1
|
Zepernick BN, McKay RML, Martin RM, Bullerjahn GS, Paerl HW, Wilhelm SW. A tale of two blooms: do ecological paradigms for algal bloom success and succession require revisiting? JOURNAL OF GREAT LAKES RESEARCH 2024; 50:102336. [PMID: 39050868 PMCID: PMC11268832 DOI: 10.1016/j.jglr.2024.102336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Lake Erie algal bloom discussions have historically focused on cyanobacteria, with foundational "blooms like it hot" and "high nutrient" paradigms considered as primary drivers behind cyanobacterial bloom success. Yet, recent surveys have rediscovered winter-spring diatom blooms, introducing another key player in the Lake Erie eutrophication and algal bloom story which has been historically overlooked. These blooms (summer vs. winter) have been treated as solitary events separated by spatial and temporal gradients. However, new evidence suggests they may not be so isolated, linked in a manner that manifests as an algal bloom cycle. Equally notable are the emerging reports of cyanobacterial blooms in cold and/or oligotrophic freshwaters, which have been interpreted by some as shifts in classical bloom paradigms. These emerging bloom reports have led many to ask "what is a bloom?". Furthermore, questioning classic paradigms has caused others to wonder if we are overlooking additional factors which constrain bloom success. In light of emerging data and ideas, we revisited foundational concepts within the context of Lake Erie algal blooms and derived five key take-aways: 1) Additional bloom-formers (diatoms) need to be included in Lake Erie algal discussions, 2) The term "bloom" must be reinforced with a clear definition and quantitative metrics for each event, 3) Algal blooms should not be studied solitarily, 4) Shifts in physiochemical conditions serve as an alternative interpretation to potential shifts in ecological paradigms, 5) Additional factors which constrain bloom success and succession (i.e., pH and light) require consideration.
Collapse
Affiliation(s)
| | - R. Michael L. McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
| | - Robbie M. Martin
- Department of Microbiology, The University of Tennessee, Knoxville, TN, USA
| | - George S. Bullerjahn
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, OH, USA
| | - Hans W. Paerl
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, Morehead City, NC, USA
| | - Steven W. Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, TN, USA
| |
Collapse
|
2
|
Blais MA, Vincent WF, Vigneron A, Labarre A, Matveev A, Coelho LF, Lovejoy C. Diverse winter communities and biogeochemical cycling potential in the under-ice microbial plankton of a subarctic river-to-sea continuum. Microbiol Spectr 2024; 12:e0416023. [PMID: 38511950 PMCID: PMC11210273 DOI: 10.1128/spectrum.04160-23] [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: 12/08/2023] [Accepted: 03/05/2024] [Indexed: 03/22/2024] Open
Abstract
Winter conditions greatly alter the limnological properties of lotic ecosystems and the availability of nutrients, carbon, and energy resources for microbial processes. However, the composition and metabolic capabilities of winter microbial communities are still largely uncharacterized. Here, we sampled the winter under-ice microbiome of the Great Whale River (Nunavik, Canada) and its discharge plume into Hudson Bay. We used a combination of 16S and 18S rRNA gene amplicon analysis and metagenomic sequencing to evaluate the size-fractionated composition and functional potential of the microbial plankton. These under-ice communities were diverse in taxonomic composition and metabolically versatile in terms of energy and carbon acquisition, including the capacity to carry out phototrophic processes and degrade aromatic organic matter. Limnological properties, community composition, and metabolic potential differed between shallow and deeper sites in the river, and between fresh and brackish water in the vertical profile of the plume. Community composition also varied by size fraction, with a greater richness of prokaryotes in the larger size fraction (>3 µm) and of microbial eukaryotes in the smaller size fraction (0.22-3 µm). The freshwater communities included cosmopolitan bacterial genera that were previously detected in the summer, indicating their persistence over time in a wide range of physico-chemical conditions. These observations imply that the microbial communities of subarctic rivers and their associated discharge plumes retain a broad taxonomic and functional diversity throughout the year and that microbial processing of complex terrestrial materials persists beneath the ice during the long winter season. IMPORTANCE Microbiomes vary over multiple timescales, with short- and long-term changes in the physico-chemical environment. However, there is a scarcity of data and understanding about the structure and functioning of aquatic ecosystems during winter relative to summer. This is especially the case for seasonally ice-covered rivers, limiting our understanding of these ecosystems that are common throughout the boreal, subpolar, and polar regions. Here, we examined the winter under-ice microbiome of a Canadian subarctic river and its entry to the sea to characterize the taxonomic and functional features of the microbial community. We found substantial diversity in both composition and functional capabilities, including the capacity to degrade complex terrestrial compounds, despite the constraints imposed by a prolonged seasonal ice-cover and near-freezing water temperatures. This study indicates the ecological complexity and importance of winter microbiomes in ice-covered rivers and the coastal marine environment that they discharge into.
Collapse
Affiliation(s)
- Marie-Amélie Blais
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- Centre for Northern Studies (CEN), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
| | - Warwick F. Vincent
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- Centre for Northern Studies (CEN), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
| | - Adrien Vigneron
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- Centre for Northern Studies (CEN), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
| | - Aurélie Labarre
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
- Québec-Océan, Université Laval, Quebec City, Quebec, Canada
| | - Alex Matveev
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Centre for Northern Studies (CEN), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
| | - Lígia Fonseca Coelho
- Centro de Química Estrutural, Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Connie Lovejoy
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
- Québec-Océan, Université Laval, Quebec City, Quebec, Canada
| |
Collapse
|
3
|
Kalinowska K, Napiórkowska-Krzebietke A, Bogacka-Kapusta E, Stawecki K, Ulikowski D. Winter dynamics of abiotic and biotic parameters in eutrophic temperate lakes. ACTA OECOLOGICA 2023. [DOI: 10.1016/j.actao.2022.103883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
4
|
Chiriac MC, Haber M, Salcher MM. Adaptive genetic traits in pelagic freshwater microbes. Environ Microbiol 2023; 25:606-641. [PMID: 36513610 DOI: 10.1111/1462-2920.16313] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
Pelagic microbes have adopted distinct strategies to inhabit the pelagial of lakes and oceans and can be broadly categorized in two groups: free-living, specialized oligotrophs and patch-associated generalists or copiotrophs. In this review, we aim to identify genomic traits that enable pelagic freshwater microbes to thrive in their habitat. To do so, we discuss the main genetic differences of pelagic marine and freshwater microbes that are both dominated by specialized oligotrophs and the difference to freshwater sediment microbes, where copiotrophs are more prevalent. We phylogenomically analysed a collection of >7700 metagenome-assembled genomes, classified habitat preferences on different taxonomic levels, and compared the metabolic traits of pelagic freshwater, marine, and freshwater sediment microbes. Metabolic differences are mainly associated with transport functions, environmental information processing, components of the electron transport chain, osmoregulation and the isoelectric point of proteins. Several lineages with known habitat transitions (Nitrososphaeria, SAR11, Methylophilaceae, Synechococcales, Flavobacteriaceae, Planctomycetota) and the underlying mechanisms in this process are discussed in this review. Additionally, the distribution, ecology and genomic make-up of the most abundant freshwater prokaryotes are described in details in separate chapters for Actinobacteriota, Bacteroidota, Burkholderiales, Verrucomicrobiota, Chloroflexota, and 'Ca. Patescibacteria'.
