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Krausfeldt LE, Lopez JV, Bilodeau CM, Won Lee H, Casali SL. Change and stasis of distinct sediment microbiomes across Port Everglades Inlet (PEI) and the adjacent coral reefs. PeerJ 2023; 11:e14288. [PMID: 36655050 PMCID: PMC9841897 DOI: 10.7717/peerj.14288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 10/02/2022] [Indexed: 01/15/2023] Open
Abstract
Deep water ports are human built coastal structures that by definition welcome ship traffic and disturbance. Evidence is accumulating that enhanced port activities such as dredging or deepening have negatively affected nearby natural habitats. Port Everglades Inlet (PEI) is a large active South Florida cargo port for over two million people and lies adjacent to coral reefs, dwindling mangroves, and recreational beaches. In this study, the microbial communities of PEI and adjacent reef sediments were characterized to serve as indicators for change due to dredging and assess anthropogenic influence on these sensitive ecosystems by sequencing the V4 region of 16S rRNA ahead of a large-scale port deepening event. For the first time, this study established baseline bacterial community characterizations and their patterns of diversity prior to and after a maintenance dredging event. PEI samples were collected for two consecutive years 2020 (Phase I, before maintenance dredging) and 2021 (Phase II, after maintenance dredging) from PEI sediments and adjacent coral reef sediments. In spite of their proximity and tidal connections through the PEI, reef and PEI sediment microbial communities were distinct. Changes in microbial diversity within the intracoastal waterway (ICW), a route for community exchange or transfers, were the greatest after maintenance dredging occurred. Microbial diversity in reef sediments also changed after dredging, indicating potential influence from resuspended sediments due to an associated increase in trace metals and decrease in cyanobacterial diversity. Sediments were identified as a possible source of human and coral pathogens, although dredging did not affect the relative abundances of these indicator microorganisms. This study highlighted the utility and relative ease of applying current molecular ecology methods to address macroscale questions with environmental management ramifications.
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Affiliation(s)
- Lauren E. Krausfeldt
- Halmos College of Arts and Sciences, Nova Southeastern University, Dania Beach, Florida, United States
| | - Jose Victor Lopez
- Halmos College of Arts and Sciences, Nova Southeastern University, Dania Beach, Florida, United States
| | | | - Hyo Won Lee
- Florida International University, Miami, Florida, USA
| | - Shelby L. Casali
- Coral Reef Conservation Program (CRCP), Florida Department of Environmental Protection, West Palm Beach, Florida, USA
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2
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Mehlrose MR, Bernard AM, Finnegan KA, Krausfeldt LE, Lopez JV, Shivji MS. Three complete mitochondrial genomes of shortfin mako sharks, Isurus oxyrinchus, from the Atlantic and Pacific Oceans. Mitochondrial DNA B Resour 2022; 7:652-654. [PMID: 35434361 PMCID: PMC9009892 DOI: 10.1080/23802359.2022.2060768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We present complete mitogenome sequences of three shortfin mako sharks (Isurus oxyrinchus) sampled from the western Pacific, and eastern and western Atlantic oceans. Mitogenome sequence lengths ranged between 16,699 bp and 16,702 bp, and all three mitogenomes contained one non-coding control region, two rRNA genes, 22 tRNA genes, and 13 protein-coding genes. Comparative assessment of five mitogenomes from globally distributed shortfin makos (the current three and two previously published mitogenomes) yielded 98.4% identity, with the protein-coding genes ATP8, ATP6, and ND5 as the most variable regions (sequence identities of 96.4%, 96.5%, and 97.6%, respectively). These mitogenome sequences contribute resources for assessing the genetic population dynamics of this endangered oceanic apex predator.
