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Cabello-Yeves PJ, Callieri C, Picazo A, Schallenberg L, Huber P, Roda-Garcia JJ, Bartosiewicz M, Belykh OI, Tikhonova IV, Torcello-Requena A, De Prado PM, Puxty RJ, Millard AD, Camacho A, Rodriguez-Valera F, Scanlan DJ. Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates. BMC Biol 2022; 20:175. [PMID: 35941649 PMCID: PMC9361551 DOI: 10.1186/s12915-022-01379-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cyanobacteria are the major prokaryotic primary producers occupying a range of aquatic habitats worldwide that differ in levels of salinity, making them a group of interest to study one of the major unresolved conundrums in aquatic microbiology which is what distinguishes a marine microbe from a freshwater one? We address this question using ecogenomics of a group of picocyanobacteria (cluster 5) that have recently evolved to inhabit geographically disparate salinity niches. Our analysis is made possible by the sequencing of 58 new genomes from freshwater representatives of this group that are presented here, representing a 6-fold increase in the available genomic data. RESULTS Overall, freshwater strains had larger genomes (≈2.9 Mb) and %GC content (≈64%) compared to brackish (2.69 Mb and 64%) and marine (2.5 Mb and 58.5%) isolates. Genomic novelties/differences across the salinity divide highlighted acidic proteomes and specific salt adaptation pathways in marine isolates (e.g., osmolytes/compatible solutes - glycine betaine/ggp/gpg/gmg clusters and glycerolipids glpK/glpA), while freshwater strains possessed distinct ion/potassium channels, permeases (aquaporin Z), fatty acid desaturases, and more neutral/basic proteomes. Sulfur, nitrogen, phosphorus, carbon (photosynthesis), or stress tolerance metabolism while showing distinct genomic footprints between habitats, e.g., different types of transporters, did not obviously translate into major functionality differences between environments. Brackish microbes show a mixture of marine (salt adaptation pathways) and freshwater features, highlighting their transitional nature. CONCLUSIONS The plethora of freshwater isolates provided here, in terms of trophic status preference and genetic diversity, exemplifies their ability to colonize ecologically diverse waters across the globe. Moreover, a trend towards larger and more flexible/adaptive genomes in freshwater picocyanobacteria may hint at a wider number of ecological niches in this environment compared to the relatively homogeneous marine system.
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Affiliation(s)
- Pedro J Cabello-Yeves
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel, Hernández, San Juan de Alicante, Alicante, Spain.
| | - Cristiana Callieri
- National Research Council (CNR), Institute of Water Research (IRSA), Verbania, Italy
| | - Antonio Picazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, E-46980, Paterna, Valencia, Spain
| | | | - Paula Huber
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Av. Intendente Marino Km 8,200, (7130) Chascomús, Buenos Aires, Argentina.,Instituto Nacional de Limnología (INALI), CONICET-UNL, Ciudad Universitaria - Paraje el Pozo s/n, (3000), Santa Fé, Argentina
| | - Juan J Roda-Garcia
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel, Hernández, San Juan de Alicante, Alicante, Spain
| | - Maciej Bartosiewicz
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Olga I Belykh
- Limnological Institute, Russian Academy of Sciences, P.O. Box 278, 664033, Irkutsk, Russia
| | - Irina V Tikhonova
- Limnological Institute, Russian Academy of Sciences, P.O. Box 278, 664033, Irkutsk, Russia
| | | | | | - Richard J Puxty
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Andrew D Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Antonio Camacho
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, E-46980, Paterna, Valencia, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel, Hernández, San Juan de Alicante, Alicante, Spain.,Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
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2
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Blais MA, Matveev A, Lovejoy C, Vincent WF. Size-Fractionated Microbiome Structure in Subarctic Rivers and a Coastal Plume Across DOC and Salinity Gradients. Front Microbiol 2022; 12:760282. [PMID: 35046910 PMCID: PMC8762315 DOI: 10.3389/fmicb.2021.760282] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/01/2021] [Indexed: 11/16/2022] Open
Abstract
Little is known about the microbial diversity of rivers that flow across the changing subarctic landscape. Using amplicon sequencing (rRNA and rRNA genes) combined with HPLC pigment analysis and physicochemical measurements, we investigated the diversity of two size fractions of planktonic Bacteria, Archaea and microbial eukaryotes along environmental gradients in the Great Whale River (GWR), Canada. This large subarctic river drains an extensive watershed that includes areas of thawing permafrost, and discharges into southeastern Hudson Bay as an extensive plume that gradually mixes with the coastal marine waters. The microbial communities differed by size-fraction (separated with a 3-μm filter), and clustered into three distinct environmental groups: (1) the GWR sites throughout a 150-km sampling transect; (2) the GWR plume in Hudson Bay; and (3) small rivers that flow through degraded permafrost landscapes. There was a downstream increase in taxonomic richness along the GWR, suggesting that sub-catchment inputs influence microbial community structure in the absence of sharp environmental gradients. Microbial community structure shifted across the salinity gradient within the plume, with changes in taxonomic composition and diversity. Rivers flowing through degraded permafrost had distinct physicochemical and microbiome characteristics, with allochthonous dissolved organic carbon explaining part of the variation in community structure. Finally, our analyses of the core microbiome indicated that while a substantial part of all communities consisted of generalists, most taxa had a more limited environmental range and may therefore be sensitive to ongoing change.