Collapse
Affiliation(s)
| | - Markus Haber
- Institute of Hydrobiology, Biology Centre CAS, Ceske Budejovice, Czechia
| | - Michaela M Salcher
- Institute of Hydrobiology, Biology Centre CAS, Ceske Budejovice, Czechia
| |
Collapse
|
5
|
Laanto E, Oksanen HM. Three Phages from a Boreal Lake during Ice Cover Infecting Xylophilus, Caulobacter, and Polaromonas Species. Viruses 2023; 15:v15020307. [PMID: 36851521 PMCID: PMC9959647 DOI: 10.3390/v15020307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
Although the important role of microbes in freshwater is well understood, studies on phage-host systems in such environments during ice cover are completely lacking. Here, we describe the isolation and characterization of three new bacteriophages infecting Xylophilus sp., Caudobacter sp., and Polaromonas sp. from freshwater samples taken under the ice cover of Lake Konnevesi, Finland. Lumi, Kuura, and Tiera bacteriophages have tailed icosahedral virions and double-stranded DNA. Lumi is a siphophage with a genome of 80,496 bp, and Kuura and Tiera are podophages, and their genomes are 43,205 and 45,327 bp in length, resembling viruses in the class Caudoviricetes. Their host ranges were very limited among the winter-isolated bacterial strains from Konnevesi, each infecting only their own hosts. They can infect efficiently at 4 °C, showing that they are adapted to living in lake water under ice cover. Analysis of the viral genome sequences showed that a significant number of the gene products of each virus are unique, indicating that there is unexplored viral diversity in freshwaters. To our knowledge, Lumi and Tiera are the first phages isolated on the Xylophilus sp. and Polaromonas sp. strains, allowing their exploitation in further studies of freshwater bacterial-phage interactions.
Collapse
Affiliation(s)
- Elina Laanto
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
- Correspondence: ; Tel.: +358-2941-59104
| |
Collapse
|
6
|
Zakharova Y, Bashenkhaeva M, Galachyants Y, Petrova D, Tomberg I, Marchenkov A, Kopyrina L, Likhoshway Y. Variability of Microbial Communities in Two Long-Term Ice-Covered Freshwater Lakes in the Subarctic Region of Yakutia, Russia. MICROBIAL ECOLOGY 2022; 84:958-973. [PMID: 34741646 DOI: 10.1007/s00248-021-01912-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
Although under-ice microbial communities are subject to a cold environment, low concentrations of nutrients, and a lack of light, they nevertheless take an active part in biogeochemical cycles. However, we still lack an understanding of how high their diversity is and how these communities are distributed during the long-term ice-cover period. Here, we assessed for the first time the composition and distribution of microbial communities during the ice-cover period in two subarctic lakes (Labynkyr and Vorota) located in the area of the lowest temperature in the Northern Hemisphere. The diversity distribution and abundance of main bacterial taxa as well as the composition of microalgae varied by time and habitat. The 16S rRNA gene sequencing method revealed, in general, a high diversity of bacterial communities where Proteobacteria (~ 45%) and Actinobacteria (~ 21%) prevailed. There were significant differences between the communities of the lakes: Chthoniobacteraceae, Moraxellaceae, and Pirellulaceae were abundant in Lake Labynkyr, while Cyanobiaceae, Oligoflexales, Ilumatobacteraceae, and Methylacidiphilaceae were more abundant in Lake Vorota. The most abundant families were evenly distributed in April, May, and June their contribution was different in different habitats. In April, Moraxellaceae and Ilumatobacteraceae were the most abundant in the water column, while Sphingomonadaceae was abundant both in water column and on the ice bottom. In May, the abundance of Comamonadaceae increased and reached the maximum in June, while Cyanobiaceae, Oxalobacteraceae, and Pirellulaceae followed. We found a correlation of the structure of bacterial communities with snow thickness, pH, Nmin concentration, and conductivity. We isolated psychrophilic heterotrophic bacteria both from dominating and minor taxa of the communities studied. This allowed for specifying their ecological function in the under-ice communities. These findings will advance our knowledge of the under-ice microbial life.
Collapse
Affiliation(s)
- Yulia Zakharova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Street, Irkutsk, 664033, Russia
| | - Maria Bashenkhaeva
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Street, Irkutsk, 664033, Russia.
