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Krausfeldt LE, Shmakova E, Lee HW, Mazzei V, Loftin KA, Smith RP, Karwacki E, Fortman PE, Rosen BH, Urakawa H, Dadlani M, Colwell RR, Lopez JV. Microbial diversity, genomics, and phage-host interactions of cyanobacterial harmful algal blooms. mSystems 2024:e0070923. [PMID: 38856205 DOI: 10.1128/msystems.00709-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/13/2023] [Indexed: 06/11/2024] Open
Abstract
The occurrence of cyanobacterial harmful algal blooms (cyanoHABs) is related to their physical and chemical environment. However, less is known about their associated microbial interactions and processes. In this study, cyanoHABs were analyzed as a microbial ecosystem, using 1 year of 16S rRNA sequencing and 70 metagenomes collected during the bloom season from Lake Okeechobee (Florida, USA). Biogeographical patterns observed in microbial community composition and function reflected ecological zones distinct in their physical and chemical parameters that resulted in bloom "hotspots" near major lake inflows. Changes in relative abundances of taxa within multiple phyla followed increasing bloom severity. Functional pathways that correlated with increasing bloom severity encoded organic nitrogen and phosphorus utilization, storage of nutrients, exchange of genetic material, phage defense, and protection against oxidative stress, suggesting that microbial interactions may promote cyanoHAB resilience. Cyanobacterial communities were highly diverse, with picocyanobacteria ubiquitous and oftentimes most abundant, especially in the absence of blooms. The identification of novel bloom-forming cyanobacteria and genomic comparisons indicated a functionally diverse cyanobacterial community with differences in its capability to store nitrogen using cyanophycin and to defend against phage using CRISPR and restriction-modification systems. Considering blooms in the context of a microbial ecosystem and their interactions in nature, physiologies and interactions supporting the proliferation and stability of cyanoHABs are proposed, including a role for phage infection of picocyanobacteria. This study displayed the power of "-omics" to reveal important biological processes that could support the effective management and prediction of cyanoHABs. IMPORTANCE Cyanobacterial harmful algal blooms pose a significant threat to aquatic ecosystems and human health. Although physical and chemical conditions in aquatic systems that facilitate bloom development are well studied, there are fundamental gaps in the biological understanding of the microbial ecosystem that makes a cyanobacterial bloom. High-throughput sequencing was used to determine the drivers of cyanobacteria blooms in nature. Multiple functions and interactions important to consider in cyanobacterial bloom ecology were identified. The microbial biodiversity of blooms revealed microbial functions, genomic characteristics, and interactions between cyanobacterial populations that could be involved in bloom stability and more coherently define cyanobacteria blooms. Our results highlight the importance of considering cyanobacterial blooms as a microbial ecosystem to predict, prevent, and mitigate them.
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Affiliation(s)
- Lauren E Krausfeldt
- Department of Biological Sciences, Guy Harvey Oceanographic Center, Nova Southeastern University, Dania Beach, Florida, USA
| | - Elizaveta Shmakova
- Department of Biological Sciences, Guy Harvey Oceanographic Center, Nova Southeastern University, Dania Beach, Florida, USA
| | - Hyo Won Lee
- Department of Biological Sciences, Guy Harvey Oceanographic Center, Nova Southeastern University, Dania Beach, Florida, USA
| | - Viviana Mazzei
- U.S. Geological Survey, Caribbean-Florida Water Science Center, Orlando, Florida, USA
| | - Keith A Loftin
- U.S. Geological Survey, Kansas Water Science Center, Lawrence, Kansas, USA
| | - Robert P Smith
- Department of Biological Sciences, Guy Harvey Oceanographic Center, Nova Southeastern University, Dania Beach, Florida, USA
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, Florida, USA
| | - Emily Karwacki
- U.S. Geological Survey, Caribbean-Florida Water Science Center, Orlando, Florida, USA
| | - P Eric Fortman
- Department of Biological Sciences, Guy Harvey Oceanographic Center, Nova Southeastern University, Dania Beach, Florida, USA
| | - Barry H Rosen
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, Florida, USA
| | - Hidetoshi Urakawa
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, Florida, USA
| | | | - Rita R Colwell
- Institute for Advanced Computer Studies, University of Maryland College Park, College Park, Maryland, USA
| | - Jose V Lopez
- Department of Biological Sciences, Guy Harvey Oceanographic Center, Nova Southeastern University, Dania Beach, Florida, USA
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Wasswa J, Perkins M, Matthews DA, Zeng T. Characterizing the Impact of Cyanobacterial Blooms on the Photoreactivity of Surface Waters from New York Lakes: A Combined Statewide Survey and Laboratory Investigation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:8020-8031. [PMID: 38629457 PMCID: PMC11080073 DOI: 10.1021/acs.est.3c09448] [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: 11/12/2023] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 05/08/2024]
Abstract
Cyanobacterial blooms introduce autochthonous dissolved organic matter (DOM) into aquatic environments, but their impact on surface water photoreactivity has not been investigated through collaborative field sampling with comparative laboratory assessments. In this work, we quantified the apparent quantum yields (Φapp,RI) of reactive intermediates (RIs), including excited triplet states of dissolved organic matter (3DOM*), singlet oxygen (1O2), and hydroxyl radicals (•OH), for whole water samples collected by citizen volunteers from more than 100 New York lakes. Multiple comparisons tests and orthogonal partial least-squares analysis identified the level of cyanobacterial chlorophyll a as a key factor in explaining the enhanced photoreactivity of whole water samples sourced from bloom-impacted lakes. Laboratory recultivation of bloom samples in bloom-free lake water demonstrated that apparent increases in Φapp,RI during cyanobacterial growth were likely driven by the production of photoreactive moieties through the heterotrophic transformation of freshly produced labile bloom exudates. Cyanobacterial proliferation also altered the energy distribution of 3DOM* and contributed to the accelerated transformation of protriptyline, a model organic micropollutant susceptible to photosensitized reactions, under simulated sunlight conditions. Overall, our study provides insights into the relationship between the photoreactivity of surface waters and the limnological characteristics and trophic state of lakes and highlights the relevance of cyanobacterial abundance in predicting the photoreactivity of bloom-impacted surface waters.
