1
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Lui LM, Nielsen TN. Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses. mSystems 2024; 9:e0024224. [PMID: 39158287 PMCID: PMC11406994 DOI: 10.1128/msystems.00242-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 07/11/2024] [Indexed: 08/20/2024] Open
Abstract
Although long-read sequencing has enabled obtaining high-quality and complete genomes from metagenomes, many challenges still remain to completely decompose a metagenome into its constituent prokaryotic and viral genomes. This study focuses on decomposing an estuarine metagenome to obtain a more accurate estimate of microbial diversity. To achieve this, we developed a new bead-based DNA extraction method, a novel bin refinement method, and obtained 150 Gbp of Nanopore sequencing. We estimate that there are ~500 bacterial and archaeal species in our sample and obtained 68 high-quality bins (>90% complete, <5% contamination, ≤5 contigs, contig length of >100 kbp, and all ribosomal and tRNA genes). We also obtained many contigs of picoeukaryotes, environmental DNA of larger eukaryotes such as mammals, and complete mitochondrial and chloroplast genomes and detected ~40,000 viral populations. Our analysis indicates that there are only a few strains that comprise most of the species abundances. IMPORTANCE Ocean and estuarine microbiomes play critical roles in global element cycling and ecosystem function. Despite the importance of these microbial communities, many species still have not been cultured in the lab. Environmental sequencing is the primary way the function and population dynamics of these communities can be studied. Long-read sequencing provides an avenue to overcome limitations of short-read technologies to obtain complete microbial genomes but comes with its own technical challenges, such as needed sequencing depth and obtaining high-quality DNA. We present here new sampling and bioinformatics methods to attempt decomposing an estuarine microbiome into its constituent genomes. Our results suggest there are only a few strains that comprise most of the species abundances from viruses to picoeukaryotes, and to fully decompose a metagenome of this diversity requires 1 Tbp of long-read sequencing. We anticipate that as long-read sequencing technologies continue to improve, less sequencing will be needed.
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Affiliation(s)
- Lauren M Lui
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Torben N Nielsen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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2
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Raposo VDMB, Costa VAF, Rodrigues AF. A review of recent developments on drought characterization, propagation, and influential factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 898:165550. [PMID: 37459986 DOI: 10.1016/j.scitotenv.2023.165550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 07/24/2023]
Abstract
Droughts have impacted human society throughout its history. However, the occurrence of severe drought events in the last century and the concerns on the potential effects of climate change have prompted remarkable advances in drought conceptualization and modeling in recent years. This review intends to present the state-of-the-art on drought characterization and propagation, as well as providing insights on how climate dynamics and anthropogenic activities might affect this phenomenon. For this purpose, we first address the distinct concepts of droughts and their relationships. Next, we present two frequently utilized methods based on the run theory for drought characterization and explain the development and recovery stages of droughts. Then, we discuss potential drivers for drought occurrence and propagation, with focus on meteorological factors, catchments' physical characteristics and human activities. Later, we describe how droughts can affect several parameters of water quality. This review also addressed flash droughts, encompassing their definitions, commonly used indices, and potential drivers. Finally, we briefly address the roles of climate change and long-term persistence on future drought scenarios. This review may be useful for researchers and stakeholders for attaining a broader understanding on drought dynamics and impacts.