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Affiliation(s)
- Marie-Amélie Blais
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Centre for Northern Studies (CEN), Université Laval, Quebec City, QC, Canada
| | - Alex Matveev
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Centre for Northern Studies (CEN), Université Laval, Quebec City, QC, Canada
| | - Connie Lovejoy
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Québec-Océan, Université Laval, Quebec City, QC, Canada
| | - Warwick F Vincent
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Centre for Northern Studies (CEN), Université Laval, Quebec City, QC, Canada
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3
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Increases in Picocyanobacteria Abundance in Agriculturally Eutrophic Pampean Lakes Inferred from Historical Records of Secchi Depth and Chlorophyll-a. WATER 2022. [DOI: 10.3390/w14020159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Phytoplankton size structure has profound consequences on food-web organization and energy transfer. Presently, picocyanobacteria (size < 2 µm) represent a major fraction of the autotrophic plankton of Pampean lakes. Glyphosate is known to stimulate the development of picocyanobacteria capable of degrading the herbicide. Due to the worldwide adoption of glyphosate-resistant crops, herbicide usage has increased sharply since the mid-1990s. Unfortunately, there are very few studies (none for the Pampa region) reporting picocyanobacteria abundance before 2000. The proliferation of µm sized particles should decrease Secchi disc depth (ZSD). Therefore ZSD, conditional to chlorophyll-a, may serve as an indicator of picocyanobacteria abundance. We use generalized additive models (GAMs) to analyze a “validation” dataset consisting of 82 records of ZSD, chlorophyll-a, and picocyanobacteria abundance from two Pampean lakes surveys (2009 and 2015). In support of the hypothesis, ZSD was negatively related to picocyanobacteria after accounting for the effect of chlorophyll-a. We then fitted a “historical” dataset using hierarchical GAMs to compare ZSD conditional to chlorophyll-a, before and after 2000. We estimated that ZSD levels during 2000–2021 were, on average, only about half as deep as those during 1980–1999. We conclude that the adoption of glyphosate-resistant crops has stimulated outbreaks of picocyanobacteria populations, resulting in lower water transparency.