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Affiliation(s)
- Marissa R. Mehlrose
- Save Our Seas Foundation Shark Research Center, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Andrea M. Bernard
- Save Our Seas Foundation Shark Research Center, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Kimberly A. Finnegan
- Save Our Seas Foundation Shark Research Center, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Lauren E. Krausfeldt
- Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Jose V. Lopez
- Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Mahmood S. Shivji
- Save Our Seas Foundation Shark Research Center, Nova Southeastern University, Fort Lauderdale, FL, USA
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Zepernick BN, Gann ER, Martin RM, Pound HL, Krausfeldt LE, Chaffin JD, Wilhelm SW. Elevated pH Conditions Associated With Microcystis spp. Blooms Decrease Viability of the Cultured Diatom Fragilaria crotonensis and Natural Diatoms in Lake Erie. Front Microbiol 2021; 12:598736. [PMID: 33717001 PMCID: PMC7943883 DOI: 10.3389/fmicb.2021.598736] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/20/2021] [Indexed: 11/13/2022] Open
Abstract
Cyanobacterial Harmful Algal Blooms (CyanoHABs) commonly increase water column pH to alkaline levels ≥9.2, and to as high as 11. This elevated pH has been suggested to confer a competitive advantage to cyanobacteria such as Microcystis aeruginosa. Yet, there is limited information regarding the restrictive effects bloom-induced pH levels may impose on this cyanobacterium’s competitors. Due to the pH-dependency of biosilicification processes, diatoms (which seasonally both precede and proceed Microcystis blooms in many fresh waters) may be unable to synthesize frustules at these pH levels. We assessed the effects of pH on the ecologically relevant diatom Fragilaria crotonensis in vitro, and on a Lake Erie diatom community in situ. In vitro assays revealed F. crotonensis monocultures exhibited lower growth rates and abundances when cultivated at a starting pH of 9.2 in comparison to pH 7.7. The suppressed growth trends in F. crotonensis were exacerbated when co-cultured with M. aeruginosa at pH conditions and cell densities that simulated a cyanobacteria bloom. Estimates demonstrated a significant decrease in silica (Si) deposition at alkaline pH in both in vitro F. crotonensis cultures and in situ Lake Erie diatom assemblages, after as little as 48 h of alkaline pH-exposure. These observations indicate elevated pH negatively affected growth rate and diatom silica deposition; in total providing a competitive disadvantage for diatoms. Our observations demonstrate pH likely plays a significant role in bloom succession, creating a potential to prolong summer Microcystis blooms and constrain diatom fall resurgence.
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Affiliation(s)
- Brittany N Zepernick
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Eric R Gann
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Robbie M Martin
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Helena L Pound
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Lauren E Krausfeldt
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Justin D Chaffin
- F.T. 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, Knoxville, TN, United States
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4
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Krausfeldt LE, Farmer AT, Castro HF, Boyer GL, Campagna SR, Wilhelm SW. Nitrogen flux into metabolites and microcystins changes in response to different nitrogen sources in Microcystis aeruginosa NIES-843. Environ Microbiol 2020; 22:2419-2431. [PMID: 32338427 DOI: 10.1111/1462-2920.15032] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/13/2020] [Accepted: 04/18/2020] [Indexed: 01/17/2023]
Abstract
The over-enrichment of nitrogen (N) in the environment has contributed to severe and recurring harmful cyanobacterial blooms, especially by the non-N2 -fixing Microcystis spp. N chemical speciation influences cyanobacterial growth, persistence and the production of the hepatotoxin microcystin, but the physiological mechanisms to explain these observations remain unresolved. Stable-labelled isotopes and metabolomics were employed to address the influence of nitrate, ammonium, and urea on cellular physiology and production of microcystins in Microcystis aeruginosa NIES-843. Global metabolic changes were driven by both N speciation and diel cycling. Tracing 15 N-labelled nitrate, ammonium, and urea through the metabolome revealed N uptake, regardless of species, was linked to C assimilation. The production of amino acids, like arginine, and other N-rich compounds corresponded with greater turnover of microcystins in cells grown on urea compared to nitrate and ammonium. However, 15 N was incorporated into microcystins from all N sources. The differences in N flux were attributed to the energetic efficiency of growth on each N source. While N in general plays an important role in sustaining biomass, these data show that N-speciation induces physiological changes that culminate in differences in global metabolism, cellular microcystin quotas and congener composition.