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Affiliation(s)
- Joseph Wasswa
- Department
of Civil and Environmental Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - MaryGail Perkins
- Upstate
Freshwater Institute, Syracuse, New York 13206, United States
| | - David A. Matthews
- Upstate
Freshwater Institute, Syracuse, New York 13206, United States
| | - Teng Zeng
- Department
of Civil and Environmental Engineering, Syracuse University, Syracuse, New York 13244, United States
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3
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Baylous HR, Gladfelter MF, Gardner MI, Foley M, Wilson AE, Steffen MM. Indole-3-acetic acid promotes growth in bloom-forming Microcystis via an antioxidant response. HARMFUL ALGAE 2024; 133:102575. [PMID: 38485434 DOI: 10.1016/j.hal.2024.102575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 03/19/2024]
Abstract
Interactions between bacteria and phytoplankton in the phycosphere facilitate and constrain biogeochemical cycling in aquatic ecosystems. Indole-3-acetic acid (IAA) is a bacterially produced chemical signal that promotes growth of phytoplankton and plants. Here, we explored the impact of IAA on bloom-forming cyanobacteria and their associated bacteria. Exposure to IAA and its precursor, tryptophan, resulted in a strong growth response in a bloom of the freshwater cyanobacterium, Microcystis. Metatranscriptome analysis revealed the induction of an antioxidant response in Microcystis upon exposure to IAA, potentially allowing populations to increase photosynthetic rate and overcome internally generated reactive oxygen. Our data reveal that co-occurring bacteria within the phycosphere microbiome exhibit a division of labor for supportive functions, such as nutrient mineralization and transport, vitamin synthesis, and reactive oxygen neutralization. These complex dynamics within the Microcystis phycosphere microbiome are an example of interactions within a microenvironment that can have ecosystem-scale consequences.
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Affiliation(s)
- Hunter R Baylous
- Department of Biology, James Madison University, Harrisonburg, VA 22801, USA
| | - Matthew F Gladfelter
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Malia I Gardner
- Department of Biology, James Madison University, Harrisonburg, VA 22801, USA
| | - Madalynn Foley
- Department of Biology, James Madison University, Harrisonburg, VA 22801, USA
| | - Alan E Wilson
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Morgan M Steffen
- Department of Biology, James Madison University, Harrisonburg, VA 22801, USA.
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4
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Li H, Bhattarai B, Barber M, Goel R. Stringent Response of Cyanobacteria and Other Bacterioplankton during Different Stages of a Harmful Cyanobacterial Bloom. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16016-16032. [PMID: 37819800 DOI: 10.1021/acs.est.3c03114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
We conducted a field study to investigate the role of stringent response in cyanobacteria and coexisting bacterioplankton during nutrient-deprived periods at various stages of bloom in a freshwater lake (Utah Lake) for the first time. Using metagenomics and metatranscriptomics analyses, we examined the cyanobacterial ecology and expression of important functional genes related to stringent response, N and P metabolism, and regulation. Our findings mark a significant advancement in understanding the mechanisms by which toxic cyanobacteria survive and proliferate during nitrogen (N) and phosphorus (P) limitations. We successfully identified and analyzed the metagenome-assembled genomes (MAGs) of the dominant bloom-forming cyanobacteria, namely, Dolichospermum circinale, Aphanizomenon flos-aquae UKL13-PB, Planktothrix agardhii, and Microcystis aeruginosa. By mapping RNA-seq data to the coding sequences of the MAGs, we observed that these four prevalent cyanobacteria species activated multiple functions to adapt to the depletion of inorganic nutrients. During and after the blooms, the four dominant cyanobacteria species expressed high levels of transcripts related to toxin production, such as microcystins (mcy), anatoxins (ana), and cylindrospermopsins (cyr). Additionally, genes associated with polyphosphate (poly-P) storage and the stringent response alarmone (p)ppGpp synthesis/hydrolysis, including ppk, relA, and spoT, were highly activated in both cyanobacteria and bacterioplankton. Under N deficiency, the main N pathways shifted from denitrification and dissimilatory nitrate reduction in bacterioplankton toward N2-fixing and assimilatory nitrate reduction in certain cyanobacteria with a corresponding shift in the community composition. P deprivation triggered a stringent response mediated by spoT-dependent (p)ppGpp accumulation and activation of the Pho regulon in both cyanobacteria and bacterioplankton, facilitating inorganic and organic P uptake. The dominant cyanobacterial MAGs exhibited the presence of multiple alkaline phosphatase (APase) transcripts (e.g., phoA in Dolichospermum, phoX in Planktothrix, and Microcystis), suggesting their ability to synthesize and release APase enzymes to convert ambient organic P into bioavailable forms. Conversely, transcripts associated with bacterioplankton-dominated pathways like denitrification were low and did not align with the occurrence of intense cyanoHABs. The strong correlations observed among N, P, stringent response metabolisms and the succession of blooms caused by dominant cyanobacterial species provide evidence that the stringent response, induced by nutrient limitation, may activate unique N and P functions in toxin-producing cyanobacteria, thereby sustaining cyanoHABs.