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FERMANI PAULINA, LAGOMARSINO LEONARDO, TORREMORRELL ANA, ESCARAY ROBERTO, BUSTINGORRY JOSÉ, LLAMES MARÍA, PÉREZ GONZALO, ZAGARESE HORACIO, MATALONI GABRIELA. Divergent dynamics of microbial components in two temperate shallow lakes with contrasting steady states in the Southern Hemisphere. AN ACAD BRAS CIENC 2022; 94:e20191545. [DOI: 10.1590/0001-3765202220191545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 08/21/2020] [Indexed: 11/22/2022] Open
Affiliation(s)
| | | | | | | | | | - MARÍA LLAMES
- Universidad Nacional de San Martín/UNSAM, Argentina
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5
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Schallenberg LA, Pearman JK, Burns CW, Wood SA. Metabarcoding Reveals Lacustrine Picocyanobacteria Respond to Environmental Change Through Adaptive Community Structuring. Front Microbiol 2021; 12:757929. [PMID: 34867882 PMCID: PMC8633389 DOI: 10.3389/fmicb.2021.757929] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/04/2021] [Indexed: 01/04/2023] Open
Abstract
Picocyanobacteria (Pcy) are important yet understudied components of lake foodwebs. While phylogenetic studies of isolated strains reveal a high diversity of freshwater genotypes, little is known about abiotic drivers associated with Pcy in different lakes. Due to methodological limitations, most previous studies assess potential drivers using total cell abundances as a response, with often conflicting and inconsistent results. In the present study, we explored how picocyanobacterial communities respond to environmental change using a combination of epifluorescence microscopy and community data determined using 16S rRNA gene metabarcoding. Temporal shifts in picocyanobacterial abundance, diversity and community dynamics were assessed in relation to potential environmental drivers in five contrasting lakes over 1year. Cell abundances alone were not consistently related to environmental variables across lakes. However, the addition of metabarcoding data revealed diverse picocyanobacterial communities that differed significantly between lakes, driven by environmental variables related to trophic state. Within each lake, communities were temporally dynamic and certain amplicon sequence variants (ASVs) were strongly associated with specific environmental drivers. Rapid shifts in community structure and composition were often related to environmental changes, indicating that lacustrine Pcy can persist at high abundances through collective community adaptation. These results demonstrate that a combination of microscopy and metabarcoding enables an in-depth characterisation of picocyanobacterial communities and reveals strain-specific drivers. We recommend that future studies cease referring to picocyanobacterial as one functional group and take strain specific variability into consideration.
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Affiliation(s)
| | - John K. Pearman
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Carolyn W. Burns
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Susanna A. Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
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6
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Chen G, Zhu N, Hu Z, Liu L, Wang GQ, Wang G. Motility changes rather than EPS production shape aggregation of Chlamydomonas microsphaera in aquatic environment. ENVIRONMENTAL TECHNOLOGY 2021; 42:2916-2924. [PMID: 31951776 DOI: 10.1080/09593330.2020.1718216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/11/2020] [Indexed: 06/10/2023]
Abstract
Microalgal aggregation is a key for both microalgae harvesting and water purification, where changes in extracellular polymeric substance (EPS) secretion and cell motility changes are of core importance. In this study, we investigated the aggregation process of Chlamydomonas microsphaera confronting resource limitation and chlorine disinfection, and tried to compare changes in the magnitude of EPS secretion and cell motility. Results show that the presence of mild chlorine solution (0.20%) dose stimulated microalgal aggregation (with an aggregated to planktonic cells ratio of 3.2), with extracellular protein concentration and mean cell velocity reaching a maximum of 43.43 ± 0.01 mg/L and 201 ± 35 µm/s, respectively. These values are 71% and 191% higher than those of the control. Comparably, nutrient availability had only a limited impact on microalgal aggregation and was associated with mild EPS secretion and cell motility. Correlation analysis revealed a strong positive impact of cell motility (mean velocity) on microalgae aggregation, with little effect on EPS excretion. Together, these quantitative estimations may shed light on understanding the mechanisms of microalgae aggregation in aqueous systems, which could help future design and practical operation of source water pretreatment or microalgae harvesting.