| | - Yuri Galachyants
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Street, Irkutsk, 664033, Russia
| | - Darya Petrova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Street, Irkutsk, 664033, Russia
| | - Irina Tomberg
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Street, Irkutsk, 664033, Russia
| | - Artyom Marchenkov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Street, Irkutsk, 664033, Russia
| | - Liubov Kopyrina
- Institute for Biological Problems of Cryolithozone, Siberian Branch of the Russian Academy of Sciences, 41 Lenin Ave, Yakutsk, 677980, Russia
| | - Yelena Likhoshway
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Street, Irkutsk, 664033, Russia
| |
Collapse
|
7
|
Zufiaurre A, Felip M, Camarero L, Sala-Faig M, Juhanson J, Bonilla-Rosso G, Hallin S, Catalan J. Bacterioplankton seasonality in deep high-mountain lakes. Front Microbiol 2022; 13:935378. [PMID: 36187988 PMCID: PMC9519062 DOI: 10.3389/fmicb.2022.935378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/08/2022] [Indexed: 12/04/2022] Open
Abstract
Due to global warming, shorter ice cover duration might drastically affect the ecology of lakes currently undergoing seasonal surface freezing. High-mountain lakes show snow-rich ice covers that determine contrasting conditions between ice-off and ice-on periods. We characterized the bacterioplankton seasonality in a deep high-mountain lake ice-covered for half a year. The lake shows a rich core bacterioplankton community consisting of three components: (i) an assemblage stable throughout the year, dominated by Actinobacteria, resistant to all environmental conditions; (ii) an ice-on-resilient assemblage dominating during the ice-covered period, which is more diverse than the other components and includes a high abundance of Verrucomicrobia; the deep hypolimnion constitutes a refuge for many of the typical under-ice taxa, many of which recover quickly during autumn mixing; and (iii) an ice-off-resilient assemblage, which members peak in summer in epilimnetic waters when the rest decline, characterized by a dominance of Flavobacterium, and Limnohabitans. The rich core community and low random elements compared to other relatively small cold lakes can be attributed to its simple hydrological network in a poorly-vegetated catchment, the long water-residence time (ca. 4 years), and the long ice-cover duration; features common to many headwater deep high-mountain lakes.
Collapse
Affiliation(s)
- Aitziber Zufiaurre
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
- Área de Biodiversidad, Gestión ambiental de Navarra-Nafarroako Ingurumenkudeaketa (GAN-NIK), Pamplona-Iruñea, Navarra, Spain
| | - Marisol Felip
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Lluís Camarero
- Centre d’Estudis Avançats de Blanes (CEAB), CSIC, Blanes, Catalonia, Spain
| | - Marc Sala-Faig
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
| | - Jaanis Juhanson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - German Bonilla-Rosso
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jordi Catalan
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
- CSIC, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
| |
Collapse
|
8
|
Diversity Distribution, Driving Factors and Assembly Mechanisms of Free-Living and Particle-Associated Bacterial Communities at a Subtropical Marginal Sea. Microorganisms 2021; 9:microorganisms9122445. [PMID: 34946047 PMCID: PMC8704526 DOI: 10.3390/microorganisms9122445] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/21/2021] [Accepted: 11/24/2021] [Indexed: 01/04/2023] Open
Abstract
Free-living (FL) and particle-associated (PA) bacterioplankton communities play critical roles in biogeochemical cycles in the ocean. However, their community composition, assembly process and functions in the continental shelf and slope regions are poorly understood. Based on 16S rRNA gene amplicon sequencing, we investigated bacterial communities’ driving factors, assembly processes and functional potentials at a subtropical marginal sea. The bacterioplankton community showed specific distribution patterns with respect to lifestyle (free living vs. particle associated), habitat (slope vs. shelf) and depth (surface vs. DCM and Bottom). Salinity and water temperature were the key factors modulating turnover in the FL community, whereas nitrite, silicate and phosphate were the key factors for the PA community. Model analyses revealed that stochastic processes outweighed deterministic processes and had stronger influences on PA than FL. Homogeneous selection (Hos) was more responsible for the assembly and turnover of FL, while drift and dispersal limitation contributed more to the assembly of PA. Importantly, the primary contributor to Hos in PA was Gammaproteobacteria:Others, whereas that in FL was Cyanobacteria:Bin6. Finally, the PICRUSt2 analysis indicated that the potential metabolisms of carbohydrates, cofactors, amino acids, terpenoids, polyketides, lipids and antibiotic resistance were markedly enriched in PA than FL.
Collapse
|
9
|
Hrycik AR, Isles PDF, Adrian R, Albright M, Bacon LC, Berger SA, Bhattacharya R, Grossart HP, Hejzlar J, Hetherington AL, Knoll LB, Laas A, McDonald CP, Merrell K, Nejstgaard JC, Nelson K, Nõges P, Paterson AM, Pilla RM, Robertson DM, Rudstam LG, Rusak JA, Sadro S, Silow EA, Stockwell JD, Yao H, Yokota K, Pierson DC. Earlier winter/spring runoff and snowmelt during warmer winters lead to lower summer chlorophyll-a in north temperate lakes. GLOBAL CHANGE BIOLOGY 2021; 27:4615-4629. [PMID: 34241940 DOI: 10.1111/gcb.15797] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 05/26/2021] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
Winter conditions, such as ice cover and snow accumulation, are changing rapidly at northern latitudes and can have important implications for lake processes. For example, snowmelt in the watershed-a defining feature of lake hydrology because it delivers a large portion of annual nutrient inputs-is becoming earlier. Consequently, earlier and a shorter duration of snowmelt are expected to affect annual phytoplankton biomass. To test this hypothesis, we developed an index of runoff timing based on the date when 50% of cumulative runoff between January 1 and May 31 had occurred. The runoff index was computed using stream discharge for inflows, outflows, or for flows from nearby streams for 41 lakes in Europe and North America. The runoff index was then compared with summer chlorophyll-a (Chl-a) concentration (a proxy for phytoplankton biomass) across 5-53 years for each lake. Earlier runoff generally corresponded to lower summer Chl-a. Furthermore, years with earlier runoff also had lower winter/spring runoff magnitude, more protracted runoff, and earlier ice-out. We examined several lake characteristics that may regulate the strength of the relationship between runoff timing and summer Chl-a concentrations; however, our tested covariates had little effect on the relationship. Date of ice-out was not clearly related to summer Chl-a concentrations. Our results indicate that ongoing changes in winter conditions may have important consequences for summer phytoplankton biomass and production.