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Affiliation(s)
- Hanyan Li
- Institute for Environmental Genomics, The University of Oklahoma, 101 David L Boren Blvd, Norman, Oklahoma 73019, United States
| | - Bishav Bhattarai
- Department of Civil and Environmental Engineering, The University of Utah, 110 S Central Campus, Salt Lake City, Utah 84112, United States
| | - Michael Barber
- Department of Civil and Environmental Engineering, The University of Utah, 110 S Central Campus, Salt Lake City, Utah 84112, United States
| | - Ramesh Goel
- Department of Civil and Environmental Engineering, The University of Utah, 110 S Central Campus, Salt Lake City, Utah 84112, United States
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Lefler FW, Barbosa M, Zimba PV, Smyth AR, Berthold DE, Laughinghouse HD. Spatiotemporal diversity and community structure of cyanobacteria and associated bacteria in the large shallow subtropical Lake Okeechobee (Florida, United States). Front Microbiol 2023; 14:1219261. [PMID: 37711696 PMCID: PMC10499181 DOI: 10.3389/fmicb.2023.1219261] [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: 05/08/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023] Open
Abstract
Lake Okeechobee is a large eutrophic, shallow, subtropical lake in south Florida, United States. Due to decades of nutrient loading and phosphorus rich sediments, the lake is eutrophic and frequently experiences cyanobacterial harmful algal blooms (cyanoHABs). In the past, surveys of the phytoplankton community structure in the lake have been conducted by morphological studies, whereas molecular based studies have been seldom employed. With increased frequency of cyanoHABs in Lake Okeechobee (e.g., 2016 and 2018 Microcystis-dominated blooms), it is imperative to determine the diversity of cyanobacterial taxa that exist within the lake and the limnological parameters that drive bloom-forming genera. A spatiotemporal study of the lake was conducted over the course of 1 year to characterize the (cyano)bacterial community structure, using 16S rRNA metabarcoding, with coincident collection of limnological parameters (e.g., nutrients, water temperature, major ions), and cyanotoxins. The objectives of this study were to elucidate spatiotemporal trends of community structure, identify drivers of community structure, and examine cyanobacteria-bacterial relationships within the lake. Results indicated that cyanobacterial communities within the lake were significantly different between the wet and dry season, but not between periods of nitrogen limitation and co-nutrient limitation. Throughout the year, the lake was primarily dominated by the picocyanobacterium Cyanobium. The bloom-forming genera Cuspidothrix, Dolichospermum, Microcystis, and Raphidiopsis were highly abundant throughout the lake and had disparate nutrient requirements and niches within the lake. Anatoxin-a, microcystins, and nodularins were detected throughout the lake across both seasons. There were no correlated (cyano)bacteria shared between the common bloom-forming cyanobacteria Dolichospermum, Microcystis, and Raphidiopsis. This study is the first of its kind to use molecular based methods to assess the cyanobacterial community structure within the lake. These data greatly improve our understanding of the cyanobacterial community structure within the lake and the physiochemical parameters which may drive the bloom-forming taxa within Lake Okeechobee.