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Affiliation(s)
| | - Abigail T Farmer
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Hector F Castro
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Gregory L Boyer
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, Syracuse, NY, USA
| | - Shawn R Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
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Pound HL, Gann ER, Tang X, Krausfeldt LE, Huff M, Staton ME, Talmy D, Wilhelm SW. The "Neglected Viruses" of Taihu: Abundant Transcripts for Viruses Infecting Eukaryotes and Their Potential Role in Phytoplankton Succession. Front Microbiol 2020; 11:338. [PMID: 32210938 PMCID: PMC7067694 DOI: 10.3389/fmicb.2020.00338] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/17/2020] [Indexed: 01/18/2023] Open
Abstract
Drivers of algal bloom dynamics remain poorly understood, but viruses have been implicated as important players. Research addressing bloom dynamics has generally been restricted to the virus-infection of the numerically dominant (i.e. bloom forming) taxa. Yet this approach neglects a broad diversity of viral groups, limiting our knowledge of viral interactions and constraints within these systems. We examined hallmark virus marker genes in metatranscriptomic libraries from a seasonal and spatial survey of a Microcystis aeruginosa bloom in Lake Tai (Taihu) China to identify active infections by nucleocytoplasmic large DNA viruses (NCLDVs), RNA viruses, ssDNA viruses, bacteriophage, and virophage. Phylogenetic analyses revealed a diverse virus population with seasonal and spatial variability. We observed disproportionately high expression of markers associated with NCLDVs and ssRNA viruses (consistent with viruses that infect photosynthetic protists) relative to bacteriophage infecting heterotrophic bacteria or cyanobacteria during the height of the Microcystis bloom event. Under a modified kill-the-winner scheme, we hypothesize viruses infecting protists help suppress the photosynthetic eukaryotic community and allow for the proliferation of cyanobacteria such as Microcystis. Our observations provide a foundation for a little considered factor promoting algal blooms.
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Affiliation(s)
- Helena L Pound
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Eric R Gann
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Lauren E Krausfeldt
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Matthew Huff
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Margaret E Staton
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - David Talmy
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
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Krausfeldt LE, Steffen MM, McKay RM, Bullerjahn GS, Boyer GL, Wilhelm SW. Insight Into the Molecular Mechanisms for Microcystin Biodegradation in Lake Erie and Lake Taihu. Front Microbiol 2019; 10:2741. [PMID: 31921001 PMCID: PMC6914704 DOI: 10.3389/fmicb.2019.02741] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/11/2019] [Indexed: 01/04/2023] Open
Abstract
Microcystins are potent hepatotoxins that are frequently detected in fresh water lakes plagued by toxic cyanobacteria. Microbial biodegradation has been referred to as the most important avenue for removal of microcystin from aquatic environments. The biochemical pathway most commonly associated with the degradation of microcystin is encoded by the mlrABCD (mlr) cassette. The ecological significance of this pathway remains unclear as no studies have examined the expression of these genes in natural environments. Six metatranscriptomes were generated from microcystin-producing Microcystis blooms and analyzed to assess the activity of this pathway in environmental samples. Seventy-eight samples were collected from Lake Erie, United States/Canada and Lake Tai (Taihu), China, and screened for the presence of mlr gene transcripts. Read mapping to the mlr cassette indicated transcripts for these genes were absent, with only 77 of the collective 3.7 billion reads mapping to any part of the mlr cassette. Analysis of the assembled metatranscriptomes supported this, with only distantly related sequences identified as mlrABC-like. These observations were made despite the presence of microcystin and over 500,000 reads mapping to the mcy cassette for microcystin production. Glutathione S-transferases and alkaline proteases have been previously hypothesized to be alternative pathways for microcystin biodegradation, and expression of these genes was detected across space and time in both lakes. While the activity of these alternative pathways needs to be experimentally confirmed, they may be individually or collectively more important than mlr genes in the natural environment. Importantly, the lack of mlr expression could indicate microcystin biodegradation was not occurring in the analyzed samples. This study raises interesting questions about the ubiquity, specificity and locality of microcystin biodegradation, and highlights the need for the characterization of relevant mechanisms in natural communities to understand the fate of microcystin in the environment and risk to public health.
