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Article ; Online: Genome Streamlining, Proteorhodopsin, and Organic Nitrogen Metabolism in Freshwater Nitrifiers.

Podowski, Justin C / Paver, Sara F / Newton, Ryan J / Coleman, Maureen L

2022 Volume 13, Issue 3, Page(s) e0237921

Abstract: Microbial nitrification is a critical process governing nitrogen availability in aquatic systems. Freshwater nitrifiers have received little attention, leaving many unanswered questions about their taxonomic distribution, functional potential, and ... ...

Abstract	Microbial nitrification is a critical process governing nitrogen availability in aquatic systems. Freshwater nitrifiers have received little attention, leaving many unanswered questions about their taxonomic distribution, functional potential, and ecological interactions. Here, we reconstructed genomes to infer the metabolism and ecology of free-living picoplanktonic nitrifiers across the Laurentian Great Lakes, a connected series of five of Earth's largest lakes. Surprisingly, ammonia-oxidizing bacteria (AOB) related to
MeSH term(s)	Ammonia/metabolism ; Archaea/genetics ; Archaea/metabolism ; Bacteria/genetics ; Bacteria/metabolism ; Ecosystem ; Genome ; Lakes/microbiology ; Nitrification ; Nitrogen/metabolism ; Oxidation-Reduction ; Phylogeny ; Rhodopsins, Microbial
Chemical Substances	Rhodopsins, Microbial ; proteorhodopsin ; Ammonia (7664-41-7) ; Nitrogen (N762921K75)
Language	English
Publishing date	2022-04-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mbio.02379-21
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Microbial communities of the Laurentian Great Lakes reflect connectivity and local biogeochemistry.

Paver, Sara F / Newton, Ryan J / Coleman, Maureen L

Environmental microbiology

2019 Volume 22, Issue 1, Page(s) 433–446

Abstract: The Laurentian Great Lakes are a vast, interconnected freshwater system spanning strong physicochemical gradients, thus constituting a powerful natural laboratory for addressing fundamental questions about microbial ecology and evolution. We present a ... ...

Abstract	The Laurentian Great Lakes are a vast, interconnected freshwater system spanning strong physicochemical gradients, thus constituting a powerful natural laboratory for addressing fundamental questions about microbial ecology and evolution. We present a comparative analysis of pelagic microbial communities across all five Laurentian Great Lakes, focusing on Bacterial and Archaeal picoplankton characterized via 16S rRNA amplicon sequencing. We collected samples throughout the water column from the major basins of each lake in spring and summer over 2 years. Two oligotypes, classified as LD12 (Alphaproteobacteria) and acI-B1 (Actinobacteria), were among the most abundant in every sample. At the same time, microbial communities showed distinct patterns with depth during summer stratification. Deep hypolimnion samples were frequently dominated by a Chloroflexi oligotype that reached up to 19% relative abundance. Stratified surface communities differed between the colder, less productive upper lakes (Superior, Michigan, Huron) and warmer, more productive lower lakes (Erie, Ontario), in part due to an Actinobacteria oligotype (acI-C2) that averaged 7.7% of sequences in the lower lakes but <0.2% in the upper lakes. Together, our findings suggest that both hydrologic connectivity and local selective pressures shape microbial communities in the Great Lakes and establish a framework for future investigations.
MeSH term(s)	Actinobacteria/classification ; Actinobacteria/genetics ; Actinobacteria/isolation & purification ; Alphaproteobacteria/classification ; Alphaproteobacteria/genetics ; Alphaproteobacteria/isolation & purification ; Archaea/classification ; Archaea/genetics ; Archaea/isolation & purification ; Chloroflexi/classification ; Chloroflexi/genetics ; Chloroflexi/isolation & purification ; Lakes/microbiology ; Michigan ; Microbiota/genetics ; Phylogeny ; Plankton/classification ; Plankton/genetics ; RNA, Ribosomal, 16S/genetics
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2019-12-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.14862
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Article: Microbial communities of the Laurentian Great Lakes reflect connectivity and local biogeochemistry