Collapse
Affiliation(s)
- Allison R Hrycik
- Biology Department/Rubenstein Ecosystem Science Laboratory, University of Vermont, Burlington, VT, USA
| | - Peter D F Isles
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Sciences (Eawag), Dübendorf, Switzerland
| | - Rita Adrian
- Department of Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | | | - Linda C Bacon
- State of Maine Department of Environmental Protection, Augusta, ME, USA
| | - Stella A Berger
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin, Germany
| | - Ruchi Bhattacharya
- Legacies of Agricultural Pollutants, Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario, Canada
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin, Germany
- Institute of Biochemistry and Biology, Postdam University, Potsdam, Germany
| | - Josef Hejzlar
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Amy Lee Hetherington
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Lesley B Knoll
- Itasca Biological Station, University of Minnesota, Lake Itasca, MN, USA
| | - Alo Laas
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Cory P McDonald
- Department of Civil and Environmental Engineering, Michigan Technological University, Houghton, MI, USA
| | - Kellie Merrell
- Vermont Department of Environmental Conservation, Montpelier, VT, USA
| | - Jens C Nejstgaard
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin, Germany
| | - Kirsten Nelson
- New Hampshire Department of Environmental Services, Concord, NH, USA
| | - Peeter Nõges
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Andrew M Paterson
- Dorset Environmental Science Centre, Ontario Ministry of Environment, Conservation and Parks, Dorset, Ontario, Canada
| | - Rachel M Pilla
- Department of Biology, Miami University, Oxford, OH, USA
| | - Dale M Robertson
- Upper Midwest Water Science Center, U.S. Geological Survey, Middleton, WI, USA
| | - Lars G Rudstam
- Cornell Biological Field Station, Cornell University, Bridgeport, NY, USA
| | - James A Rusak
- Dorset Environmental Science Centre, Ontario Ministry of Environment, Conservation and Parks, Dorset, Ontario, Canada
| | - Steven Sadro
- Department of Environmental Science and Policy, University of California, Davis, CA, USA
| | - Eugene A Silow
- Institute of Biology, Irkutsk State University, Irkutsk, Russian Federation
| | - Jason D Stockwell
- Rubenstein Ecosystem Science Laboratory, University of Vermont, Burlington, VT, USA
| | - Huaxia Yao
- Dorset Environmental Science Centre, Ontario Ministry of Environment, Conservation and Parks, Dorset, Ontario, Canada
| | - Kiyoko Yokota
- Biology Department, State University of New York College at Oneonta, Oneonta, NY, USA
| | - Donald C Pierson
- Section of Limnology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| |
Collapse
|
10
|
Shahraki AH, Chaganti SR, Heath D. Spatio-temporal dynamics of bacterial communities in the shoreline of Laurentian great Lake Erie and Lake St. Clair's large freshwater ecosystems. BMC Microbiol 2021; 21:253. [PMID: 34548037 PMCID: PMC8454060 DOI: 10.1186/s12866-021-02306-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 09/01/2021] [Indexed: 11/16/2022] Open
Abstract
Background Long-term trends in freshwater bacterial community composition (BCC) and dynamics are not yet well characterized, particularly in large lake ecosystems. We addressed this gap by temporally (15 months) and spatially (6 sampling locations) characterizing BCC variation in lakes Erie and St. Clair; two connected ecosystems in the Laurentian Great Lakes. Results We found a spatial variation of the BCC between the two lakes and among the sampling locations (significant changes in the relative abundance of 16% of the identified OTUs at the sampling location level). We observed five distinct temporal clusters (UPGMA broad-scale temporal variation) corresponding to seasonal variation over the 15 months of sampling. Temporal variation among months was high, with significant variation in the relative abundance of 69% of the OTUs. We identified significant differences in taxonomic composition between summer months of 2016 and 2017, with a corresponding significant reduction in the diversity of BCC in summer 2017. Conclusions As bacteria play a key role in biogeochemical cycling, and hence in healthy ecosystem function our study defines the scope for temporal and spatial variation in large lake ecosystems. Our data also show that freshwater BCC could serve as an effective proxy and monitoring tool to access large lake health. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02306-y.
Collapse
Affiliation(s)
| | - Subba Rao Chaganti
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada. .,Present Address: Cooperative Institute for Great Lakes Research, School of Environmental and Sustainability, University of Michigan, Ann Arbor, MI, USA.
| | - Daniel Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada. .,Department of Integrative Biology, University of Windsor, Windsor, Ontario, Canada.
| |
Collapse
|
11
|
Knepp ZJ, Ghaner A, Root KT. Purification and refolding protocol for cold-active recombinant esterase AaSGNH1 from Aphanizomenon flos-aquae expressed as insoluble inclusion bodies. Prep Biochem Biotechnol 2021; 52:394-403. [PMID: 34355672 DOI: 10.1080/10826068.2021.1952601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Microbial esterases are a highly desirable tool for numerous biosynthetic and biotechnological applications requiring ester bond cleavage. Once identified, microbial esterases are often produced recombinantly in Escherichia coli to enhance yield and ease of purification. In this study a polyhistidine-tagged SGNH esterase gene (AaSGNH1), originating from the cyanobacterium Aphanizomenon flos-aquae, was cloned into an over-expression plasmid and expressed in BL21(DE3) cells. The recombinant esterase enzyme was produced as inactive inclusion bodies which were insoluble in 8 M urea but readily solubilized by the detergent Empigen BB®. Crucially, the procurement of active enzyme required controlled removal of detergent during column chromatography and dialysis steps. The refolded esterase was characterized with respect to its ability to catalyze the cleavage of p-nitrophenol esters of different chain lengths (C2, C8, C16). In addition, the temperature and pH optima were determined and it was found that the enzyme was most active at low temperatures (5-15 °C) and under alkaline conditions (pH 8-10). It was found that the kinetic properties of AaSGNH1 were remarkably similar to other SGNH esterases described thereby validating that the protein was effectively refolded. Overall, this study provides a simple strategy for isolating cold-active recombinant esterase enzyme when expressed as inclusion bodies.