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Affiliation(s)
- Forrest W. Lefler
- Agronomy Department, Fort Lauderdale Research and Education Center, University of Florida—IFAS, Davie, FL, United States
| | - Maximiliano Barbosa
- Agronomy Department, Fort Lauderdale Research and Education Center, University of Florida—IFAS, Davie, FL, United States
| | - Paul V. Zimba
- Rice Rivers Center, Virginia Commonwealth University, Charles City, VA, United States
| | - Ashley R. Smyth
- Soil, Water and Ecosystem Sciences Department, Tropical Research and Education Center, University of Florida—IFAS, Homestead, FL, United States
| | - David E. Berthold
- Agronomy Department, Fort Lauderdale Research and Education Center, University of Florida—IFAS, Davie, FL, United States
| | - H. Dail Laughinghouse
- Agronomy Department, Fort Lauderdale Research and Education Center, University of Florida—IFAS, Davie, FL, United States
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6
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Louati I, Nunan N, Tambosco K, Bernard C, Humbert JF, Leloup J. The phyto-bacterioplankton couple in a shallow freshwater ecosystem: Who leads the dance? HARMFUL ALGAE 2023; 126:102436. [PMID: 37290884 DOI: 10.1016/j.hal.2023.102436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 04/20/2023] [Accepted: 04/20/2023] [Indexed: 06/10/2023]
Abstract
Bloom-forming phytoplankton dynamics are still unpredictable, even though it is known that several abiotic factors, such as nutrient availability and temperature, are key factors for bloom development. We investigated whether biotic factors, i.e. the bacterioplankton composition (via 16SrDNA metabarcoding), were correlated with phytoplankton dynamics, through a weekly monitoring of a shallow lake known to host recurrent cyanobacterial blooms. We detected concomitant changes in both bacterial and phytoplankton community biomass and diversity. During the bloom event, a significant decrease in phytoplankton diversity, was detected, with a first co-dominance of Ceratium, Microcystis and Aphanizomenon, followed by a co-dominance of the two cyanobacterial genera. In the same time, we observed a decrease of the particle-associated (PA) bacterial richness and the emergence of a specific bacterial consortium that was potentially better adapted to the new nutritional niche. Unexpectedly, changes in PA bacterial communities occurred just before the development the emergence of the phytoplanktonic bloom and the associated modification of the phytoplanktonic community composition, suggesting that changes in environmental conditions leading to the bloom, were first sensed by the bacterial PA community. This last was quite stable throughout the bloom event, even though there were changes in the blooming species, suggesting that the association between cyanobacterial species and bacterial communities may not be as tight as previously described for monospecific blooming communities. Finally, the dynamics of the free-living (FL) bacterial communities displayed a different trajectory from those of the PA and phytoplankton communities. This FL communities can be viewed as a reservoir for bacterial recruitment for the PA fraction. Altogether, these data also highlight s that the spatial organization within these different microenvironments in the water column is a relevant factor in the structuring of these communities.
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Affiliation(s)
- Imen Louati
- Sorbonne Université, UMR 7618 CNRS-INRA- RD-Paris Cité-UPEC, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 4 place Jussieu, Paris cedex 05 75252, France
| | - Naoise Nunan
- Sorbonne Université, UMR 7618 CNRS-INRA- RD-Paris Cité-UPEC, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 4 place Jussieu, Paris cedex 05 75252, France; Department of Soil and Environment, Swedish University of Agricultural Sciences, P.O. Box 7014, Uppsala 75007, Sweden
| | - Kevin Tambosco
- Sorbonne Université, UMR 7618 CNRS-INRA- RD-Paris Cité-UPEC, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 4 place Jussieu, Paris cedex 05 75252, France
| | - Cécile Bernard
- Muséum National d'Histoire Naturelle, UMR 7245 CNRS-MNHN, Molécules de Communication et Adaptation des Microorganismes, Paris, France
| | - Jean-François Humbert
- Sorbonne Université, UMR 7618 CNRS-INRA- RD-Paris Cité-UPEC, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 4 place Jussieu, Paris cedex 05 75252, France
| | - Julie Leloup
- Sorbonne Université, UMR 7618 CNRS-INRA- RD-Paris Cité-UPEC, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 4 place Jussieu, Paris cedex 05 75252, France.
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7
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Chen J, Zhang T, Sun L, Liu Y, Li D, Leng X, An S. Abundance trade-offs and dominant taxa maintain the stability of the bacterioplankton community underlying Microcystis blooms. Front Microbiol 2023; 14:1181341. [PMID: 37275174 PMCID: PMC10235547 DOI: 10.3389/fmicb.2023.1181341] [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: 03/07/2023] [Accepted: 05/09/2023] [Indexed: 06/07/2023] Open
Abstract
Microcystis blooms are an intractable global environmental problem that pollute water and compromise ecosystem functioning. Closed-lake management practices keep lakes free of sewage and harmful algae invasions and have succeeded in controlling local Microcystis blooms; however, there is little understanding of how the bacterioplankton communities associated with Microcystis have changed. Here, based on metagenomic sequencing, the phyla, genera, functional genes and metabolic functions of the bacterioplankton communities were compared between open lakes (underlying Microcystis blooms) and closed lakes (no Microcystis blooms). Water properties and zooplankton density were investigated and measured as factors influencing blooms. The results showed that (1) the water quality of closed lakes was improved, and the nitrogen and phosphorus concentrations were significantly reduced. (2) The stability of open vs. closed-managed lakes differed notably at the species and genus levels (p < 0.01), but no significant variations were identified at the phylum and functional genes levels (p > 0.05). (3) The relative abundance of Microcystis (Cyanobacteria) increased dramatically in the open lakes (proportions from 1.44 to 41.76%), whereas the relative abundance of several other dominant genera of Cyanobacteria experienced a trade-off and decreased with increasing Microcystis relative abundance. (4) The main functions of the bacterioplankton communities were primarily related to dominant genera of Proteobacteria and had no significant relationship with Microcystis. Overall, the closed-lake management practices significantly reduced nutrients and prevented Microcystis blooms, but the taxonomic and functional structures of bacterioplankton communities remained stable overall.