Paver, Sara F / Newton, Ryan J / Coleman, Maureen L

Environmental microbiology. 2020 Jan., v. 22, no. 1

2020

Abstract	The Laurentian Great Lakes are a vast, interconnected freshwater system spanning strong physicochemical gradients, thus constituting a powerful natural laboratory for addressing fundamental questions about microbial ecology and evolution. We present a comparative analysis of pelagic microbial communities across all five Laurentian Great Lakes, focusing on Bacterial and Archaeal picoplankton characterized via 16S rRNA amplicon sequencing. We collected samples throughout the water column from the major basins of each lake in spring and summer over 2 years. Two oligotypes, classified as LD12 (Alphaproteobacteria) and acI‐B1 (Actinobacteria), were among the most abundant in every sample. At the same time, microbial communities showed distinct patterns with depth during summer stratification. Deep hypolimnion samples were frequently dominated by a Chloroflexi oligotype that reached up to 19% relative abundance. Stratified surface communities differed between the colder, less productive upper lakes (Superior, Michigan, Huron) and warmer, more productive lower lakes (Erie, Ontario), in part due to an Actinobacteria oligotype (acI‐C2) that averaged 7.7% of sequences in the lower lakes but <0.2% in the upper lakes. Together, our findings suggest that both hydrologic connectivity and local selective pressures shape microbial communities in the Great Lakes and establish a framework for future investigations.
Keywords	Actinobacteria ; Archaea ; Chloroflexi ; alpha-Proteobacteria ; basins ; biogeochemistry ; freshwater ; lakes ; microbial communities ; ribosomal RNA ; sequence analysis ; spring ; summer ; Great Lakes ; Michigan ; Ontario
Language	English
Dates of publication	2020-01
Size	p. 433-446.
Publishing place	John Wiley & Sons, Inc.
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.14862
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Article: Direct and contextâdependent effects of light, temperature, and phytoplankton shape bacterial community composition

Paver, Sara F / Angela D. Kent

Ecosphere. 2017 Sept., v. 8, no. 9

2017

Abstract: Species interactions, environmental conditions, and stochastic processes work in concert to bring about changes in community structure. However, the relative importance of specific factors and how their combined influence affects community composition ... ...

Abstract	Species interactions, environmental conditions, and stochastic processes work in concert to bring about changes in community structure. However, the relative importance of specific factors and how their combined influence affects community composition remain largely unclear. We conducted a multiâfactorial experiment to (1) disentangle the direct and interactionâmediated effects of environmental conditions and (2) augment our understanding of how environmental context modulates species interactions. We focus on a planktonic system where interactions with phytoplankton effect changes in the composition of bacterial communities. Further, light and temperature conditions can influence bacteria directly as well as through their interactions with phytoplankton. Epilimnetic bacteria from two humic lakes were combined with phytoplankton assemblages from each lake (home or away) or a noâphytoplankton control and incubated for 5Â d under all combinations of light (surface, ~25% surface irradiance) and temperature (five levels from 10Â° to 25Â°C). Observed light effects were primarily direct, while phytoplankton and temperature effects on bacterial community composition were highly interdependent. The influence of temperature on aquatic bacteria was consistently mediated by phytoplankton and most pronounced for bacteria incubated with âawayâ phytoplankton treatments, likely due to the availability of novel phytoplanktonâderived resources. The effects of phytoplankton on bacterial community composition were generally increased at higher temperatures. Incorporating mechanisms underlying the observed interdependent effects of species interactions and environmental conditions into modeling frameworks may improve our ability to forecast ecological responses to environmental change.
Keywords	aquatic bacteria ; bacterial communities ; community structure ; environmental factors ; lakes ; light intensity ; models ; phytoplankton ; stochastic processes ; temperature
Language	English
Dates of publication	2017-09
Size	p. .
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2572257-8
ISSN	2150-8925
ISSN	2150-8925
DOI	10.1002/ecs2.1948
Database	NAL-Catalogue (AGRICOLA)

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Article: Reevaluating the Salty Divide: Phylogenetic Specificity of Transitions between Marine and Freshwater Systems.

Paver, Sara F / Muratore, Daniel / Newton, Ryan J / Coleman, Maureen L

mSystems

2018 Volume 3, Issue 6

Abstract: Marine and freshwater microbial communities are phylogenetically distinct, and transitions between habitat types are thought to be infrequent. We compared the phylogenetic diversity of marine and freshwater microorganisms and identified specific lineages ...