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Affiliation(s)
- Guowei Chen
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, People's Republic of China
- Department of Civil Engineering, Hefei University of Technology, Hefei, People's Republic of China
| | - Ning Zhu
- Department of Civil Engineering, Hefei University of Technology, Hefei, People's Republic of China
| | - Zhen Hu
- Department of Civil Engineering, Hefei University of Technology, Hefei, People's Republic of China
| | - Li Liu
- Department of Civil Engineering, Hefei University of Technology, Hefei, People's Republic of China
| | - Guo-Qing Wang
- Nanjing Hydraulic Research Institute, Nanjing, People's Republic of China
| | - Gang Wang
- Department of Soil and Water Sciences, China Agricultural University, Beijing, People's Republic of China
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7
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Marmen S, Fadeev E, Al Ashhab A, Benet-Perelberg A, Naor A, Patil HJ, Cytryn E, Viner-Mozzini Y, Sukenik A, Lalzar M, Sher D. Seasonal Dynamics Are the Major Driver of Microbial Diversity and Composition in Intensive Freshwater Aquaculture. Front Microbiol 2021; 12:679743. [PMID: 34248892 PMCID: PMC8264503 DOI: 10.3389/fmicb.2021.679743] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/31/2021] [Indexed: 01/04/2023] Open
Abstract
Aquaculture facilities such as fishponds are one of the most anthropogenically impacted freshwater ecosystems. The high fish biomass reared in aquaculture is associated with an intensive input into the water of fish-feed and fish excrements. This nutrients load may affect the microbial community in the water, which in turn can impact the fish health. To determine to what extent aquaculture practices and natural seasonal cycles affect the microbial populations, we characterized the microbiome of an inter-connected aquaculture system at monthly resolution, over 3 years. The system comprised two fishponds, where fish are grown, and an operational water reservoir in which fish are not actively stocked. Clear natural seasonal cycles of temperature and inorganic nutrients concentration, as well as recurring cyanobacterial blooms during summer, were observed in both the fishponds and the reservoir. The structure of the aquatic bacterial communities in the system, characterized using 16S rRNA sequencing, was explained primarily by the natural seasonality, whereas aquaculture-related parameters had only a minor explanatory power. However, the cyanobacterial blooms were characterized by different cyanobacterial clades dominating at each fishpond, possibly in response to distinct nitrogen and phosphate ratios. In turn, nutrient ratios may have been affected by the magnitude of fish feed input. Taken together, our results show that, even in strongly anthropogenically impacted aquatic ecosystems, the structure of bacterial communities is mainly driven by the natural seasonality, with more subtle effects of aquaculture-related factors.
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Affiliation(s)
- Sophi Marmen
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Eduard Fadeev
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Ashraf Al Ashhab
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
- Microbial Metagenomics Division, The Dead Sea and Arava Science Center, Masada, Israel
| | - Ayana Benet-Perelberg
- Dor Aquaculture Research Station, Fisheries Department, Israel Ministry of Agriculture and Rural Development, Dor, Israel
| | - Alon Naor
- Dor Aquaculture Research Station, Fisheries Department, Israel Ministry of Agriculture and Rural Development, Dor, Israel
| | - Hemant J. Patil
- Institute of Soil, Water and Environmental Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
| | - Yehudit Viner-Mozzini
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, Israel
| | - Assaf Sukenik
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, Israel
| | - Maya Lalzar
- Bioinformatics Service Unit, University of Haifa, Haifa, Israel
| | - Daniel Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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8
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Schallenberg LA, Pearman JK, Burns CW, Wood SA. Spatial abundance and distribution of picocyanobacterial communities in two contrasting lakes revealed using environmental DNA metabarcoding. FEMS Microbiol Ecol 2021; 97:fiab075. [PMID: 34100943 DOI: 10.1093/femsec/fiab075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 06/03/2021] [Indexed: 01/04/2023] Open
Abstract
Freshwater picocyanobacteria (Pcy) are important yet understudied components of lake ecosystems. Most previous studies have relied on cell abundances to assess Pcy dynamics in largely oligotrophic lakes, while little is known about spatial diversity and dynamics across different lake types. In the present study we assessed the horizontal-spatial abundance and community structure of Pcy in two contrasting (oligotrophic and hypertrophic) New Zealand lakes using epifluorescence microscopy and 16S rRNA metabarcoding. Pcy abundance and community composition differed significantly both between and within the oligotrophic and hypertrophic lakes. While spatial variability was observed in both study lakes, these differences were particularly pronounced in the oligotrophic, morphometrically complex Lake Wanaka where cell abundances were typically higher in bays than open-water sites and community structure differed significantly between sites. Community structuring appeared to be driven by localised environmental conditions, with different factors influencing each lake. These results suggest that single spot-samples are insufficient to gain an understanding of Pcy dynamics and consequently, phytoplankton dynamics in lakes.