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Affiliation(s)
- Jun Chen
- School of Life Science and Institute of Wetland Ecology, Nanjing University, Nanjing, China
- Nanjing University Ecology Research Institute of Changshu (NJUecoRICH), Changshu, China
| | - Tiange Zhang
- School of Life Science and Institute of Wetland Ecology, Nanjing University, Nanjing, China
- Nanjing University Ecology Research Institute of Changshu (NJUecoRICH), Changshu, China
| | - Lingyan Sun
- School of Life Science and Institute of Wetland Ecology, Nanjing University, Nanjing, China
- Nanjing University Ecology Research Institute of Changshu (NJUecoRICH), Changshu, China
| | - Yan Liu
- School of Life Science and Institute of Wetland Ecology, Nanjing University, Nanjing, China
- Nanjing University Ecology Research Institute of Changshu (NJUecoRICH), Changshu, China
| | - Dianpeng Li
- School of Life Science and Institute of Wetland Ecology, Nanjing University, Nanjing, China
- Nanjing University Ecology Research Institute of Changshu (NJUecoRICH), Changshu, China
| | - Xin Leng
- School of Life Science and Institute of Wetland Ecology, Nanjing University, Nanjing, China
- Nanjing University Ecology Research Institute of Changshu (NJUecoRICH), Changshu, China
| | - Shuqing An
- School of Life Science and Institute of Wetland Ecology, Nanjing University, Nanjing, China
- Nanjing University Ecology Research Institute of Changshu (NJUecoRICH), Changshu, China
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8
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Feng J, Zhou L, Zhao X, Chen J, Li Z, Liu Y, Ou L, Xie Z, Wang M, Yin X, Zhang X, Li Y, Luo M, Zeng L, Yan Q, Xie L, Sun L. Evaluation of environmental factors and microbial community structure in an important drinking-water reservoir across seasons. Front Microbiol 2023; 14:1091818. [PMID: 36865780 PMCID: PMC9971975 DOI: 10.3389/fmicb.2023.1091818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/09/2023] [Indexed: 02/18/2023] Open
Abstract
The composition of microbial communities varies in water and sediments, and changes in environmental factors have major effects on microbiomes. Here, we characterized variations in microbial communities and physicochemical factors at two sites in a large subtropical drinking water reservoir in southern China. The microbiomes of all sites, including the diversity and abundance of microbial species, were determined via metagenomics, and the relationships between microbiomes and physicochemical factors were determined via redundancy analysis. The dominant species in sediment and water samples differed; Dinobryon sp. LO226KS and Dinobryon divergens were dominant in sediment samples, whereas Candidatus Fonsibacter ubiquis and Microcystis elabens were dominant in water. The diversity was also significantly different in microbial alpha diversity between water and sediment habitats (p < 0.01). The trophic level index (TLI) was the major factor affecting the microbial community in water samples; Mycolicibacterium litorale and Mycolicibacterium phlei were significantly positively related to TLI. Furthermore, we also studied the distribution of algal toxin-encoding genes and antibiotic-resistant genes (ARGs) in the reservoir. It found that water samples contained more phycotoxin genes, with the cylindrospermopsin gene cluster most abundant. We found three genera highly related to cylindrospermopsin and explored a new cyanobacteria Aphanocapsa montana that may produce cylindrospermopsin based on the correlation through network analysis. The multidrug resistance gene was the most abundant ARG, while the relationship between ARGs and bacteria in sediment samples was more complicated than in water. The results of this study enhance our understanding of the effects of environmental factors on microbiomes. In conclusion, research on the properties, including profiles of algal toxin-encoding genes and ARGs, and microbial communities can aid water quality monitoring and conservation.