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Affiliation(s)
- Lauren E. Krausfeldt
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Morgan M. Steffen
- Department of Biology, James Madison University, Harrisonburg, VA, United States
| | - Robert M. McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - George S. Bullerjahn
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States
| | - Gregory L. Boyer
- Department of Chemistry, College of Environmental Science and Forestry, State University of New York, Syracuse, NY, United States
| | - Steven W. Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
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7
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Davenport EJ, Neudeck MJ, Matson PG, Bullerjahn GS, Davis TW, Wilhelm SW, Denney MK, Krausfeldt LE, Stough JMA, Meyer KA, Dick GJ, Johengen TH, Lindquist E, Tringe SG, McKay RML. Metatranscriptomic Analyses of Diel Metabolic Functions During a Microcystis Bloom in Western Lake Erie (United States). Front Microbiol 2019; 10:2081. [PMID: 31551998 PMCID: PMC6746948 DOI: 10.3389/fmicb.2019.02081] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 08/23/2019] [Indexed: 12/02/2022] Open
Abstract
This study examined diel shifts in metabolic functions of Microcystis spp. during a 48-h Lagrangian survey of a toxin-producing cyanobacterial bloom in western Lake Erie in the aftermath of the 2014 Toledo Water Crisis. Transcripts mapped to the genomes of recently sequenced lower Great Lakes Microcystis isolates showed distinct patterns of gene expression between samples collected across day (10:00 h, 16:00 h) and night (22:00 h, 04:00 h). Daytime transcripts were enriched in functions related to Photosystem II (e.g., psbA), nitrogen and phosphate acquisition, cell division (ftsHZ), heat shock response (dnaK, groEL), and uptake of inorganic carbon (rbc, bicA). Genes transcribed during nighttime included those involved in phycobilisome protein synthesis and Photosystem I core subunits. Hierarchical clustering and principal component analysis (PCA) showed a tightly clustered group of nighttime expressed genes, whereas daytime transcripts were separated from each other over the 48-h duration. Lack of uniform clustering within the daytime transcripts suggested that the partitioning of gene expression in Microcystis is dependent on both circadian regulation and physicochemical changes within the environment.
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Affiliation(s)
- Emily J. Davenport
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States,Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, MI, United States
| | - Michelle J. Neudeck
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States
| | - Paul G. Matson
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States
| | - George S. Bullerjahn
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States,*Correspondence: George S. Bullerjahn,
| | - Timothy W. Davis
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States
| | - Steven W. Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Maddie K. Denney
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Lauren E. Krausfeldt
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Joshua M. A. Stough
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Kevin A. Meyer
- Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, MI, United States,Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, United States
| | - Gregory J. Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, United States
| | - Thomas H. Johengen
- Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, MI, United States
| | - Erika Lindquist
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Susannah G. Tringe
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Robert Michael L. McKay
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States,Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
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Krausfeldt LE, Farmer AT, Castro Gonzalez HF, Zepernick BN, Campagna SR, Wilhelm SW. Urea Is Both a Carbon and Nitrogen Source for Microcystis aeruginosa: Tracking 13C Incorporation at Bloom pH Conditions. Front Microbiol 2019; 10:1064. [PMID: 31164875 PMCID: PMC6536089 DOI: 10.3389/fmicb.2019.01064] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/26/2019] [Indexed: 12/03/2022] Open
Abstract
The use of urea as a nitrogenous fertilizer has increased over the past two decades, with urea itself being readily detected at high concentrations in many lakes. Urea has been linked to cyanobacterial blooms as it is a readily assimilated nitrogen (N) - source for cyanobacteria that possess the enzyme urease. We tested the hypothesis that urea may also act as a carbon (C) source to supplemental growth requirements during the alkaline conditions created by dense cyanobacterial blooms, when concentrations of dissolved CO2 are vanishingly low. High rates of photosynthesis markedly reduce dissolved CO2 concentrations and drive up pH. This was observed in Lake Erie during the largest bloom on record (2015) over long periods (months) and short periods (days) of time, suggesting blooms experience periods of CO2-limitation on a seasonal and daily basis. We used 13C-urea to demonstrate that axenic cultures of the model toxic cyanobacterium, Microcystis aeruginosa NIES843, assimilated C at varying environmentally relevant pH conditions directly into a spectrum of metabolic pools during urea hydrolysis. Primarily, 13C from urea was assimilated into central C metabolism and amino acid biosynthesis pathways, including those important for the production of the hepatotoxin, microcystin, and incorporation into these pathways was at a higher percentage during growth at higher pH. This corresponded to increased growth rates on urea as the sole N source with increasing pH. We propose this ability to incorporate C from urea represents yet another competitive advantage for this cyanobacterium during dense algal blooms.