Collapse
Affiliation(s)
- Zachary J Knepp
- Department of Chemistry, Lock Haven University, Lock Haven, PA, USA
| | - Ashlea Ghaner
- Department of Chemistry, Lock Haven University, Lock Haven, PA, USA
| | - Kyle T Root
- Department of Chemistry, Lock Haven University, Lock Haven, PA, USA
| |
Collapse
|
12
|
Kalinowska K, Napiórkowska-Krzebietke A, Ulikowski D, Bogacka-Kapusta E, Stawecki K, Traczuk P. Under-ice environmental conditions, planktonic communities and ichthyofauna in dystrophic lakes. THE EUROPEAN ZOOLOGICAL JOURNAL 2021. [DOI: 10.1080/24750263.2021.1889054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- K. Kalinowska
- Department of Lake Fisheries, S. Sakowicz Inland Fisheries Institute in Olsztyn, Giżycko, Poland
| | - A. Napiórkowska-Krzebietke
- Department of Ichthyology, Hydrobiology and Aquatic Ecology, S. Sakowicz Inland Fisheries Institute in Olsztyn, Olsztyn, Poland
| | - D. Ulikowski
- Department of Lake Fisheries, S. Sakowicz Inland Fisheries Institute in Olsztyn, Giżycko, Poland
| | - E. Bogacka-Kapusta
- Department of Lake Fisheries, S. Sakowicz Inland Fisheries Institute in Olsztyn, Giżycko, Poland
| | - K. Stawecki
- Department of Ichthyology, Hydrobiology and Aquatic Ecology, S. Sakowicz Inland Fisheries Institute in Olsztyn, Olsztyn, Poland
| | - P. Traczuk
- Department of Lake Fisheries, S. Sakowicz Inland Fisheries Institute in Olsztyn, Giżycko, Poland
| |
Collapse
|
13
|
Bock C, Jensen M, Forster D, Marks S, Nuy J, Psenner R, Beisser D, Boenigk J. Factors shaping community patterns of protists and bacteria on a European scale. Environ Microbiol 2020; 22:2243-2260. [PMID: 32202362 DOI: 10.1111/1462-2920.14992] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 03/18/2020] [Indexed: 01/19/2023]
Abstract
Factors shaping community patterns of microorganisms are controversially discussed. Physical and chemical factors certainly limit the survival of individual taxa and maintenance of diversity. In recent years, a contribution of geographic distance and dispersal barriers to distribution patterns of protists and bacteria has been demonstrated. Organismic interactions such as competition, predation and mutualism further modify community structure and maintenance of distinct taxa. Here, we address the relative importance of these different factors in shaping protists and bacterial communities on a European scale using high-throughput sequencing data obtained from lentic freshwater ecosystems. We show that community patterns of protists are similar to those of bacteria. Our results indicate that cross-domain organismic factors are important variables with a higher influence on protists as compared with bacteria. Abiotic physical and chemical factors also contributed significantly to community patterns. The contribution of these latter factors was higher for bacteria, which may reflect a stronger biogeochemical coupling. The contribution of geographical distance was similar for both microbial groups.
Collapse
Affiliation(s)
- Christina Bock
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Manfred Jensen
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Dominik Forster
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger-Str. 14, 67663, Kaiserslautern, Germany
| | - Sabina Marks
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Julia Nuy
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Roland Psenner
- Lake and Glacier Research, Institute of Ecology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Daniela Beisser
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Jens Boenigk
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| |
Collapse
|
14
|
Bižić M, Klintzsch T, Ionescu D, Hindiyeh MY, Günthel M, Muro-Pastor AM, Eckert W, Urich T, Keppler F, Grossart HP. Aquatic and terrestrial cyanobacteria produce methane. SCIENCE ADVANCES 2020; 6:eaax5343. [PMID: 31998836 PMCID: PMC6962044 DOI: 10.1126/sciadv.aax5343] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 11/19/2019] [Indexed: 05/08/2023]
Abstract
Evidence is accumulating to challenge the paradigm that biogenic methanogenesis, considered a strictly anaerobic process, is exclusive to archaea. We demonstrate that cyanobacteria living in marine, freshwater, and terrestrial environments produce methane at substantial rates under light, dark, oxic, and anoxic conditions, linking methane production with light-driven primary productivity in a globally relevant and ancient group of photoautotrophs. Methane production, attributed to cyanobacteria using stable isotope labeling techniques, was enhanced during oxygenic photosynthesis. We suggest that the formation of methane by cyanobacteria contributes to methane accumulation in oxygen-saturated marine and limnic surface waters. In these environments, frequent cyanobacterial blooms are predicted to further increase because of global warming potentially having a direct positive feedback on climate change. We conclude that this newly identified source contributes to the current natural methane budget and most likely has been producing methane since cyanobacteria first evolved on Earth.
Collapse
Affiliation(s)
- M. Bižić
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhuette 2, D-16775 Stechlin, Germany
- Corresponding author. (M.B.); (H.-P.G.)
| | - T. Klintzsch
- Institute of Earth Sciences, Biogeochemistry Group, Heidelberg University, Heidelberg, Germany
| | - D. Ionescu
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhuette 2, D-16775 Stechlin, Germany
| | - M. Y. Hindiyeh
- Department of Water and Environmental Engineering, German Jordanian University, Amman, Jordan
| | - M. Günthel
- Department of Biosciences, Swansea University, SA2 8PP Swansea, UK
- Medical University of Gdańsk, Department of International Research Agenda 3P–Medicine, Marii Skłodowskiej-Curie 3a, 80-210 Gdańsk, Poland
| | - A. M. Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Sevilla, Spain
| | - W. Eckert
- Israel Oceanographic and Limnological Research, Yigal Allon Kinneret Limnological Laboratory, Migdal 14650, Israel
| | - T. Urich
- Institute of Microbiology, Center for Functional Genomics, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
| | - F. Keppler
- Institute of Earth Sciences, Biogeochemistry Group, Heidelberg University, Heidelberg, Germany
- Heidelberg Center for the Environment (HCE), Heidelberg University, 69120 Heidelberg, Germany
| | - H.-P. Grossart
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhuette 2, D-16775 Stechlin, Germany
- Institute of Biochemistry and Biology, Potsdam University, Maulbeerallee 2, 14469 Potsdam, Germany
- Corresponding author. (M.B.); (H.-P.G.)