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Affiliation(s)
- Jie Feng
- State Environmental Protection Key Laboratory of Drinking Water Source Management and Technology, Shenzhen Academy of Environmental Sciences, Shenzhen, China
| | - Letian Zhou
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Xiaochao Zhao
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Jianyi Chen
- State Environmental Protection Key Laboratory of Drinking Water Source Management and Technology, Shenzhen Academy of Environmental Sciences, Shenzhen, China
| | - Zhi Li
- State Environmental Protection Key Laboratory of Drinking Water Source Management and Technology, Shenzhen Academy of Environmental Sciences, Shenzhen, China
| | - Yongfeng Liu
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Lei Ou
- State Environmental Protection Key Laboratory of Drinking Water Source Management and Technology, Shenzhen Academy of Environmental Sciences, Shenzhen, China
| | - Zixin Xie
- State Environmental Protection Key Laboratory of Drinking Water Source Management and Technology, Shenzhen Academy of Environmental Sciences, Shenzhen, China
| | - Miao Wang
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Xue Yin
- State Environmental Protection Key Laboratory of Drinking Water Source Management and Technology, Shenzhen Academy of Environmental Sciences, Shenzhen, China
| | - Xin Zhang
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Yan Li
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Mingjie Luo
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Lidong Zeng
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Qin Yan
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Linshen Xie
- State Environmental Protection Key Laboratory of Drinking Water Source Management and Technology, Shenzhen Academy of Environmental Sciences, Shenzhen, China,*Correspondence: Linshen Xie,
| | - Lei Sun
- GeneMind Biosciences Company Limited, Shenzhen, China,*Correspondence: Linshen Xie,
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Crevecoeur S, Edge TA, Watson LC, Watson SB, Greer CW, Ciborowski JJH, Diep N, Dove A, Drouillard KG, Frenken T, McKay RM, Zastepa A, Comte J. Spatio-temporal connectivity of the aquatic microbiome associated with cyanobacterial blooms along a Great Lake riverine-lacustrine continuum. Front Microbiol 2023; 14:1073753. [PMID: 36846788 PMCID: PMC9947797 DOI: 10.3389/fmicb.2023.1073753] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/16/2023] [Indexed: 02/11/2023] Open
Abstract
Lake Erie is subject to recurring events of cyanobacterial harmful algal blooms (cHABs), but measures of nutrients and total phytoplankton biomass seem to be poor predictors of cHABs when taken individually. A more integrated approach at the watershed scale may improve our understanding of the conditions that lead to bloom formation, such as assessing the physico-chemical and biological factors that influence the lake microbial community, as well as identifying the linkages between Lake Erie and the surrounding watershed. Within the scope of the Government of Canada's Genomics Research and Development Initiative (GRDI) Ecobiomics project, we used high-throughput sequencing of the 16S rRNA gene to characterize the spatio-temporal variability of the aquatic microbiome in the Thames River-Lake St. Clair-Detroit River-Lake Erie aquatic corridor. We found that the aquatic microbiome was structured along the flow path and influenced mainly by higher nutrient concentrations in the Thames River, and higher temperature and pH downstream in Lake St. Clair and Lake Erie. The same dominant bacterial phyla were detected along the water continuum, changing only in relative abundance. At finer taxonomical level, however, there was a clear shift in the cyanobacterial community, with Planktothrix dominating in the Thames River and Microcystis and Synechococcus in Lake St. Clair and Lake Erie. Mantel correlations highlighted the importance of geographic distance in shaping the microbial community structure. The fact that a high proportion of microbial sequences found in the Western Basin of Lake Erie were also identified in the Thames River, indicated a high degree of connectivity and dispersal within the system, where mass effect induced by passive transport play an important role in microbial community assembly. Nevertheless, some cyanobacterial amplicon sequence variants (ASVs) related to Microcystis, representing less than 0.1% of relative abundance in the upstream Thames River, became dominant in Lake St. Clair and Erie, suggesting selection of those ASVs based on the lake conditions. Their extremely low relative abundances in the Thames suggest additional sources are likely to contribute to the rapid development of summer and fall blooms in the Western Basin of Lake Erie. Collectively, these results, which can be applied to other watersheds, improve our understanding of the factors influencing aquatic microbial community assembly and provide new perspectives on how to better understand the occurrence of cHABs in Lake Erie and elsewhere.
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Affiliation(s)
- Sophie Crevecoeur
- Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Burlington, ON, Canada,*Correspondence: Sophie Crevecoeur, ✉
| | - Thomas A. Edge
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Linet Cynthia Watson
- Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Burlington, ON, Canada
| | - Susan B. Watson
- Department of Biology, Trent University, Peterborough, ON, Canada
| | - Charles W. Greer
- Energy, Mining and Environment, National Research Council of Canada, Montreal, QC, Canada
| | - Jan J. H. Ciborowski
- Department of Integrative Biology, University of Windsor, Windsor, ON, Canada,Department of Biological Sciences University of Calgary, Calgary, AB, Canada
| | - Ngan Diep
- Ontario Ministry of the Environment, Conservation and Parks, Environmental Monitoring and Reporting Branch, Etobicoke, ON, Canada
| | - Alice Dove
- Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Burlington, ON, Canada
| | - Kenneth G. Drouillard