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Affiliation(s)
- Lauren E. Krausfeldt
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Abigail T. Farmer
- Department of Chemistry, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | | | - Brittany N. Zepernick
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Shawn R. Campagna
- Department of Chemistry, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Steven W. Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
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Tang X, Krausfeldt LE, Shao K, LeCleir GR, Stough JMA, Gao G, Boyer GL, Zhang Y, Paerl HW, Qin B, Wilhelm SW. Seasonal Gene Expression and the Ecophysiological Implications of Toxic Microcystis aeruginosa Blooms in Lake Taihu. Environ Sci Technol 2018; 52:11049-11059. [PMID: 30168717 DOI: 10.1021/acs.est.8b01066] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Harmful cyanobacterial blooms represent an increasing threat to freshwater resources globally. Despite increased research, the physiological basis of how the dominant bloom-forming cyanobacteria, Microcystis spp., proliferate and then maintain high population densities through changing environmental conditions is poorly understood. In this study, we examined the transcriptional profiles of the microbial community in Lake Taihu, China at 9 stations sampled monthly from June to October in 2014. To target Microcystis populations, we collected metatranscriptomic data and mapped reads to the M. aeruginosa NIES 843 genome. Our results revealed significant temporal gene expression patterns, with many genes separating into either early or late bloom clusters. About one-third of genes observed from M. aeruginosa were differentially expressed between these two clusters. Conductivity and nutrient availability appeared to be the environmental factors most strongly associated with these temporal gene expression shifts. Compared with the early bloom season (June and July), genes involved in N and P transport, energy metabolism, translation, and amino acid biosynthesis were down-regulated during the later season (August to October). In parallel, genes involved in regulatory functions as well as transposases and the production of microcystin and extracellular polysaccharides were up-regulated in the later season. Our observation indicates an eco-physiological shift occurs within the Microcystis spp. transcriptome as cells move from the rapid growth of early summer to bloom maintenance in late summer and autumn.
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Affiliation(s)
- 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 , Jiangsu 210008 , China
| | - Lauren E Krausfeldt
- Department of Microbiology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - 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 , Jiangsu 210008 , China
| | - Gary R LeCleir
- Department of Microbiology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Joshua M A Stough
- Department of Microbiology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - 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 , Jiangsu 210008 , China
| | - Gregory L Boyer
- Department of Chemistry , SUNY College of Environmental Science and Forestry , Syracuse , New York 13210 , United States
| | - Yunlin Zhang
- 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 , Jiangsu 210008 , China
| | - Hans W Paerl
- Institute of Marine Sciences , The University of North Carolina at Chapel Hill , Morehead City , North Carolina 28557 , United States
- College of Environment , Hohai University , Nanjing , Jiangsu 210098 , China
| | - Boqiang Qin
- 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 , Jiangsu 210008 , China
| | - Steven W Wilhelm
- Department of Microbiology , University of Tennessee , Knoxville , Tennessee 37996 , United States
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10
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Stough JMA, Tang X, Krausfeldt LE, Steffen MM, Gao G, Boyer GL, Wilhelm SW. Molecular prediction of lytic vs lysogenic states for Microcystis phage: Metatranscriptomic evidence of lysogeny during large bloom events. PLoS One 2017; 12:e0184146. [PMID: 28873456 PMCID: PMC5584929 DOI: 10.1371/journal.pone.0184146] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/18/2017] [Indexed: 11/18/2022] Open
Abstract
Microcystis aeruginosa is a freshwater bloom-forming cyanobacterium capable of producing the potent hepatotoxin, microcystin. Despite increased interest in this organism, little is known about the viruses that infect it and drive nutrient mobilization and transfer of genetic material between organisms. The genomic complement of sequenced phage suggests these viruses are capable of integrating into the host genome, though this activity has not been observed in the laboratory. While analyzing RNA-sequence data obtained from Microcystis blooms in Lake Tai (Taihu, China), we observed that a series of lysogeny-associated genes were highly expressed when genes involved in lytic infection were down-regulated. This pattern was consistent, though not always statistically significant, across multiple spatial and temporally distinct samples. For example, samples from Lake Tai (2014) showed a predominance of lytic virus activity from late July through October, while genes associated with lysogeny were strongly expressed in the early months (June–July) and toward the end of bloom season (October). Analyses of whole phage genome expression shows that transcription patterns are shared across sampling locations and that genes consistently clustered by co-expression into lytic and lysogenic groups. Expression of lytic-cycle associated genes was positively correlated to total dissolved nitrogen, ammonium concentration, and salinity. Lysogeny-associated gene expression was positively correlated with pH and total dissolved phosphorous. Our results suggest that lysogeny may be prevalent in Microcystis blooms and support the hypothesis that environmental conditions drive switching between temperate and lytic life cycles during bloom proliferation.