| |
Collapse
|
15
|
Tran P, Ramachandran A, Khawasik O, Beisner BE, Rautio M, Huot Y, Walsh DA. Microbial life under ice: Metagenome diversity and in situ activity of Verrucomicrobia in seasonally ice-covered Lakes. Environ Microbiol 2019; 20:2568-2584. [PMID: 29921005 DOI: 10.1111/1462-2920.14283] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 05/15/2018] [Indexed: 01/25/2023]
Abstract
Northern lakes are ice-covered for a large part of the year, yet our understanding of microbial diversity and activity during winter lags behind that of the ice-free period. In this study, we investigated under-ice diversity and metabolism of Verrucomicrobia in seasonally ice-covered lakes in temperate and boreal regions of Quebec, Canada using 16S rRNA sequencing, metagenomics and metatranscriptomics. Verrucomicrobia, particularly the V1, V3 and V4 subdivisions, were abundant during ice-covered periods. A diversity of Verrucomicrobia genomes were reconstructed from Quebec lake metagenomes. Several genomes were associated with the ice-covered period and were represented in winter metatranscriptomes, supporting the notion that Verrucomicrobia are metabolically active under ice. Verrucomicrobia transcriptome analysis revealed a range of metabolisms potentially occurring under ice, including carbohydrate degradation, glycolate utilization, scavenging of chlorophyll degradation products, and urea use. Genes for aerobic sulfur and hydrogen oxidation were expressed, suggesting chemolithotrophy may be an adaptation to conditions where labile carbon may be limited. The expression of genes for flagella biosynthesis and chemotaxis was detected, suggesting Verrucomicrobia may be actively sensing and responding to winter nutrient pulses, such as phytoplankton blooms. These results increase our understanding on the diversity and metabolic processes occurring under ice in northern lakes ecosystems.© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.
Collapse
Affiliation(s)
- Patricia Tran
- Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, Quebec, H4B 1R6, Canada.,Groupe de Recherche Interuniversitaire en Limnologie et Environnement Aquatique (GRIL), Montréal, Québec, Canada
| | - Arthi Ramachandran
- Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, Quebec, H4B 1R6, Canada
| | - Ola Khawasik
- Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, Quebec, H4B 1R6, Canada
| | - Beatrix E Beisner
- Groupe de Recherche Interuniversitaire en Limnologie et Environnement Aquatique (GRIL), Montréal, Québec, Canada.,Département des Sciences Biologiques, Université du Québec à Montréal, Montreal, Québec, Canada
| | - Milla Rautio
- Groupe de Recherche Interuniversitaire en Limnologie et Environnement Aquatique (GRIL), Montréal, Québec, Canada.,Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Québec, Canada
| | - Yannick Huot
- Groupe de Recherche Interuniversitaire en Limnologie et Environnement Aquatique (GRIL), Montréal, Québec, Canada.,Département de Géomatique Appliquée, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - David A Walsh
- Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, Quebec, H4B 1R6, Canada.,Groupe de Recherche Interuniversitaire en Limnologie et Environnement Aquatique (GRIL), Montréal, Québec, Canada
| |
Collapse
|
16
|
Butler TM, Wilhelm AC, Dwyer AC, Webb PN, Baldwin AL, Techtmann SM. Microbial Community Dynamics During Lake Ice Freezing. Sci Rep 2019; 9:6231. [PMID: 30996247 PMCID: PMC6470161 DOI: 10.1038/s41598-019-42609-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 03/27/2019] [Indexed: 01/22/2023] Open
Abstract
Many freshwater environments experience dramatic seasonal changes with some systems remaining ice-covered for most of the winter. Freshwater systems are also highly sensitive to environmental change. However, little is known about changes in microbial abundance and community composition during lake ice formation and times of persistent ice cover. The goal of this study is to characterize temporal dynamics of microbial communities during ice formation and persistent ice cover. Samples were collected in triplicate, five days per week from surface water in the Keweenaw Waterway between November and April. Environmental conditions along with microbial abundance and microbial community composition was determined. Distinct community composition was found between ice-free and ice-covered time periods with significantly different community composition between months. The microbial community underwent dramatic shifts in microbial abundance and diversity during the transitions into and out of ice cover. The richness of the microbial community increased during times of ice cover. Relatives of microbes involved in nitrogen cycling bloomed during times of ice cover as sequences related to known nitrifying taxa were significantly enriched during ice cover. These results help to elucidate how microbial abundance and diversity change over drastic seasonal transitions and how ice cover may affect microbial abundance and diversity.
Collapse
Affiliation(s)
- Timothy M Butler
- Department of Biological Sciences, Michigan Technology University, Houghton, MI, USA
| | | | - Amber C Dwyer
- Department of Biological Sciences, Michigan Technology University, Houghton, MI, USA
| | - Paige N Webb
- Department of Biological Sciences, Michigan Technology University, Houghton, MI, USA
| | - Andrew L Baldwin
- Department of Biological Sciences, Michigan Technology University, Houghton, MI, USA
| | - Stephen M Techtmann
- Department of Biological Sciences, Michigan Technology University, Houghton, MI, USA.
| |
Collapse
|
17
|
Bock C, Salcher M, Jensen M, Pandey RV, Boenigk J. Synchrony of Eukaryotic and Prokaryotic Planktonic Communities in Three Seasonally Sampled Austrian Lakes. Front Microbiol 2018; 9:1290. [PMID: 29963032 PMCID: PMC6014231 DOI: 10.3389/fmicb.2018.01290] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/28/2018] [Indexed: 01/15/2023] Open
Abstract
Freshwater systems are characterized by an enormous diversity of eukaryotic protists and prokaryotic taxa. The community structures in different lakes are thereby influenced by factors such as habitat size, lake chemistry, biotic interactions, and seasonality. In our study, we used high throughput 454 sequencing to study the diversity and temporal changes of prokaryotic and eukaryotic planktonic communities in three Austrian lakes during the ice-free season. In the following year, one lake was sampled again with a reduced set of sampling dates to observe reoccurring patterns. Cluster analyses (based on SSU V9 (eukaryotic) and V4 (prokaryotic) OTU composition) grouped samples according to their origin followed by separation into seasonal clusters, indicating that each lake has a unique signature based on OTU composition. These results suggest a strong habitat-specificity of microbial communities and in particular of community patterns at the OTU level. A comparison of the prokaryotic and eukaryotic datasets via co-inertia analysis (CIA) showed a consistent clustering of prokaryotic and eukaryotic samples, probably reacting to the same environmental forces (e.g., pH, conductivity). In addition, the shifts in eukaryotic and bacterioplanktonic communities generally occurred at the same time and on the same scale. Regression analyses revealed a linear relationship between an increase in Bray-Curtis dissimilarities and elapsed time. Our study shows a pronounced coupling between bacteria and eukaryotes in seasonal samplings of the three analyzed lakes. However, our temporal resolution (biweekly sampling) and data on abiotic factors were insufficient to determine if this was caused by direct biotic interactions or by reacting to the same seasonally changing environmental forces.