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Thijs Frenken
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada,Cluster Nature & Society, HAS University of Applied Sciences, s-Hertogenbosch, Netherlands
| | - Robert Michael McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada,Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, OH, United States
| | - Arthur Zastepa
- Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Burlington, ON, Canada
| | - Jérôme Comte
- Centre Eau Terre Environnement, Institut National de la Recherche Scientifique, Quebec City, QC, Canada,Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Université de Montréal, Montreal, QC, Canada
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10
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Zepernick BN, Wilhelm SW, Bullerjahn GS, Paerl HW. Climate change and the aquatic continuum: A cyanobacterial comeback story. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:3-12. [PMID: 36096485 PMCID: PMC10103762 DOI: 10.1111/1758-2229.13122] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/11/2022] [Indexed: 05/20/2023]
Abstract
Billions of years ago, the Earth's waters were dominated by cyanobacteria. These microbes amassed to such formidable numbers, they ushered in a new era-starting with the Great Oxidation Event-fuelled by oxygenic photosynthesis. Throughout the following eon, cyanobacteria ceded portions of their global aerobic power to new photoautotrophs with the rise of eukaryotes (i.e. algae and higher plants), which co-existed with cyanobacteria in aquatic ecosystems. Yet while cyanobacteria's ecological success story is one of the most notorious within our planet's biogeochemical history, scientists to this day still seek to unlock the secrets of their triumph. Now, the Anthropocene has ushered in a new era fuelled by excessive nutrient inputs and greenhouse gas emissions, which are again reshaping the Earth's biomes. In response, we are experiencing an increase in global cyanobacterial bloom distribution, duration, and frequency, leading to unbalanced, and in many instances degraded, ecosystems. A critical component of the cyanobacterial resurgence is the freshwater-marine continuum: which serves to transport blooms, and the toxins they produce, on the premise that "water flows downhill". Here, we identify drivers contributing to the cyanobacterial comeback and discuss future implications in the context of environmental and human health along the aquatic continuum. This Minireview addresses the overlooked problem of the freshwater to marine continuum and the effects of nutrients and toxic cyanobacterial blooms moving along these waters. Marine and freshwater research have historically been conducted in isolation and independently of one another. Yet, this approach fails to account for the interchangeable transit of nutrients and biology through and between these freshwater and marine systems, a phenomenon that is becoming a major problem around the globe. This Minireview highlights what we know and the challenges that lie ahead.
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Affiliation(s)
- Brittany N. Zepernick
- Department of MicrobiologyThe University of Tennessee KnoxvilleKnoxvilleTennesseeUSA
| | - Steven W. Wilhelm
- Department of MicrobiologyThe University of Tennessee KnoxvilleKnoxvilleTennesseeUSA
| | - George S. Bullerjahn
- NIEHS/NSF Great Lakes Center for Fresh Waters and Human HealthBowling Green State UniversityBowling GreenOhioUSA
| | - Hans W. Paerl
- Institute of Marine SciencesUniversity of North Carolina at Chapel HillMorehead CityNorth CarolinaUSA
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11
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Zhou Y, Xu J, MacIsaac HJ, McKay RM, Xu R, Pei Y, Zi Y, Li J, Qian Y, Chang X. Comparative metabolomic analysis of exudates of microcystin-producing and microcystin-free Microcystis aeruginosa strains. Front Microbiol 2023; 13:1075621. [PMID: 36741884 PMCID: PMC9894096 DOI: 10.3389/fmicb.2022.1075621] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/29/2022] [Indexed: 01/20/2023] Open
Abstract
Cyanobacterial harmful algal blooms (cHABs) dominated by Microcystis aeruginosa threaten the ecological integrity and beneficial uses of lakes globally. In addition to producing hepatotoxic microcystins (MC), M. aeruginosa exudates (MaE) contain various compounds with demonstrated toxicity to aquatic biota. Previously, we found that the ecotoxicity of MaE differed between MC-producing and MC-free strains at exponential (E-phase) and stationary (S-phase) growth phases. However, the components in these exudates and their specific harmful effects were unclear. In this study, we performed untargeted metabolomics based on liquid chromatography-mass spectrometry to reveal the constituents in MaE of a MC-producing and a MC-free strain at both E-phase and S-phase. A total of 409 metabolites were identified and quantified based on their relative abundance. These compounds included lipids, organoheterocyclic compounds, organic acid, benzenoids and organic oxygen compounds. Multivariate analysis revealed that strains and growth phases significantly influenced the metabolite profile. The MC-producing strain had greater total metabolites abundance than the MC-free strain at S-phase, whereas the MC-free strain released higher concentrations of benzenoids, lipids, organic oxygen, organic nitrogen and organoheterocyclic compounds than the MC-producing strain at E-phase. Total metabolites had higher abundance in S-phase than in E- phase in both strains. Analysis of differential metabolites (DMs) and pathways suggest that lipids metabolism and biosynthesis of secondary metabolites were more tightly coupled to growth phases than to strains. Abundance of some toxic lipids and benzenoids DMs were significantly higher in the MC-free strain than the MC-producing one. This study builds on the understanding of MaE chemicals and their biotoxicity, and adds to evidence that non-MC-producing strains of cyanobacteria may also pose a threat to ecosystem health.