Abstract	Marine and freshwater microbial communities are phylogenetically distinct, and transitions between habitat types are thought to be infrequent. We compared the phylogenetic diversity of marine and freshwater microorganisms and identified specific lineages exhibiting notably high or low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA gene tag-sequencing data sets. As expected, marine and freshwater microbial communities differed in the relative abundance of major phyla and contained habitat-specific lineages. At the same time, and contrary to expectations, many shared taxa were observed in both habitats. Based on several metrics, we found that
Language	English
Publishing date	2018-11-13
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN	2379-5077
DOI	10.1128/mSystems.00232-18
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Article ; Online: Temporal patterns in glycolate-utilizing bacterial community composition correlate with phytoplankton population dynamics in humic lakes.

Paver, Sara F / Kent, Angela D

Microbial ecology

2010 Volume 60, Issue 2, Page(s) 406–418

Abstract: Previous observations of correlated community dynamics between phytoplankton and bacteria in lakes indicate that phytoplankton populations may influence bacterial community structure. To investigate the possibility that bacterial use of phytoplankton ... ...

Abstract	Previous observations of correlated community dynamics between phytoplankton and bacteria in lakes indicate that phytoplankton populations may influence bacterial community structure. To investigate the possibility that bacterial use of phytoplankton exudates contributes to observed patterns of community change, we characterized the diversity and dynamics of heterotrophic bacterioplankton with genetic potential to use glycolate, a photorespiration-specific exudate, in five lakes over a 15-week period. Culture-independent approaches were used to track different bacterial phylotypes represented by DNA sequence variation in the functional gene glycolate oxidase subunit D (glcD). glcD gene sequences from freshwater bacteria exhibited broad phylogenetic diversity, including sequences representing the Alpha-, Beta-, and Gammaproteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Verrucomicrobia. The majority of glcD gene sequences were betaproteobacterial, with 48% of the sequences clustering with the glcD gene from the cosmopolitan freshwater species Polynucleobacter necessarius. Terminal restriction fragment length polymorphism fingerprinting of the glcD gene revealed changes in glycolate-utilizing assemblages over time. An average of 39% of within-lake temporal variation in glycolate-utilizing assemblages across five lakes was explained by phytoplankton community composition and dynamics. The interaction between phytoplankton populations and the environment explained an additional 17% of variation on average. These observations offer new insight into the diversity and temporal dynamics of freshwater bacteria with genetic potential to use glycolate and support the hypothesis that algal exudates influence the structure of bacterial communities.
MeSH term(s)	Alcohol Oxidoreductases/genetics ; Bacteria/classification ; Bacteria/genetics ; Bacteria/growth & development ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Fresh Water/microbiology ; Genes, Bacterial ; Glycolates/metabolism ; Microbial Consortia ; Phylogeny ; Phytoplankton/growth & development ; Phytoplankton/microbiology ; Polymorphism, Restriction Fragment Length ; Population Dynamics ; Sequence Analysis, DNA ; Time Factors ; Water Microbiology
Chemical Substances	DNA, Bacterial ; Glycolates ; glycolic acid (0WT12SX38S) ; Alcohol Oxidoreductases (EC 1.1.-) ; glycollate oxidase (EC 1.1.3.15)
Language	English
Publishing date	2010-07-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1462065-0
ISSN	1432-184X ; 0095-3628
ISSN (online)	1432-184X
ISSN	0095-3628
DOI	10.1007/s00248-010-9722-6
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Article ; Online: Temporal succession of putative glycolate-utilizing bacterioplankton tracks changes in dissolved organic matter in a high-elevation lake.

Paver, Sara F / Nelson, Craig E / Kent, Angela D

FEMS microbiology ecology

2013 Volume 83, Issue 3, Page(s) 541–551

Abstract: Shifts in the composition of dissolved organic matter (DOM) may be a principal factor effecting changes in bacterial community composition. Emerald Lake, a high-elevation lake with DOM dominated by terrestrial sources in the spring with increasing ... ...