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Affiliation(s)
- Joshua M. A. Stough
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States of America
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, Nanjing, PR China
| | - Lauren E. Krausfeldt
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States of America
| | - Morgan M. Steffen
- Department of Biology, James Madison University, Harrisonburg, VA, United States of America
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, Nanjing, PR China
| | - Gregory L. Boyer
- College of Environmental Science and Forestry, The State University of New York, Syracuse, NY, United States of America
| | - Steven W. Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States of America
- * E-mail:
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Steffen MM, Davis TW, McKay RML, Bullerjahn GS, Krausfeldt LE, Stough JMA, Neitzey ML, Gilbert NE, Boyer GL, Johengen TH, Gossiaux DC, Burtner AM, Palladino D, Rowe MD, Dick GJ, Meyer KA, Levy S, Boone BE, Stumpf RP, Wynne TT, Zimba PV, Gutierrez D, Wilhelm SW. Ecophysiological Examination of the Lake Erie Microcystis Bloom in 2014: Linkages between Biology and the Water Supply Shutdown of Toledo, OH. Environ Sci Technol 2017; 51:6745-6755. [PMID: 28535339 DOI: 10.1021/acs.est.7b00856] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Annual cyanobacterial blooms dominated by Microcystis have occurred in western Lake Erie (U.S./Canada) during summer months since 1995. The production of toxins by bloom-forming cyanobacteria can lead to drinking water crises, such as the one experienced by the city of Toledo in August of 2014, when the city was rendered without drinking water for >2 days. It is important to understand the conditions and environmental cues that were driving this specific bloom to provide a scientific framework for management of future bloom events. To this end, samples were collected and metatranscriptomes generated coincident with the collection of environmental metrics for eight sites located in the western basin of Lake Erie, including a station proximal to the water intake for the city of Toledo. These data were used to generate a basin-wide ecophysiological fingerprint of Lake Erie Microcystis populations in August 2014 for comparison to previous bloom communities. Our observations and analyses indicate that, at the time of sample collection, Microcystis populations were under dual nitrogen (N) and phosphorus (P) stress, as genes involved in scavenging of these nutrients were being actively transcribed. Targeted analysis of urea transport and hydrolysis suggests a potentially important role for exogenous urea as a nitrogen source during the 2014 event. Finally, simulation data suggest a wind event caused microcystin-rich water from Maumee Bay to be transported east along the southern shoreline past the Toledo water intake. Coupled with a significant cyanophage infection, these results reveal that a combination of biological and environmental factors led to the disruption of the Toledo water supply. This scenario was not atypical of reoccurring Lake Erie blooms and thus may reoccur in the future.