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Affiliation(s)
- Yuan Zhou
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Department of Ecology and Environment of Yunnan Province, Kunming Ecology and Environment Monitoring Station, Kunming, China
| | - Jun Xu
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Hugh J. MacIsaac
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Robert Michael McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Runbing Xu
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Ying Pei
- College of Agronomy and Life Sciences, Kunming University, Kunming, China
| | - Yuanyan Zi
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Jiaojiao Li
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Yu Qian
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Xuexiu Chang
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
- College of Agronomy and Life Sciences, Kunming University, Kunming, China
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12
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Pound HL, Martin RM, Zepernick BN, Christopher CJ, Howard SM, Castro HF, Campagna SR, Boyer GL, Bullerjahn GS, Chaffin JD, Wilhelm SW. Changes in Microbiome Activity and Sporadic Viral Infection Help Explain Observed Variability in Microcosm Studies. Front Microbiol 2022; 13:809989. [PMID: 35369463 PMCID: PMC8966487 DOI: 10.3389/fmicb.2022.809989] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/10/2022] [Indexed: 11/13/2022] Open
Abstract
The environmental conditions experienced by microbial communities are rarely fully simulated in the laboratory. Researchers use experimental containers ("bottles"), where natural samples can be manipulated and evaluated. However, container-based methods are subject to "bottle effects": changes that occur when enclosing the plankton community that are often times unexplained by standard measures like pigment and nutrient concentrations. We noted variability in a short-term, nutrient amendment experiment during a 2019 Lake Erie, Microcystis spp. bloom. We observed changes in heterotrophic bacteria activity (transcription) on a time-frame consistent with a response to experimental changes in nutrient availability, demonstrating how the often overlooked microbiome of cyanobacterial blooms can be altered. Samples processed at the time of collection (T0) contained abundant transcripts from Bacteroidetes, which reduced in abundance during incubation in all bottles, including controls. Significant biological variability in the expression of Microcystis-infecting phage was observed between replicates, with phosphate-amended treatments showing a 10-fold variation. The expression patterns of Microcystis-infecting phage were significantly correlated with ∼35% of Microcystis-specific functional genes and ∼45% of the cellular-metabolites measured across the entire microbial community, suggesting phage activity not only influenced Microcystis dynamics, but the biochemistry of the microbiome. Our observations demonstrate how natural heterogeneity among replicates can be harnessed to provide further insight on virus and host ecology.
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Affiliation(s)
- Helena L Pound
- Department of Microbiology, The University of Tennessee, Knoxville, TN, United States
| | - Robbie M Martin
- Department of Microbiology, The University of Tennessee, Knoxville, TN, United States
| | - Brittany N Zepernick
- Department of Microbiology, The University of Tennessee, Knoxville, TN, United States
| | - Courtney J Christopher
- Biological and Small Molecule Mass Spectrometry Core, The University of Tennessee, Knoxville, TN, United States
| | - Sara M Howard
- Biological and Small Molecule Mass Spectrometry Core, The University of Tennessee, Knoxville, TN, United States
| | - Hector F Castro
- Biological and Small Molecule Mass Spectrometry Core, The University of Tennessee, Knoxville, TN, United States
| | - Shawn R Campagna
- Biological and Small Molecule Mass Spectrometry Core, The University of Tennessee, Knoxville, TN, United States
| | - Gregory L Boyer
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, Syracuse, NY, United States
| | - George S Bullerjahn
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States
| | - Justin D Chaffin
- Stone Laboratory and Ohio Sea Grant, The Ohio State University, Put-In-Bay, OH, United States
| | - Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, TN, United States
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13
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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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14
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Pound HL, Gann ER, Wilhelm SW. A comparative study of metatranscriptomic assessment methods to characterize Microcystis blooms. LIMNOLOGY AND OCEANOGRAPHY, METHODS 2021; 19:846-854. [PMID: 35528780 PMCID: PMC9075346 DOI: 10.1002/lom3.10465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/28/2021] [Accepted: 10/19/2021] [Indexed: 06/14/2023]
Abstract
Harmful algal blooms are increasing in duration and severity globally, resulting in increased research interest. The use of genetic sequencing technologies has provided a wealth of opportunity to advance knowledge, but also poses a risk to that knowledge if handled incorrectly. The vast numbers of sequence processing tools and protocols provide a method to test nearly every hypothesis, but each method has inherent strengths and weaknesses. Here, we tested six methods to classify and quantify metatranscriptomic activity from a harmful algal bloom dominated by Microcystis spp. Three online tools were evaluated (Kaiju, MG-RAST, and GhostKOALA) in addition to three local tools that included a command line BLASTx approach, recruitment of reads to individual Microcystis genomes, and recruitment to a combined Microcystis composite genome generated from sequenced isolates with complete, closed genomes. Based on the analysis of each tool presented in this study, two recommendations are made that are dependent on the hypothesis to be tested. For researchers only interested in the function and physiology of Microcystis spp., read recruitments to the composite genome, referred to as "Frankenstein's Microcystis", provided the highest total estimates of transcript expression. However, for researchers interested in the entire bloom microbiome, the online GhostKOALA annotation tool, followed by subsequent read recruitments, provided functional and taxonomic characterization, in addition to transcript expression estimates. This study highlights the critical need for careful evaluation of methods before data analysis.
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Affiliation(s)
- Helena L. Pound
- Department of MicrobiologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Eric R. Gann
- Department of MicrobiologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Steven W. Wilhelm
- Department of MicrobiologyUniversity of TennesseeKnoxvilleTennesseeUSA
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