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Affiliation(s)
- Lena A Schallenberg
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin 9010, New Zealand
| | - John K Pearman
- Cawthron Institute, 98 Halifax St East, Private Bag 2, Nelson 7042, New Zealand
| | - Carolyn W Burns
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin 9010, New Zealand
| | - Susanna A Wood
- Cawthron Institute, 98 Halifax St East, Private Bag 2, Nelson 7042, New Zealand
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9
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Quiroga MV, Huber P, Ospina-Serna J, Diovisalvi N, Odriozola M, Cueto GR, Lagomarsino L, Fermani P, Bustingorry J, Escaray R, Zagarese H, Unrein F. The dynamics of picocyanobacteria from a hypereutrophic shallow lake is affected by light-climate and small-bodied zooplankton: a 10-year cytometric time-series analysis. FEMS Microbiol Ecol 2021; 97:6204701. [PMID: 33784379 DOI: 10.1093/femsec/fiab055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/26/2021] [Indexed: 11/12/2022] Open
Abstract
In aquatic systems, an interplay between bottom-up and top-down processes determines the dynamic of picocyanobacteria (Pcy) abundance and community structure. Here, we analyzed a 10-year time series (sampled fortnightly) from a hypereutrophic turbid shallow lake located within the Pampa Region of South America, generating the first long-term record of freshwater Pcy from the Southern Hemisphere. We used a cytometric approach to study Pcy community, and focused on its relations with nutrient and light conditions (bottom-up) and potential grazers (top-down). A novel Pcy abundance seasonality with winter maximums was observed for years with relatively stable hydrological levels, related with decreased abundance of seasonal rotifers during colder seasons. Pcy showed lower abundance and higher cytometric alpha diversity during summer, probably due to a strong predation exerted by rotifers. In turn, a direct effect of the non-seasonal small cladocerans Bosmina spp. decreased Pcy abundance and induced a shift from single-cell Pcy into aggregated forms. This structuring effect of Bosmina spp. was further confirmed by Pcy cytometric (dis)similarity analyses from the time series and in situ experimental data. Remarkably, Pcy showed acclimatization to underwater light variations, resembling the relevance of light in this turbid system.
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Affiliation(s)
- María Victoria Quiroga
- Instituto Tecnológico de Chascomús (INTECH), Universidad Nacional de San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Intendente Marino Km 8.200, (7130) Chascomús, Buenos Aires, Argentina
| | - Paula Huber
- Instituto Tecnológico de Chascomús (INTECH), Universidad Nacional de San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Intendente Marino Km 8.200, (7130) Chascomús, Buenos Aires, Argentina.,Instituto Nacional de Limnología (INALI), Universidad Nacional del Litoral-Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Universitaria, Paraje El Pozo, (3000) Santa Fe, Argentina
| | - Juliana Ospina-Serna
- Instituto Tecnológico de Chascomús (INTECH), Universidad Nacional de San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Intendente Marino Km 8.200, (7130) Chascomús, Buenos Aires, Argentina
| | - Nadia Diovisalvi
- Instituto Tecnológico de Chascomús (INTECH), Universidad Nacional de San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Intendente Marino Km 8.200, (7130) Chascomús, Buenos Aires, Argentina
| | - Mariana Odriozola
- Instituto Tecnológico de Chascomús (INTECH), Universidad Nacional de San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Intendente Marino Km 8.200, (7130) Chascomús, Buenos Aires, Argentina
| | - Gerardo R Cueto
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Universitaria, (1428) Ciudad Autónoma de Buenos Aires, Argentina
| | - Leonardo Lagomarsino
- Instituto Tecnológico de Chascomús (INTECH), Universidad Nacional de San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Intendente Marino Km 8.200, (7130) Chascomús, Buenos Aires, Argentina
| | - Paulina Fermani
- Instituto Tecnológico de Chascomús (INTECH), Universidad Nacional de San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Intendente Marino Km 8.200, (7130) Chascomús, Buenos Aires, Argentina
| | - José Bustingorry
- Instituto Tecnológico de Chascomús (INTECH), Universidad Nacional de San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Intendente Marino Km 8.200, (7130) Chascomús, Buenos Aires, Argentina
