyanobacteria in Lake Taihu, but not in the other two lakes, thus highlighting the potential compatibility of this method in the study of PA assemblage in eutrophic lakes. The high bacterial diversity and low relative percentage of Cyanobacteria was in samples retained on 5.0 μm filters in all lakes. These results suggest that collecting PA samples in lakes using filters with 5.0 μm pore size is the preferred protocol, if species diversity and heterotrophic bacteria are the top research priorities, when comparing bacterial communities in different trophic lakes at the same time. The present study offers the possibility of collecting PA samples using unified methods in oligotrophic to eutrophic lakes.
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Affiliation(s)
- Guijuan Xie
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiangming Tang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yi Gong
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Keqiang Shao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Guang Gao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
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Cook KV, Li C, Cai H, Krumholz LR, Hambright KD, Paerl HW, Steffen MM, Wilson AE, Burford MA, Grossart H, Hamilton DP, Jiang H, Sukenik A, Latour D, Meyer EI, Padisák J, Qin B, Zamor RM, Zhu G. The global Microcystis interactome. LIMNOLOGY AND OCEANOGRAPHY 2020; 65:S194-S207. [PMID: 32051648 PMCID: PMC7003799 DOI: 10.1002/lno.11361] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 07/22/2019] [Accepted: 09/24/2019] [Indexed: 05/06/2023]
Abstract
Bacteria play key roles in the function and diversity of aquatic systems, but aside from study of specific bloom systems, little is known about the diversity or biogeography of bacteria associated with harmful cyanobacterial blooms (cyanoHABs). CyanoHAB species are known to shape bacterial community composition and to rely on functions provided by the associated bacteria, leading to the hypothesized cyanoHAB interactome, a coevolved community of synergistic and interacting bacteria species, each necessary for the success of the others. Here, we surveyed the microbiome associated with Microcystis aeruginosa during blooms in 12 lakes spanning four continents as an initial test of the hypothesized Microcystis interactome. We predicted that microbiome composition and functional potential would be similar across blooms globally. Our results, as revealed by 16S rRNA sequence similarity, indicate that M. aeruginosa is cosmopolitan in lakes across a 280° longitudinal and 90° latitudinal gradient. The microbiome communities were represented by a wide range of operational taxonomic units and relative abundances. Highly abundant taxa were more related and shared across most sites and did not vary with geographic distance, thus, like Microcystis, revealing no evidence for dispersal limitation. High phylogenetic relatedness, both within and across lakes, indicates that microbiome bacteria with similar functional potential were associated with all blooms. While Microcystis and the microbiome bacteria shared many genes, whole-community metagenomic analysis revealed a suite of biochemical pathways that could be considered complementary. Our results demonstrate a high degree of similarity across global Microcystis blooms, thereby providing initial support for the hypothesized Microcystis interactome.
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Affiliation(s)
- Katherine V. Cook
- Plankton Ecology and Limnology Laboratory, Department of BiologyThe University of OklahomaNormanOklahoma
- Program in Ecology and Evolutionary Biology and the Geographical Ecology Group, Department of BiologyThe University of OklahomaNormanOklahoma
| | - Chuang Li
- Department of Microbiology and Plant Biology and Institute for Energy and the EnvironmentThe University of OklahomaNormanOklahoma
| | - Haiyuan Cai
- Plankton Ecology and Limnology Laboratory, Department of BiologyThe University of OklahomaNormanOklahoma
| | - Lee R. Krumholz
- Department of Microbiology and Plant Biology and Institute for Energy and the EnvironmentThe University of OklahomaNormanOklahoma
| | - K. David Hambright
- Plankton Ecology and Limnology Laboratory, Department of BiologyThe University of OklahomaNormanOklahoma
- Program in Ecology and Evolutionary Biology and the Geographical Ecology Group, Department of BiologyThe University of OklahomaNormanOklahoma
| | - Hans W. Paerl
- Institute of Marine Sciences, The University of North Carolina at Chapel HillMorehead CityNorth Carolina
| | | | - Alan E. Wilson
- School of Fisheries, Aquaculture, and Aquatic SciencesAuburn UniversityAuburnAlabama
| | - Michele A. Burford
- Australian Rivers Institute and School of Environment and Science, Griffith UniversityNathanQueenslandAustralia
| | - Hans‐Peter Grossart
- Department of Experimental Limnology, Leibniz Institute for Freshwater Ecology and Inland Fisheries, Stechlin, and Institute for Biochemistry and BiologyPotsdam UniversityPotsdamGermany
| | - David P. Hamilton
- Australian Rivers Institute and School of Environment and Science, Griffith UniversityNathanQueenslandAustralia
- Environmental Research Institute, University of WaikatoWaikatoNew Zealand
| | - Helong Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and LimnologyChinese Academy of SciencesNanjingChina
| | - Assaf Sukenik
- Israel Oceanographic and Limnological ResearchThe Yigal Allon Kinneret Limnological LaboratoryMigdalIsrael
| | | | - Elisabeth I. Meyer
- Institute for Evolution and Biodiversity, University of MünsterMünsterGermany