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Affiliation(s)
- Vinícius de Matos Brandão Raposo
- Federal University of Minas Gerais, Sanitation, Environment and Water Resources Postgraduate Program, Antonio Carlos Avenue, 6627, School of Engineering, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| | - Veber Afonso Figueiredo Costa
- Federal University of Minas Gerais, Sanitation, Environment and Water Resources Postgraduate Program, Antonio Carlos Avenue, 6627, School of Engineering, Belo Horizonte 31270-901, Minas Gerais, Brazil
| | - André Ferreira Rodrigues
- Federal University of Minas Gerais, Sanitation, Environment and Water Resources Postgraduate Program, Antonio Carlos Avenue, 6627, School of Engineering, Belo Horizonte 31270-901, Minas Gerais, Brazil
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3
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Lehman PW, Kurobe T, Huynh K, Lesmeister S, Teh SJ. Covariance of Phytoplankton, Bacteria, and Zooplankton Communities Within Microcystis Blooms in San Francisco Estuary. Front Microbiol 2021; 12:632264. [PMID: 34163439 PMCID: PMC8215387 DOI: 10.3389/fmicb.2021.632264] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 04/21/2021] [Indexed: 11/25/2022] Open
Abstract
Microcystis blooms have occurred in upper San Francisco Estuary (USFE) since 1999, but their potential impacts on plankton communities have not been fully quantified. Five years of field data collected from stations across the freshwater reaches of the estuary were used to identify the plankton communities that covaried with Microcystis blooms, including non-photosynthetic bacteria, cyanobacteria, phytoplankton, zooplankton, and benthic genera using a suite of analyses, including microscopy, quantitative PCR (qPCR), and shotgun metagenomic analysis. Coherence between the abundance of Microcystis and members of the plankton community was determined by hierarchal cluster analysis (CLUSTER) and type 3 similarity profile analysis (SIMPROF), as well as correlation analysis. Microcystis abundance varied with many cyanobacteria and phytoplankton genera and was most closely correlated with the non-toxic cyanobacterium Merismopoedia, the green algae Monoraphidium and Chlamydomonas, and the potentially toxic cyanobacteria Pseudoanabaena, Dolichospermum, Planktothrix, Sphaerospermopsis, and Aphanizomenon. Among non-photosynthetic bacteria, the xenobiotic bacterium Phenylobacterium was the most closely correlated with Microcystis abundance. The coherence of DNA sequences for phyla across trophic levels in the plankton community also demonstrated the decrease in large zooplankton and increase in small zooplankton during blooms. The breadth of correlations between Microcystis and plankton across trophic levels suggests Microcystis influences ecosystem production through bottom-up control during blooms. Importantly, the abundance of Microcystis and other members of the plankton community varied with wet and dry conditions, indicating climate was a significant driver of trophic structure during blooms.
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Affiliation(s)
- Peggy W. Lehman
- Division of Environmental Services, California Department of Water Resources, West Sacramento, CA, United States
| | - Tomofumi Kurobe
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Khiet Huynh
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Sarah Lesmeister
- Division of Environmental Services, California Department of Water Resources, West Sacramento, CA, United States
| | - Swee J. Teh
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
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4
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Martini GDA, Montagner CC, Viveiros W, Quinaglia GA, França DD, Munin NCG, Lopes-Ferreira M, Rogero SO, Rogero JR. Emerging contaminant occurrence and toxic effects on zebrafish embryos to assess the adverse effects caused by mixtures of substances in the environment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:20313-20329. [PMID: 33405144 DOI: 10.1007/s11356-020-11963-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
The contaminants of emerging concern (CECs) have been receiving global attention due to their worldwide presence in water bodies. The CECs could be originated from synthetic or natural sources, and they are not commonly monitored, although these substances are continuously reaching the aquatic environment. The main goal of this study was to determine the occurrence of some target CECs in São Paulo state surface water, once there is practically no information on the presence and concentration range of these substances at the studied sites. In addition, the present study aimed to assess adverse effects in the non-target fish embryo of Danio rerio (zebrafish) after exposure to surface water organic extract samples during 96 h using FET test. The CECs in surface water samples were determined by solid-phase extraction and liquid chromatography coupled by mass spectrometry. A 2-year study was assessed in 7 rivers and 3 reservoirs at São Paulo state, where 25 of the 30 analyzed substances were quantified, being caffeine the substance with the highest concentration range (5.5 ng L-1 to 69 μg L-1) and detected in 95% of analyzed samples, followed by bisphenol A (6.5-1300 ng L-1) and carbendazim (4.7-285 ng L-1), found in 50% and 85% of the analyzed samples, respectively. The chemical analysis and biological test were not performed in order to show a direct relationship between concentrations and observed effects on embryos; however, the combined approach can provide a better understanding of the adverse effects caused by mixtures of substances at relevant environmental concentrations. Regarding the adverse effects, it was observed that in the samples from sites with higher anthropogenic activity in the surroundings, there was also a higher mortality rate in organisms. At the Ribeirão Pires River and Sapucaí-Guaçu River, the mortality rate during the 2-year study was 21.6% and 9.3%, respectively. The morphological abnormality rates were higher at Ribeirão Grande (21.4%) and Ribeirão Pires (29.5%) Rivers. The obtained results aim to show that even in low concentrations (ng-μg L-1) the CECs can cause adverse effects on non-target species, and because of that, new chemical indicators would be important to monitor the water quality and protect the aquatic biota.