Collapse
Affiliation(s)
- Christina Bock
- Biodiversity, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Michaela Salcher
- Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland.,Institute of Hydrobiology, Biology Centre CAS, České Budějovice, Czechia
| | - Manfred Jensen
- Biodiversity, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Ram Vinay Pandey
- Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Vienna, Austria.,Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Jens Boenigk
- Biodiversity, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| |
Collapse
|
18
|
Wurzbacher C, Attermeyer K, Kettner MT, Flintrop C, Warthmann N, Hilt S, Grossart HP, Monaghan MT. DNA metabarcoding of unfractionated water samples relates phyto-, zoo- and bacterioplankton dynamics and reveals a single-taxon bacterial bloom. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:383-388. [PMID: 28429584 DOI: 10.1111/1758-2229.12540] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 04/02/2017] [Indexed: 06/07/2023]
Abstract
Most studies of aquatic plankton focus on either macroscopic or microbial communities, and on either eukaryotes or prokaryotes. This separation is primarily for methodological reasons, but can overlook potential interactions among groups. Here we tested whether DNA metabarcoding of unfractionated water samples with universal primers could be used to qualitatively and quantitatively study the temporal dynamics of the total plankton community in a shallow temperate lake. Significant changes in the relative proportions of normalized sequence reads of eukaryotic and prokaryotic plankton communities over a 3-month period in spring were found. Patterns followed the same trend as plankton estimates measured using traditional microscopic methods. The bloom of a conditionally rare bacterial taxon belonging to Arcicella was characterized, which rapidly came to dominate the whole lake ecosystem and would have remained unnoticed without metabarcoding. The data demonstrate the potential of universal DNA metabarcoding applied to unfractionated samples for providing a more holistic view of plankton communities.
Collapse
Affiliation(s)
- Christian Wurzbacher
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, Göteborg, 40530, Sweden
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587, Germany
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775, Germany
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195, Germany
| | - Katrin Attermeyer
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775, Germany
- Department of Ecology and Genetics, Limnology, Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Marie Therese Kettner
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775, Germany
- Potsdam University, Institute of Biochemistry and Biology, Maulbeerallee 2, Potsdam, 14469, Germany
| | - Clara Flintrop
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195, Germany
- Helmholtz Young Investigator Group SEAPUMP, Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, and MARUM, University of Bremen, Leobener Strasse, Bremen, 28359, Germany
| | - Norman Warthmann
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587, Germany
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195, Germany
- Research School of Biology, The Australian National University, Linnaeus Way, Canberra, ACT, 2601, Australia
| | - Sabine Hilt
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587, Germany
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775, Germany
- Potsdam University, Institute of Biochemistry and Biology, Maulbeerallee 2, Potsdam, 14469, Germany
| | - Michael T Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587, Germany
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195, Germany
| |
Collapse
|
19
|
Wurzbacher C, Attermeyer K, Kettner MT, Flintrop C, Warthmann N, Hilt S, Grossart HP, Monaghan MT. DNA metabarcoding of unfractionated water samples relates phyto-, zoo- and bacterioplankton dynamics and reveals a single-taxon bacterial bloom. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:383-388. [PMID: 28429584 DOI: 10.1101/058628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 04/02/2017] [Indexed: 05/25/2023]
Abstract
Most studies of aquatic plankton focus on either macroscopic or microbial communities, and on either eukaryotes or prokaryotes. This separation is primarily for methodological reasons, but can overlook potential interactions among groups. Here we tested whether DNA metabarcoding of unfractionated water samples with universal primers could be used to qualitatively and quantitatively study the temporal dynamics of the total plankton community in a shallow temperate lake. Significant changes in the relative proportions of normalized sequence reads of eukaryotic and prokaryotic plankton communities over a 3-month period in spring were found. Patterns followed the same trend as plankton estimates measured using traditional microscopic methods. The bloom of a conditionally rare bacterial taxon belonging to Arcicella was characterized, which rapidly came to dominate the whole lake ecosystem and would have remained unnoticed without metabarcoding. The data demonstrate the potential of universal DNA metabarcoding applied to unfractionated samples for providing a more holistic view of plankton communities.
Collapse
Affiliation(s)
- Christian Wurzbacher
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, Göteborg, 40530, Sweden
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587, Germany
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775, Germany
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195, Germany
| | - Katrin Attermeyer
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775, Germany
- Department of Ecology and Genetics, Limnology, Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Marie Therese Kettner
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775, Germany
- Potsdam University, Institute of Biochemistry and Biology, Maulbeerallee 2, Potsdam, 14469, Germany
| | - Clara Flintrop
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195, Germany
- Helmholtz Young Investigator Group SEAPUMP, Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, and MARUM, University of Bremen, Leobener Strasse, Bremen, 28359, Germany
| | - Norman Warthmann
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587, Germany
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195, Germany
- Research School of Biology, The Australian National University, Linnaeus Way, Canberra, ACT, 2601, Australia
| | - Sabine Hilt
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587, Germany
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775, Germany
- Potsdam University, Institute of Biochemistry and Biology, Maulbeerallee 2, Potsdam, 14469, Germany
| | - Michael T Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587, Germany
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195, Germany
| |
Collapse
|
20
|
Frisia S, Weyrich LS, Hellstrom J, Borsato A, Golledge NR, Anesio AM, Bajo P, Drysdale RN, Augustinus PC, Rivard C, Cooper A. The influence of Antarctic subglacial volcanism on the global iron cycle during the Last Glacial Maximum. Nat Commun 2017; 8:15425. [PMID: 28598412 PMCID: PMC5472753 DOI: 10.1038/ncomms15425] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 03/27/2017] [Indexed: 11/09/2022] Open
Abstract
Marine sediment records suggest that episodes of major atmospheric CO2 drawdown during the last glacial period were linked to iron (Fe) fertilization of subantarctic surface waters. The principal source of this Fe is thought to be dust transported from southern mid-latitude deserts. However, uncertainty exists over contributions to CO2 sequestration from complementary Fe sources, such as the Antarctic ice sheet, due to the difficulty of locating and interrogating suitable archives that have the potential to preserve such information. Here we present petrographic, geochemical and microbial DNA evidence preserved in precisely dated subglacial calcites from close to the East Antarctic Ice-Sheet margin, which together suggest that volcanically-induced drainage of Fe-rich waters during the Last Glacial Maximum could have reached the Southern Ocean. Our results support a significant contribution of Antarctic volcanism to subglacial transport and delivery of nutrients with implications on ocean productivity at peak glacial conditions.