| | - Roberto Escaray
- Instituto Tecnológico de Chascomús (INTECH), Universidad Nacional de San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Intendente Marino Km 8.200, (7130) Chascomús, Buenos Aires, Argentina
| | - Horacio Zagarese
- Instituto Tecnológico de Chascomús (INTECH), Universidad Nacional de San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Intendente Marino Km 8.200, (7130) Chascomús, Buenos Aires, Argentina
| | - Fernando Unrein
- Instituto Tecnológico de Chascomús (INTECH), Universidad Nacional de San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Intendente Marino Km 8.200, (7130) Chascomús, Buenos Aires, Argentina
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10
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Seasonal Distribution of Cyanobacteria in Three Urban Eutrophic Lakes Results from an Epidemic-like Response to Environmental Conditions. Curr Microbiol 2021; 78:2298-2316. [PMID: 33904973 DOI: 10.1007/s00284-021-02498-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/16/2021] [Indexed: 10/21/2022]
Abstract
Cyanobacterial communities of three co-located eutrophic sandpit lakes were surveyed during 2016 and 2017 over season and depth using high-throughput DNA sequencing of the 16S rRNA gene. All three lakes were stratified except during April 2017 when the lakes were recovering from a strong mixing event. 16S rRNA gene V4 sequences were parsed into operational taxonomic units (OTUs) at 99% sequence identity. After rarefaction of 139 samples to 25,000 sequences per sample, a combined total of 921,529 partial 16S rRNA gene sequences were identified as cyanobacteria. They were binned into 19,588 unique cyanobacterial OTUs. Of these OTUs, 11,303 were Cyanobium. Filamentous Planktothrix contributed 1537 and colonial Microcystis contributed 265. The remaining 6482 OTUs were considered unclassified. For Planktothrix and Microcystis one OTU accounted for greater than 95% of the total sequences for each genus. However, in both cases the non-dominant OTUs clustered with the dominant OTUs by date, lake, and depth. All Planktothrix OTUs and a single Cyanobium OTU were detected below the oxycline. All other Cyanobium and Microcystis OTUs were detected above the oxycline. The distribution of Cyanobium OTUs between lakes and seasons can be explained by an epidemic-like response where individual OTUs clonally rise from a diverse hypolimnion population when conditions are appropriate. The importance of using 99% identity over the more commonly used 97% is discussed with respect to cyanobacterial community structure. The approach described here can provide another valuable tool for assessing cyanobacterial populations and provide greater insight into the controls of cyanobacterial blooms.
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11
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Ospina-Serna J, Huber P, Odriozola M, Fermani P, Unrein F. Picocyanobacteria aggregation as a response to predation pressure: direct contact is not necessary. FEMS Microbiol Ecol 2020; 96:5899723. [DOI: 10.1093/femsec/fiaa153] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 08/28/2020] [Indexed: 01/08/2023] Open
Abstract
ABSTRACT
Picocyanobacteria (cells <2 µm) can be found either as single-cells (Pcy) or embedded in a mucilaginous sheath as microcolonies or colonies (CPcy). It has been demonstrated that phenotypic plasticity in picocyanobacteria (i.e. the capability of single-cells to aggregate into colonies) can be induced as a response to grazing pressure. The effect of the presence of different predators (cladocerans and rotifers) on the morphological composition of picocyanobacteria was studied in a natural community, and it was observed that the abundance of CPcy significantly increased in all treatments with zooplankton compared with the control without zooplankton. The aggregation capability was also evaluated in a single-cell strain by adding a conditioned medium of flagellates, rotifers and cladocerans. The proportion of cells forming colonies was significantly higher in all treatments with conditioned medium regardless of the predator. These results suggest that the aggregation of Pcy can be induced as a response to the predation pressure exerted by protists and different zooplankters, and also that Pcy has the capability to aggregate into CPcy even without direct contact with any predator, most probably due to the presence of an infochemical dissolved in the water that does not come from disrupted Pcy cells.