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Affiliation(s)
- Morgan M Steffen
- Department of Biology, James Madison University , Harrisonburg, Virginia 22807, United States
| | - Timothy W Davis
- NOAA-GLERL, 4840 South State Rd., Ann Arbor, Michigan 48108, United States
| | - R Michael L McKay
- Department of Biological Sciences, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - George S Bullerjahn
- Department of Biological Sciences, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Lauren E Krausfeldt
- Department of Microbiology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Joshua M A Stough
- Department of Microbiology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Michelle L Neitzey
- Department of Biology, James Madison University , Harrisonburg, Virginia 22807, United States
| | - Naomi E Gilbert
- Department of Biology, James Madison University , Harrisonburg, Virginia 22807, United States
| | - Gregory L Boyer
- Department of Chemistry, State University of New York, Environmental Science and Forestry , Syracuse, New York 13210, United States
| | - Thomas H Johengen
- Cooperative Institute for Limnology and Ecosystems Research, University of Michigan , Ann Arbor, Michigan 48108, United States
| | - Duane C Gossiaux
- NOAA-GLERL, 4840 South State Rd., Ann Arbor, Michigan 48108, United States
| | - Ashley M Burtner
- Cooperative Institute for Limnology and Ecosystems Research, University of Michigan , Ann Arbor, Michigan 48108, United States
| | - Danna Palladino
- Cooperative Institute for Limnology and Ecosystems Research, University of Michigan , Ann Arbor, Michigan 48108, United States
| | - Mark D Rowe
- Cooperative Institute for Limnology and Ecosystems Research, University of Michigan , Ann Arbor, Michigan 48108, United States
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Kevin A Meyer
- Department of Earth and Environmental Sciences, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Shawn Levy
- Genomic Service Laboratory, Hudson Alpha Institute for Biotechnology , Huntsville, Alabama 35806, United States
| | - Braden E Boone
- Genomic Service Laboratory, Hudson Alpha Institute for Biotechnology , Huntsville, Alabama 35806, United States
| | - Richard P Stumpf
- NOAA National Ocean Service, National Centers for Coastal Ocean Sciences, Silver Spring, Maryland 20910, United States
| | - Timothy T Wynne
- NOAA National Ocean Service, National Centers for Coastal Ocean Sciences, Silver Spring, Maryland 20910, United States
| | - Paul V Zimba
- Department of Life Sciences, Texas A&M Corpus Christi , Corpus Christi, Texas 78412, United States
| | - Danielle Gutierrez
- Department of Life Sciences, Texas A&M Corpus Christi , Corpus Christi, Texas 78412, United States
| | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee , Knoxville, Tennessee 37996, United States
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Krausfeldt LE, Tang X, van de Kamp J, Gao G, Bodrossy L, Boyer GL, Wilhelm SW. Spatial and temporal variability in the nitrogen cyclers of hypereutrophic Lake Taihu. FEMS Microbiol Ecol 2017; 93:3045885. [PMID: 28334116 DOI: 10.1093/femsec/fix024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 02/21/2017] [Indexed: 11/14/2022] Open
Abstract
Harmful cyanobacterial blooms (cyanoHABs) are a major threat to freshwater ecosystems worldwide. Evidence suggests that both nitrogen and phosphorus are important nutrients in the development and proliferation of blooms, yet much less is known about nitrogen cycling dynamics in these systems. To assess the potential nitrogen cycling function of the cyanoHAB community, surface water samples were collected in Lake Tai (Taihu), China over a 5-month bloom event in 2014. The expression of six nitrogen cycling genes (nifH, hzsA, nxrB, nrfA, amoA, nosZ) was surveyed using a targeted microarray with probes designed to provide phylogenetic information. N-Cycling gene expression varied spatially across Taihu, most notably near the mouth of the Dapu River. Expression of nifH was observed across the lake and attributable to both Proteobacteria and Cyanobacteria: Proteobacteria were major contributors to nifH signal near shore. Other N transformations such as anaerobic ammonia oxidation and denitrification were evident in the surface waters as well. Observations in this study highlight the potential importance of heterotrophic bacteria in N-cycling associated with cyanoHABs.
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Affiliation(s)
- Lauren E Krausfeldt
- Department of Microbiology, The University of Tennessee, Knoxville, TN 37919, USA
| | - 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 210008, China
| | - Jodie van de Kamp
- CSIRO Oceans and Atmosphere, Castray Esplanade, Hobart, Tasmania 7004, Australia
| | - 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 210008, China
| | - Levente Bodrossy
- CSIRO Oceans and Atmosphere, Castray Esplanade, Hobart, Tasmania 7004, Australia
| | - Gregory L Boyer
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, TN 37919, USA
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