Abstract	Shifts in the composition of dissolved organic matter (DOM) may be a principal factor effecting changes in bacterial community composition. Emerald Lake, a high-elevation lake with DOM dominated by terrestrial sources in the spring with increasing phytoplankton-derived inputs throughout the ice-free season, provided a natural experiment with which to investigate the importance of resource-mediated drivers. Glycolate-utilizing bacteria, a subset of the bacterial community able to use algal exudates, were characterized using DNA analysis of glycolate oxidase subunit D (glcD) genes from Emerald Lake samples collected approximately biweekly from ice-cover (June) through fall turnover (September). glcD genes were not detected in early-season samples when the lake was ice-covered and phytoplankton-derived resources were scarce. Following this period, glcD gene composition exhibited significant changes through time, which were strongly correlated with the combination of fluorescence index, an indicator of the proportion of lake vs. terrestrially derived DOM, and dissolved inorganic nitrate + nitrite. These results suggest that seasonal shifts in DOM source and environmental variables that affect the composition of algal-derived dissolved resources drive changes in the relative abundance and composition of putative glycolate-utilizing bacteria. These findings strengthen the evidence for shifts in DOM structuring bacterial communities.
MeSH term(s)	Alcohol Oxidoreductases/genetics ; Alcohol Oxidoreductases/isolation & purification ; Bacteria/enzymology ; Bacteria/genetics ; DNA, Bacterial/genetics ; DNA, Bacterial/isolation & purification ; Fresh Water/microbiology ; Glycolates/metabolism ; Lakes/microbiology ; Phylogeny ; Phytoplankton ; Polymorphism, Restriction Fragment Length ; Seasons ; Sequence Analysis, DNA
Chemical Substances	DNA, Bacterial ; Glycolates ; Alcohol Oxidoreductases (EC 1.1.-) ; glycollate oxidase (EC 1.1.3.15)
Language	English
Publishing date	2013-03
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	283722-5
ISSN	1574-6941 ; 0168-6496
ISSN (online)	1574-6941
ISSN	0168-6496
DOI	10.1111/1574-6941.12012
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Article ; Online: Phytoplankton succession affects the composition of Polynucleobacter subtypes in humic lakes.

Paver, Sara F / Youngblut, Nicholas D / Whitaker, Rachel J / Kent, Angela D

Environmental microbiology

2015 Volume 17, Issue 3, Page(s) 816–828

Abstract: Phytoplankton influence the composition of bacterial communities, but the taxonomic specificity of algal-bacterial interactions is unclear due to the aggregation of ecologically distinct bacterial populations by community characterization methods. Here ... ...

Abstract	Phytoplankton influence the composition of bacterial communities, but the taxonomic specificity of algal-bacterial interactions is unclear due to the aggregation of ecologically distinct bacterial populations by community characterization methods. Here we examine whether phytoplankton seasonal succession affects the composition of subtypes within the cosmopolitan freshwater bacterial genus Polynucleobacter. Changes in the composition of Polynucleobacter subtypes were characterized in samples collected weekly from May to August in 2003 and 2008 from three humic lakes using terminal restriction fragment length polymorphism fingerprinting of the protein-encoding cytochrome c oxidase ccoN gene. Changes in phytoplankton population abundances explained, on average, 30% of temporal variation in the composition of Polynucleobacter subtypes and the interaction between phytoplankton and the environment explained an additional 18% of temporal variation. The effect of phytoplankton on specific Polynucleobacter subtypes was experimentally confirmed by changes in Polynucleobacter subtype composition following incubation with different phytoplankton assemblages or a no-phytoplankton control. Phytoplankton-associated subtypes and differentiation in substrate use among subtypes likely contribute to the effects of phytoplankton on Polynucleobacter subtype composition. Interactions between unique Polynucleobacter populations and phytoplankton highlight the ecological significance and specificity of species interactions in freshwater communities.
MeSH term(s)	Burkholderiaceae/classification ; Burkholderiaceae/genetics ; Ecosystem ; Genotype ; Lakes/microbiology ; Microbial Consortia/genetics ; Phytoplankton/microbiology ; Polymorphism, Restriction Fragment Length
Language	English
Publishing date	2015-03
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.12529
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Article: Phytoplankton succession affects the composition of Polynucleobacter subtypes in humic lakes

Paver, Sara F / Youngblut, Nicholas D / Whitaker, Rachel J / Kent, Angela D

Environmental microbiology. 2015 Mar., v. 17, no. 3

2015

Abstract: Phytoplankton influence the composition of bacterial communities, but the taxonomic specificity of algal–bacterial interactions is unclear due to the aggregation of ecologically distinct bacterial populations by community characterization methods. Here ... ...