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Affiliation(s)
- Juliana Ospina-Serna
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET. Av. Intendente Marino Km 8,200, (7130) Chascomús, Buenos Aires, Argentina
| | - Paula Huber
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET. Av. Intendente Marino Km 8,200, (7130) Chascomús, Buenos Aires, Argentina
- Instituto Nacional de Limnología (INALI), CONICET-UNL. Ciudad Universitaria - Paraje el Pozo s/n, (3000) Santa Fé, Argentina
| | - Mariana Odriozola
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET. Av. Intendente Marino Km 8,200, (7130) Chascomús, Buenos Aires, Argentina
| | - Paulina Fermani
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET. Av. Intendente Marino Km 8,200, (7130) Chascomús, Buenos Aires, Argentina
| | - Fernando Unrein
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET. Av. Intendente Marino Km 8,200, (7130) Chascomús, Buenos Aires, Argentina
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Zhao R, Chen G, Liu L, Zhang W, Sun Y, Li B, Wang G. Bacterial foraging facilitates aggregation of Chlamydomonas microsphaera in an organic carbon source-limited aquatic environment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 259:113924. [PMID: 31926396 DOI: 10.1016/j.envpol.2020.113924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/06/2019] [Accepted: 01/05/2020] [Indexed: 06/10/2023]
Abstract
Microalgal aggregation is a key to many ecosystem functions in aquatic environments. Yet mechanistic understanding of microalgae aggregation, especially the interactions with ubiquitous bacteria populations, remains elusive. We reported an experimental study illustrating how the emerging bacterial populations interacted with a model microalga (Chlamydomonas microsphaera) cells and the consequent aggregation patterns. Results showed that the emergence of bacterial populations significantly stimulated C. microsphaera aggregation. Both bacterial and C. microsphaera motilities were remarkably excited upon coculturing, with the mean cell velocity being up to 2.67 and 1.80 times of those of separate bacterial and C. microsphaera cultures, respectively. The stimulated bacterial and C. microsphaera cell velocity upon coculturing would likely provide a mechanism for enhanced probability of cell-cell collisions that led to amplified aggregation of C. microsphaera population. Correlation analysis revealed that bacterial resource foraging (for polysaccharides) was likely a candidate mechanism for stimulated cell motility in an organic carbon source-limited environment, whereby C. microsphaera-derived polysaccharides serve as the sole organic carbon source for heterotrophic bacteria which in turns facilitates bacteria-C. microsphaera aggregation. Additional analysis showed that bacterial populations capable of successive decomposing algal-derived organic matters dominated the cocultures, with the top five abundant genera of Brevundimonas (24.78%), Shinella (17.94%), Sphingopyxis (11.62%), Dongia (5.82%) and Hyphomicrobium (5.45%). These findings provide new insights into full understanding of microalgae-bacteria interactions and consequent microbial aggregation characteristics in aquatic ecosystems.
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Affiliation(s)
- Ranran Zhao
- Department of Civil Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Guowei Chen
- Department of Civil Engineering, Hefei University of Technology, Hefei, 230009, China; State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China.
| | - Li Liu
- Department of Civil Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Wei Zhang
- Department of Plant, Soil and Microbial Sciences, and Environmental Science and Policy Program, Michigan State University, East Lansing, MI, 48824, United States
| | - Yifei Sun
- Department of Soil and Water Sciences, China Agricultural University, Beijing, 100193, China
| | - Baoguo Li
- Department of Soil and Water Sciences, China Agricultural University, Beijing, 100193, China
| | - Gang Wang
- Department of Soil and Water Sciences, China Agricultural University, Beijing, 100193, China
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Primer Design for an Accurate View of Picocyanobacterial Community Structure by Using High-Throughput Sequencing. Appl Environ Microbiol 2019; 85:AEM.02659-18. [PMID: 30709827 DOI: 10.1128/aem.02659-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/30/2019] [Indexed: 12/26/2022] Open
Abstract
High-throughput sequencing (HTS) of the 16S rRNA gene has been used successfully to describe the structure and dynamics of microbial communities. Picocyanobacteria are important members of bacterioplankton communities, and, so far, they have predominantly been targeted using universal bacterial primers, providing a limited resolution of the picocyanobacterial community structure and dynamics. To increase such resolution, the study of a particular target group is best approached with the use of specific primers. Here, we aimed to design and evaluate specific primers for aquatic picocyanobacterial genera to be used with high-throughput sequencing. Since the various regions of the 16S rRNA gene have different degrees of conservation in different bacterial groups, we therefore first determined which hypervariable region of the 16S rRNA gene provides the highest taxonomic and phylogenetic resolution for the genera Synechococcus, Prochlorococcus, and Cyanobium An in silico analysis showed that the V5, V6, and V7 hypervariable regions appear to be the most informative for this group. We then designed primers flanking these hypervariable regions and tested them in natural marine and freshwater communities. We successfully detected that most (97%) of the obtained reads could be assigned to picocyanobacterial genera. We defined operational taxonomic units as exact sequence variants (zero-radius operational taxonomic units [zOTUs]), which allowed us to detect higher genetic diversity and infer ecologically relevant information about picocyanobacterial community composition and dynamics in different aquatic systems. Our results open the door to future studies investigating picocyanobacterial diversity in aquatic systems.IMPORTANCE The molecular diversity of the aquatic picocyanobacterial community cannot be accurately described using only the available universal 16S rRNA gene primers that target the whole bacterial and archaeal community. We show that the hypervariable regions V5, V6, and V7 of the 16S rRNA gene are better suited to study the diversity, community structure, and dynamics of picocyanobacterial communities at a fine scale using Illumina MiSeq sequencing. Due to its variability, it allows reconstructing phylogenies featuring topologies comparable to those generated when using the complete 16S rRNA gene sequence. Further, we successfully designed a new set of primers flanking the V5 to V7 region whose specificity for picocyanobacterial genera was tested in silico and validated in several freshwater and marine aquatic communities. This work represents a step forward for understanding the diversity and ecology of aquatic picocyanobacteria and sets the path for future studies on picocyanobacterial diversity.