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Affiliation(s)
- Gisela de Assis Martini
- Centro de Química e Meio Ambiente, Instituto de Pesquisas Energéticas e Nucleares, São Paulo, Brazil.
| | | | | | | | | | - Nívea Cristina Guedes Munin
- Instituto de Química, Universidade Estadual de Campinas, São Paulo, Brazil
- Universidade Federal do Amazonas, Manaus, Brazil
| | | | - Sizue Ota Rogero
- Centro de Química e Meio Ambiente, Instituto de Pesquisas Energéticas e Nucleares, São Paulo, Brazil
| | - José Roberto Rogero
- Centro de Química e Meio Ambiente, Instituto de Pesquisas Energéticas e Nucleares, São Paulo, Brazil
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Jin J, Kurobe T, Hammock BG, Lam CH, Lin L, Teh SJ. Toxic effects of fluridone on early developmental stages of Japanese Medaka (Oryzias latipes). THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 700:134495. [PMID: 31693955 DOI: 10.1016/j.scitotenv.2019.134495] [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: 06/17/2019] [Revised: 09/11/2019] [Accepted: 09/15/2019] [Indexed: 06/10/2023]
Abstract
The herbicide fluridone is intensively applied to control invasive aquatic plants globally, including in the Sacramento and San Joaquin Delta (the Delta), California, USA. Our previous study revealed that the adult stage of Delta Smelt showed acute and sub-lethal adverse effects following 6 h of exposure to environmentally relevant concentrations of fluridone. To further investigate mechanisms of toxicity of fluridone and to assess its toxicity to early life stages of fish, we performed additional exposures using the fish model Japanese Medaka (Oryzias latipes). Male and female Medaka embryos were exposed to concentrations of fluridone for 14 d and showed reduced hatching success in a dose dependent manner. The half maximal effective concentration for the hatching success was 2.3 mg L-1. In addition, male and female Medaka larvae were acute exposed to fluridone for 6 h to assess their swimming behavior and gene expression patterns. Fish exposed to fluridone at 4.2 mg L-1 or higher became lethargic and showed abnormal swimming behavior. The response to the stimuli was significantly impaired by fluridone at 21 mg L-1 and above in males, and at 104 mg L-1 in females. Transcriptome analysis identified a total of 799 genes that were significantly differentially expressed, comprising 555 up-regulated and 244 down-regulated genes in males exposed to 21 mg L-1 of fluridone. The gene set enrichment analysis indicated a number of biological processes altered by fluridone. Among the genes involved in those biological processes, the expression of the genes, acetylcholinesterase, retinoic acid receptor, insulin receptor substrate, glutathione reductase, and glutathione S transferase, exhibited dose- and sex-dependent responses to fluridone. The study indicated that fluridone exposure led to detrimental toxic effects at early developmental stages of fish, by disturbing the biological processes of growth and development, and the nervous system, inducing oxidative stress and endocrine disruption.