| | - Judit Padisák
- Department of LimnologyInstitute of Environmental Science, University of PannoniaVeszprémHungary
| | - Boqiang Qin
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and LimnologyChinese Academy of SciencesNanjingChina
| | | | - Guangwei Zhu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and LimnologyChinese Academy of SciencesNanjingChina
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Tu J, Chen L, Gao S, Zhang J, Bi C, Tao Y, Lu N, Lu Z. Obtaining Genome Sequences of Mutualistic Bacteria in Single Microcystis Colonies. Int J Mol Sci 2019; 20:ijms20205047. [PMID: 31614621 PMCID: PMC6829522 DOI: 10.3390/ijms20205047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 01/01/2023] Open
Abstract
Cells of Microcystis are associated with heterotrophic bacteria and organized in colonies in natural environment, which are basic elements in the mass occurrence of cyanobacterial species. Analyzing these colonies by using metagenomics is helpful to understand species composition and relationship. Meanwhile, the difference in population abundance among Microcystis colonies could be used to recover genome bins from metagenome assemblies. Herein, we designed a pipeline to obtain high-quality genomes of mutualistic bacteria from single natural Microcystis colonies. Single colonies were lysed, and then amplified by using multiple displacement amplification to overcome the DNA quantity limit. A two-step assembly was performed after sequencing and scaffolds were grouped into putative bins based on their differential-coverage among species. We analyzed six natural colonies of three prevailing Microcystis species from Lake Taihu. Clustering results proved that colonies of the same species were similar in the microbial community composition. Eight putative population genome bins with wide bacterial diversity and different GC content were identified based on coverage difference among colonies. At the phylum level, proteobacteria was the most abundant besides cyanobacteria. Six of the population bins were further refined into nearly complete genomes (completeness > 90%).
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Affiliation(s)
- Jing Tu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Liang Chen
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Shen Gao
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Junyi Zhang
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
- Wuxi Environmental Monitoring Center, Wuxi 210096, China.
| | - Changwei Bi
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Yuhan Tao
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Na Lu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Zuhong Lu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
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Shi L, Huang Y, Zhang M, Shi X, Cai Y, Gao S, Tang X, Chen F, Lu Y, Kong F. Large buoyant particles dominated by cyanobacterial colonies harbor distinct bacterial communities from small suspended particles and free-living bacteria in the water column. Microbiologyopen 2018; 7:e00608. [PMID: 29573241 PMCID: PMC6291827 DOI: 10.1002/mbo3.608] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/20/2018] [Accepted: 01/22/2018] [Indexed: 11/29/2022] Open
Abstract
Worldwide cyanobacterial blooms greatly impair ecosystems in many eutrophic lakes and impact the microbial environment. In particular, large cyanobacterial colonies that are buoyant on the water surface may provide a distinct habitat for bacteria from other small particles that are suspended stably in the water column. To test this hypothesis, bacterial communities (excluding cyanobacteria) attached to large particles dominated by cyanobacterial colonies (>120 μm, LA), small particles (3–36 μm, SA), and free‐living bacteria (0.2–3 μm, FL) were investigated monthly for a year in Lake Taihu, China. Results confirmed that the Shannon diversity index of LA was significantly lower than that of FL, which was lower than that of SA. Cytophagia and Alphaproteobacteria were specially enriched in LA. Although samples in each habitat collected during high‐ (May to November) and low‐bloom seasons (December to April) were separated, all samples in LA were clustered and separated from SA and FL, which were also clustered during the same sampling seasons. In addition, the bacterial communities in LA were correlated with nitrate level, whereas FL and SA were correlated with nitrate level and temperature. Mantel analysis revealed that bacterial composition significantly correlated with the cyanobacterial composition in LA and FL but not in SA. These results indicate that LA provides distinct niches to bacteria, whereas the differentiation of bacterial communities in FL and SA is seasonally dependent.
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Affiliation(s)
- Limei Shi
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Yaxin Huang
- Biological Experiment Teaching Center, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Min Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Xiaoli Shi
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Yuanfeng Cai
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu Province, China
| | - Shengling Gao
- Biological Experiment Teaching Center, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Feizhou Chen
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Yaping Lu
- Biological Experiment Teaching Center, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Fanxiang Kong
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
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