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Albrecht M, Pröschold T, Schumann R. Identification of Cyanobacteria in a Eutrophic Coastal Lagoon on the Southern Baltic Coast. Front Microbiol 2017; 8:923. [PMID: 28611738 PMCID: PMC5446986 DOI: 10.3389/fmicb.2017.00923] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 05/08/2017] [Indexed: 12/20/2022] Open
Abstract
Cyanobacteria are found worldwide in various habitats. Members of the picocyanobacteria genera Synechococcus and Prochlorococcus dominate in oligotrophic ocean waters. Other picocyanobacteria dominate in eutrophic fresh or brackish waters. Usually, these are morphologically determined as species of the order Chroococcales/clade B2. The phytoplankton of a shallow, eutrophic brackish lagoon was investigated. Phytoplankton was dominated by Aphanothece-like morphospecies year-round for more than 20 years, along a trophy and salinity gradient. A biphasic approach using a culture-independent and a culture-dependent analysis was applied to identify the dominant species genetically. The 16S rRNA gene phylogeny of clone sequences and isolates indicated the dominance of Cyanobium species (order Synechococcales sensu Komárek/clade C1 sensu Shih). This difference between morphologically and genetically based species identifications has consequences for applying the Reynolds functional-groups system, and for validity long-term monitoring data. The literature shows the same pattern as our results: morphologically, Aphanothece-like species are abundant in eutrophic shallow lagoons, and genetically, Cyanobium is found in similar habitats. This discrepancy is found worldwide in the literature on fresh- and brackish-water habitats. Thus, most Aphanothece-like morphospecies may be, genetically, members of Cyanobium.
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Affiliation(s)
- Martin Albrecht
- Applied Ecology and Phycology, University of RostockRostock, Germany
| | - Thomas Pröschold
- Research Institute for Limnology, University of InnsbruckMondsee, Austria
| | - Rhena Schumann
- Applied Ecology and Phycology, Biological Station Zingst, University of RostockRostock, Germany
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Stal LJ. Gregarious cyanobacteria. Environ Microbiol 2017; 19:2105-2109. [PMID: 28370986 DOI: 10.1111/1462-2920.13739] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 03/23/2017] [Indexed: 11/29/2022]
Abstract
Huber and collaborators reported in this issue of Environmental Microbiology about freshwater picocyanobacteria that showed phenotypic plasticity in the sense that they appeared as single cells as well as in aggregates. The authors suggested that aggregation might be an inducible defense as a response to the presence of grazers. This has been described for eukaryotic phytoplankton and for the cyanobacterium Microcystis but thus far not for picocyanobacteria. Although inducible defense as an explanation is an attractive possibility, it is also problematic. Aggregation is common among cyanobacteria and it offers many advantages as compared with a free-living lifestyle. Here these advantages are highlighted and the possibility of inducible defense is critically assessed.
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Affiliation(s)
- Lucas J Stal
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, P.O.Box 59, The Netherlands.,University of Amsterdam, IBED Department of Aquatic Microbiology, Amsterdam, P.O.Box 94248, The Netherlands
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