Abstract	Phytoplankton influence the composition of bacterial communities, but the taxonomic specificity of algal–bacterial interactions is unclear due to the aggregation of ecologically distinct bacterial populations by community characterization methods. Here we examine whether phytoplankton seasonal succession affects the composition of subtypes within the cosmopolitan freshwater bacterial genus Polynucleobacter. Changes in the composition of Polynucleobacter subtypes were characterized in samples collected weekly from May to August in 2003 and 2008 from three humic lakes using terminal restriction fragment length polymorphism fingerprinting of the protein‐encoding cytochrome c oxidase ccoN gene. Changes in phytoplankton population abundances explained, on average, 30% of temporal variation in the composition of Polynucleobacter subtypes and the interaction between phytoplankton and the environment explained an additional 18% of temporal variation. The effect of phytoplankton on specific Polynucleobacter subtypes was experimentally confirmed by changes in Polynucleobacter subtype composition following incubation with different phytoplankton assemblages or a no‐phytoplankton control. Phytoplankton‐associated subtypes and differentiation in substrate use among subtypes likely contribute to the effects of phytoplankton on Polynucleobacter subtype composition. Interactions between unique Polynucleobacter populations and phytoplankton highlight the ecological significance and specificity of species interactions in freshwater communities.
Keywords	Polynucleobacter ; bacterial communities ; cytochrome-c oxidase ; freshwater ; genes ; lakes ; phytoplankton ; restriction fragment length polymorphism ; temporal variation
Language	English
Dates of publication	2015-03
Size	p. 816-828.
Publishing place	Blackwell Science
Document type	Article
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.12529
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Article: Temporal Patterns in Glycolate-Utilizing Bacterial Community Composition Correlate with Phytoplankton Population Dynamics in Humic Lakes

Paver, Sara F / Kent, Angela D

Microbial ecology. 2010 Aug., v. 60, no. 2

2010

Abstract	Previous observations of correlated community dynamics between phytoplankton and bacteria in lakes indicate that phytoplankton populations may influence bacterial community structure. To investigate the possibility that bacterial use of phytoplankton exudates contributes to observed patterns of community change, we characterized the diversity and dynamics of heterotrophic bacterioplankton with genetic potential to use glycolate, a photorespiration-specific exudate, in five lakes over a 15-week period. Culture-independent approaches were used to track different bacterial phylotypes represented by DNA sequence variation in the functional gene glycolate oxidase subunit D (glcD). glcD gene sequences from freshwater bacteria exhibited broad phylogenetic diversity, including sequences representing the Alpha-, Beta-, and Gammaproteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Verrucomicrobia. The majority of glcD gene sequences were betaproteobacterial, with 48% of the sequences clustering with the glcD gene from the cosmopolitan freshwater species Polynucleobacter necessarius. Terminal restriction fragment length polymorphism fingerprinting of the glcD gene revealed changes in glycolate-utilizing assemblages over time. An average of 39% of within-lake temporal variation in glycolate-utilizing assemblages across five lakes was explained by phytoplankton community composition and dynamics. The interaction between phytoplankton populations and the environment explained an additional 17% of variation on average. These observations offer new insight into the diversity and temporal dynamics of freshwater bacteria with genetic potential to use glycolate and support the hypothesis that algal exudates influence the structure of bacterial communities.
Keywords	(S)-2-hydroxy-acid oxidase ; Actinobacteria ; Polynucleobacter necessarius ; bacteria ; bacterial communities ; bacterioplankton ; community structure ; gamma-Proteobacteria ; lakes ; multigene family ; nucleotide sequences ; phytoplankton ; population dynamics ; restriction fragment length polymorphism ; temporal variation
Language	English
Dates of publication	2010-08
Size	p. 406-418.
Publisher	Springer-Verlag
Publishing place	New York
Document type	Article
ZDB-ID	1462065-0
ISSN	1432-184X ; 0095-3628
ISSN (online)	1432-184X
ISSN	0095-3628
DOI	10.1007/s00248-010-9722-6
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