Collapse
Affiliation(s)
- Silvia Frisia
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Laura S. Weyrich
- Australian Centre for Ancient DNA (ACAD), The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - John Hellstrom
- School of Earth Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andrea Borsato
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Nicholas R. Golledge
- Antarctic Research Centre, Victoria University of Wellington, Wellington 6140, New Zealand
- GNS Science, Avalon, Lower Hut 5011, New Zealand
| | - Alexandre M. Anesio
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, Bristol BS8 1SS, UK
| | - Petra Bajo
- School of Geography, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Russell N. Drysdale
- School of Geography, The University of Melbourne, Parkville, Victoria 3010, Australia
- Environnements, Dynamiques et Territoires de la Montagne, UMR CNRS, Université de Savoie-Mont Blanc, 73376 Le Bourget du Lac, France
| | - Paul C. Augustinus
- School of Environment, The University of Auckland, Private Bag, Auckland 92019, New Zealand
| | - Camille Rivard
- European Synchrotron Radiation Facility, 38000 Grenoble, France
| | - Alan Cooper
- Australian Centre for Ancient DNA (ACAD), The University of Adelaide, Adelaide, South Australia 5005, Australia
| |
Collapse
|
21
|
Pernthaler J. Competition and niche separation of pelagic bacteria in freshwater habitats. Environ Microbiol 2017; 19:2133-2150. [PMID: 28370850 DOI: 10.1111/1462-2920.13742] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 03/19/2017] [Accepted: 03/23/2017] [Indexed: 11/29/2022]
Abstract
Freshwater bacterioplankton assemblages are composed of sympatric populations that can be delineated, for example, by ribosomal RNA gene relatedness and that differ in key ecophysiological properties. They may be free-living or attached, specialized for particular concentrations or subsets of substrates, or invest a variable amount of their resources in defence traits against protistan predators and viruses. Some may be motile and tactic whereas others are not, with far-reaching implications for their respective life styles and niche partitioning. The co-occurrence of competitors with overlapping growth requirements has profound consequences for the stability of community functions; it can to some extent be explained by habitat factors such as the microscale complexity and spatiotemporal variability of the lacustrine environments. On the other hand, the composition and diversity of freshwater microbial assemblages also reflects non-equilibrium states, dispersal and the stochasticity of community assembly processes. This review synoptically discusses the competition and niche separation of heterotrophic bacterial populations (defined at various levels of phylogenetic resolution) in the pelagic zone of inland surface waters from a variety of angles, focusing on habitat heterogeneity and the resulting biogeographic distribution patterns, the ecophysiological adaptations to the substrate field and the interactions of prokaryotes with predators and viruses.
Collapse
Affiliation(s)
- Jakob Pernthaler
- Limnological Station Kilchberg, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| |
Collapse
|
22
|
Watson SB, Miller C, Arhonditsis G, Boyer GL, Carmichael W, Charlton MN, Confesor R, Depew DC, Höök TO, Ludsin SA, Matisoff G, McElmurry SP, Murray MW, Peter Richards R, Rao YR, Steffen MM, Wilhelm SW. The re-eutrophication of Lake Erie: Harmful algal blooms and hypoxia. HARMFUL ALGAE 2016; 56:44-66. [PMID: 28073496 DOI: 10.1016/j.hal.2016.04.010] [Citation(s) in RCA: 167] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 05/12/2023]
Abstract
Lake Erie supplies drinking water to more than 11 million consumers, processes millions of gallons of wastewater, provides important species habitat and supports a substantial industrial sector, with >$50 billion annual income to tourism, recreational boating, shipping, fisheries, and other industries. These and other key ecosystem services are currently threatened by an excess supply of nutrients, manifested in particular by increases in the magnitude and extent of harmful planktonic and benthic algal blooms (HABs) and hypoxia. Widespread concern for this important international waterbody has been manifested in a strong focus of scientific and public material on the subject, and commitments for Canada-US remedial actions in recent agreements among Federal, Provincial and State agencies. This review provides a retrospective synthesis of past and current nutrient inputs, impairments by planktonic and benthic HABs and hypoxia, modelling and Best Management Practices in the Lake Erie basin. The results demonstrate that phosphorus reduction is of primary importance, but the effects of climate, nitrogen and other factors should also be considered in the context of adaptive management. Actions to reduce nutrient levels by targeted Best Management Practices will likely need to be tailored for soil types, topography, and farming practices.
Collapse
Affiliation(s)
- Susan B Watson
- Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Burlington, ON L7S 1A1, Canada.
| | - Carol Miller
- Department of Civil and Environmental Engineering, Urban Watershed Environmental Research Group, Wayne State University, Detroit, MI 48202, USA
| | - George Arhonditsis
- Department of Physical & Environmental Sciences, University of Toronto, Toronto, ON M1C 1A4, Canada
| | - Gregory L Boyer
- Department of Chemistry, State University of New York - College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - Wayne Carmichael
- Department of Biological Sciences, Wright State University, Dayton, OH 45435, USA
| | | | - Remegio Confesor
- National Center for Water Quality Research, Heidelberg University, Tiffin, OH 44883, USA
| | - David C Depew
- Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Burlington, ON L7S 1A1, Canada
| | - Tomas O Höök
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907-2033, USA
| | - Stuart A Ludsin
- Aquatic Ecology Laboratory, Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43212, USA
| | - Gerald Matisoff
- Department of Earth, Environmental and Planetary Sciences Case Western Reserve University, Cleveland, OH 44106-7216, USA
| | - Shawn P McElmurry
- Department of Civil and Environmental Engineering, Urban Watershed Environmental Research Group, Wayne State University, Detroit, MI 48202, USA
| | - Michael W Murray
- National Wildlife Federation Great Lakes Regional Center, Ann Arbor, MI 48104, USA
| | | | - Yerubandi R Rao
- Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Burlington, ON L7S 1A1, Canada
| | - Morgan M Steffen
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, TN 37996-0845, USA
| |
Collapse
|