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Affiliation(s)
- Jiali Jin
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; Aquatic Health Program, Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA.
| | - Tomofumi Kurobe
- Aquatic Health Program, Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Bruce G Hammock
- Aquatic Health Program, Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Chelsea H Lam
- Aquatic Health Program, Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Li Lin
- Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong 510225, China
| | - Swee J Teh
- Aquatic Health Program, Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
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6
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Silva MOD, Pernthaler J. Priming of microcystin degradation in carbon-amended membrane biofilm communities is promoted by oxygen-limited conditions. FEMS Microbiol Ecol 2019; 95:5582606. [PMID: 31589311 PMCID: PMC6804753 DOI: 10.1093/femsec/fiz157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/04/2019] [Indexed: 01/09/2023] Open
Abstract
Microbial biofilms are an important element of gravity-driven membrane (GDM) filtration systems for decentralized drinking water production. Mature biofilms fed with biomass from the toxic cyanobacterium Microcystis aeruginosa efficiently remove the cyanotoxin microcystin (MC). MC degradation can be ‘primed’ by prior addition of biomass from a non-toxic M. aeruginosa strain. Increased proportions of bacteria with an anaerobic metabolism in M. aeruginosa-fed biofilms suggest that this ‘priming’ could be due to higher productivity and the resulting changes in habitat conditions. We, therefore, investigated GDM systems amended with the biomass of toxic (WT) or non-toxic (MUT) M. aeruginosa strains, of diatoms (DT), or with starch solution (ST). After 25 days, these treatments were changed to receiving toxic cyanobacterial biomass. MC degradation established significantly more rapidly in MUT and ST than in DT. Oxygen measurements suggested that this was due to oxygen-limited conditions in MUT and ST already prevailing before addition of MC-containing biomass. Moreover, the microbial communities in the initial ST biofilms featured high proportions of facultative anaerobic taxa, whereas aerobes dominated in DT biofilms. Thus, the ‘priming’ of MC degradation in mature GDM biofilms seems to be related to the prior establishment of oxygen-limited conditions mediated by higher productivity.
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Affiliation(s)
- Marisa O D Silva
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Seestrasse 187, CH-8802 Kilchberg, Switzerland
| | - Jakob Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Seestrasse 187, CH-8802 Kilchberg, Switzerland
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7
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Lam CH, Kurobe T, Lehman PW, Berg M, Hammock BG, Stillway ME, Pandey PK, Teh SJ. Toxicity of herbicides to cyanobacteria and phytoplankton species of the San Francisco Estuary and Sacramento-San Joaquin River Delta, California, USA. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2019; 55:107-118. [PMID: 31642727 DOI: 10.1080/10934529.2019.1672458] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 06/10/2023]
Abstract
The herbicides glyphosate, imazamox and fluridone are herbicides, with low toxicity towards fish and invertebrates, which are applied to waterways to control invasive aquatic weeds. However, the effects of these herbicides on natural isolates of phytoplankton and cyanobacteria are unknown. Three species of microalgae found in the San Francisco Estuary (SFE)/Sacramento-San Joaquin River Delta (Delta) (Microcystis aeruginosa, Chlamydomonas debaryana, and Thalassiosira pseudonana) were exposed to the three herbicides at a range of concentrations in 96-well plates for 5-8 days. All three algal species were the most sensitive to fluridone, with IC50 of 46.9, 21, and 109 µg L-1 for M. aeruginosa, T. pseudonana and C. debaryana, respectively. Imazamox inhibited M. aeruginosa and T. pseudonana growth at 3.6 × 104 µg L-1 or higher, and inhibited C. debaryana growth at 1.0 × 105 µg L-1 or higher. Glyphosate inhibited growth in all species at ca. 7.0 × 104 µg L-1 or higher. Fluridone was the only herbicide that inhibited the microalgae at environmentally relevant concentrations in this study and susceptibility to the herbicide depended on the species. Thus, the application of fluridone may affect cyanobacteria and phytoplankton community composition in water bodies where it is applied.
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Affiliation(s)
- Chelsea H Lam
- Aquatic Health Program, Department of Anatomy, Physiology and Cell Biology, University of California, Davis, Davis, California, USA
| | - Tomofumi Kurobe
- Aquatic Health Program, Department of Anatomy, Physiology and Cell Biology, University of California, Davis, Davis, California, USA
| | - Peggy W Lehman
- California Department of Water Resources, Division of Environmental Services, Special Studies Section, West Sacramento, California, USA
| | - Mine Berg
- Applied Marine Sciences, Santa Cruz, California, USA
| | - Bruce G Hammock
- Aquatic Health Program, Department of Anatomy, Physiology and Cell Biology, University of California, Davis, Davis, California, USA
| | - Marie E Stillway
- Aquatic Health Program, Department of Anatomy, Physiology and Cell Biology, University of California, Davis, Davis, California, USA
| | - Pramod K Pandey
- Department of Population Health and Reproduction, University of California, Davis, Davis, California, USA
| | - Swee J Teh
- Aquatic Health Program, Department of Anatomy, Physiology and Cell Biology, University of California, Davis, Davis, California, USA
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8
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Zhang D, Ye Q, Zhang F, Shao X, Fan Y, Zhu X, Li Y, Yao L, Tian Y, Zheng T, Xu H. Flocculating properties and potential of Halobacillus sp. strain H9 for the mitigation of Microcystis aeruginosa blooms. CHEMOSPHERE 2019; 218:138-146. [PMID: 30471494 DOI: 10.1016/j.chemosphere.2018.11.082] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/12/2018] [Accepted: 11/12/2018] [Indexed: 06/09/2023]
Abstract
Microcystis aeruginosa can cause harmful algal blooms in freshwaters worldwide. It has already seriously affected human lives and prevented the use of water resources. Therefore, there is an urgent need to develop ecofriendly and effective methods to control and eliminate M. aeruginosa in aquatic environments. In this study, Halobacillus sp. strain H9, a bacterium that showed high M. aeruginosa flocculation activity, was isolated and selected to assess its potential for the removal of M. aeruginosa. The analyses of flocculation activity and mode indicated that the strain H9 induced M. aeruginosa flocculation by secreting active flocculating substance rather than by directly contacting algal cells. A 5% concentration of the H9 supernatant could efficiently flocculate M. aeruginosa cells with a density of up to 5 × 107 cells/mL. Dramatic increases in the zeta potential indicated that charge neutralization could be the mechanism of the flocculation process. The strain H9 flocculated M. aeruginosa with no damage to the algal cell membrane, and did not result in microcystin being released into the surrounding environment. The flocculated algal culture was less toxic to zebrafish larvae, suggesting an environmentally friendly benefit of the H9 supernatant. In addition to M. aeruginosa, the H9 strain was also able to flocculate two other species causing harmful algal blooms, Phaeocystis globose and Heterosigma akashiwo. Furthermore, the flocculation activity of the H9 supernatant was stable at different temperatures and over a wide pH range. These characteristics give the H9 strain great potential for mitigating the influences of harmful algal blooms.
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Affiliation(s)
- Danyang Zhang
- State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Qian Ye
- State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Fuxing Zhang
- State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Xueping Shao
- State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Yongxiang Fan
- State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Xiaoying Zhu
- State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Yinan Li
- State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Luming Yao
- State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, and School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Tianling Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, and School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Hong Xu
- State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, Fujian, 361102, PR China; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, and School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China.
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9
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Thees A, Atari E, Birbeck J, Westrick JA, Huntley JF. Isolation and Characterization of Lake Erie Bacteria that Degrade the Cyanobacterial Microcystin Toxin MC-LR. JOURNAL OF GREAT LAKES RESEARCH 2019; 45:138-149. [PMID: 32753778 PMCID: PMC7402192 DOI: 10.1016/j.jglr.2018.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Microcystin-LR (MC-LR) is a cyclic hepatotoxin produced by cyanobacteria, including Microcystis sp. and Planktothrix sp. Harmful algal blooms (HABs) in Lake Erie have become a major human health concern in recent years, highlighted by the August 2014 city of Toledo, Ohio, municipal water "do not drink" order that affected nearly 500,000 residents for 3 days. Given that microcystin degrading bacteria have been reported from HAB-affected waters around the world, we hypothesized that MC-LR degrading bacteria could be isolated from Lake Erie. To test this hypothesis, 13 water samples were collected from various Lake Erie locations during the summers of 2014 and 2015, MC-LR was continuously added to each water sample for 3 to 5 weeks to enrich for MC-LR-degrading bacteria, and MC-LR was quantitated over time. Whereas MC-LR was relatively stable in sterile-filtered lake water, robust MC-LR degradation (up to 19 ppb/day) was observed in some water samples. Following the MC-LR selection process, 67 individual bacterial isolates were isolated from MC-LR degrading water samples and genotyped to exclude potential human pathogens, and MC-LR degradation by smaller groups of bacterial isolates (e.g., groups of 22 isolates, groups of 11 isolates, etc.) was examined. Of those smaller groups, selected groups of four to five bacterial isolates were found to degrade MC-LR into non-toxic forms and form robust biofilms on siliconized glass tubes. Taken together, these studies support the potential use of isolated bacterial isolates to remove MC-LR from drinking water.
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Affiliation(s)
- Alison Thees
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, 43614, U.S.A
| | - Ealla Atari
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, 43614, U.S.A
| | - Johnna Birbeck
- Lumigen Instrumentation Center, Department of Chemistry, Wayne State University, Detroit, Michigan, 49202, U.S.A
| | - Judy A. Westrick
- Lumigen Instrumentation Center, Department of Chemistry, Wayne State University, Detroit, Michigan, 49202, U.S.A
| | - Jason F. Huntley
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, 43614, U.S.A
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10
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Kurobe T, Lehman PW, Hammock BG, Bolotaolo MB, Lesmeister S, Teh SJ. Biodiversity of cyanobacteria and other aquatic microorganisms across a freshwater to brackish water gradient determined by shotgun metagenomic sequencing analysis in the San Francisco Estuary, USA. PLoS One 2018; 13:e0203953. [PMID: 30248115 PMCID: PMC6152961 DOI: 10.1371/journal.pone.0203953] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 08/30/2018] [Indexed: 11/19/2022] Open
Abstract
Blooms of Microcystis and other harmful cyanobacteria can degrade water quality by producing cyanotoxins or other toxic compounds. The goals of this study were (1) to facilitate understanding of community structure for various aquatic microorganisms in brackish water and freshwater regions with emphasis on cyanobacteria, and (2) to test a hypothesis that Microcystis genotypes that tolerate higher salinity were blooming in brackish water environments during the severe drought, 2014. Shotgun metagenomic analysis revealed that cyanobacteria dominated the brackish water region while bacteria dominated the freshwater region. A group of cyanobacteria (e.g., Aphanizomenon, Microcystis, Planktothrix, Pseudanabaena), bacteria (e.g., Bacillus, Porphyrobacter), and diatoms (Phaeodactylum and Thalassiosira) were abundant in the brackish water region. In contrast, Hassallia (cyanobacteria) and green algae (Nannochloropsis, Chlamydomonas, and Volvox) were abundant in the landward freshwater region. Station variation was also apparent. One landward sampling station located downstream of an urbanized area differed substantially from the other stations in terms of both water chemistry and community structure, with a higher percentage of arthropods, green algae, and eukaryotes. Screening of the Microcystis internal transcribed spacer region revealed six representative genotypes, and two of which were successfully quantified using qPCR (Genotypes I and VI). Both genotypes occurred predominantly in the freshwater region, so the data from this study did not support the hypothesis that salinity tolerant Microcystis genotypes bloomed in the brackish water region in 2014.
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Affiliation(s)
- Tomofumi Kurobe
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, California, United States of America
| | - Peggy W. Lehman
- California Department of Fish and Wildlife, Stockton, California, United States of America
| | - Bruce G. Hammock
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, California, United States of America
| | - Melissa B. Bolotaolo
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, California, United States of America
| | - Sarah Lesmeister
- California Department of Water Resources, West Sacramento, California, United States of America
| | - Swee J. Teh
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, California, United States of America
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11
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Affe HMDJ, Rigonato J, Nunes JMDC, Menezes M. Metagenomic Analysis of Cyanobacteria in an Oligotrophic Tropical Estuary, South Atlantic. Front Microbiol 2018; 9:1393. [PMID: 29997603 PMCID: PMC6029486 DOI: 10.3389/fmicb.2018.01393] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 06/07/2018] [Indexed: 11/20/2022] Open
Abstract
This study assessed the species composition, distribution, and functional profiles of cyanobacteria in Camamu Bay, a tropical oligotrophic estuarine system on the northeast coast of Brazil, using shotgun metagenomic sequencing. Surface-water samples were evaluated in two different rainfall periods (rainy and dry seasons), at nine stations in the three hydrodynamic regions of the bay. At a fixed sampling station, on each season, samples were taken over a tidal cycle at 3-h intervals over 12 h. A total of 219 cyanobacterial taxa were identified, demonstrating a diverse community of freshwater, euryhaline, and marine cyanobacteria. The genera of greater relative abundance, Synechococcus and Prochlorococcus, corresponded to the picoplankton fraction. Although Camamu Bay has conspicuous marine characteristics, the contribution of freshwater during the rainy season caused variation in cyanobacteria community, with an increase in species richness. Due the high prevalence of Synechococcus (90% of the sequences), the functional analysis revealed only minor differences in gene content between the dry and rainy seasons. In both rainy and dry seasons, an increase in Prochlorococcus relative abundance occurred during high tide, demonstrating the tidal influence in the bay. The environmental characteristics of the bay provide niche conditions for a wide variety of cyanobacteria, including freshwater, euryhaline, and marine strains.
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Affiliation(s)
- Helen M de Jesus Affe
- Laboratório de Algas Marinhas, Instituto de Biologia, Universidade Federal da Bahia, Salvador, Brazil
| | - Janaina Rigonato
- Centro de Energia Nuclear e Agricultura, Universidade de São Paulo, Piracicaba, Brazil.,CEA, Centre de Sequençage Genoscope, Institut de Biologie François Jacob, Evry, France
| | - José M de Castro Nunes
- Laboratório de Algas Marinhas, Instituto de Biologia, Universidade Federal da Bahia, Salvador, Brazil
| | - Mariângela Menezes
- Laboratório de Ficologia, Departamento de Botânica, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Paerl HW, Otten TG, Kudela R. Mitigating the Expansion of Harmful Algal Blooms Across the Freshwater-to-Marine Continuum. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:5519-5529. [PMID: 29656639 DOI: 10.1021/acs.est.7b05950] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Anthropogenic nutrient overenrichment, coupled with rising temperatures, and an increasing frequency of extreme hydrologic events (storms and droughts) are accelerating eutrophication and promoting the expansion of harmful algal blooms (HABs) across the freshwater-to-marine continuum. All HABs-with a focus here on cyanobacterial blooms-pose serious consequences for water supplies, fisheries, recreational uses, tourism, and property values. As nutrient loads grow in watersheds, they begin to compound the effects of legacy stores. This has led to a paradigm shift in our understanding of how nutrients control eutrophication and blooms. Phosphorus (P) reductions have been traditionally prescribed exclusively for freshwater systems, while nitrogen (N) reductions were mainly stressed for brackish and coastal waters. However, because most systems are hydrologically interconnected, single nutrient (e.g., P only) reductions upstream may not necessarily reduce HAB impacts downstream. Reducing both N and P inputs is the only viable nutrient management solution for long-term control of HABs along the continuum. This article highlights where paired physical, chemical, or biological controls may improve beneficial uses in the short term, and offers management strategies that should be enacted across watershed scales to combat the global expansion of HABs across geographically broad freshwater-to-marine continua.
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Affiliation(s)
- Hans W Paerl
- Institute of Marine Sciences , University of North Carolina at Chapel Hill , 3431 Arendell Street , Morehead City , North Carolina 28557 , United States
| | - Timothy G Otten
- Bend Genetics , 87 Scripps Drive, Ste. 108 , Sacramento , California 95825 , United States
| | - Raphael Kudela
- Ocean Sciences & Institute for Marine Sciences , University of California Santa Cruz , 1156 High Street , Santa Cruz , California 95064 , United States
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