Freshwater bacterioplankton richness in oligotrophic lakes depends on nutrient availability rather than on species–area relationships

Logue, Jürg Brendan; Langenheder, Silke; Andersson, Anders F.; Bertilsson, Stefan; Drakare, Stina; Lanzén, Anders; Lindström, Eva S.

doi:10.1038/ismej.2011.184

Cited by 94 publications

(75 citation statements)

References 59 publications

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“…The factors that shape this bacterial diversity and in turn how the bacterial community contributes to ecosystem functioning have become a subject of intense research. The variability in bacterial community structure on different temporal and spatial scales has been shown to correlate with changes in biotic and abiotic environmental factors, indicating their selective control of bacterial communities (Ramette 2007, Logue et al 2012. These studies have further provided insight into the co-occurrence of different phylotypes, suggesting environmentally driven interactions among bacterial groups (Fuhrman et al 2006, Gilbert et al 2012.…”

Section: Introductionmentioning

confidence: 84%

Changes in bacterial diversity in response to dissolved organic matter supply in a continuous culture experiment

Landa¹,

Cottrell²,

Kirchman³

et al. 2013

Aquat. Microb. Ecol.

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Heterotrophic bacterial metabolism is tightly linked to the availability of dissolved organic matter (DOM), but the relationship between substrate supply and bacterial diversity remains unresolved. The objective of the present study was to determine how an increase in the supply of bioavailable DOM affects bacterial metabolism and diversity. We addressed this issue by growing a natural bacterial community over 5 generations in continuous cultures either on seawater (dissolved organic carbon concentration equal to 74 µM) or on seawater amended with 13 µM of diatom-derived DOM. Bacteria markedly responded to the additional DOM supply, as revealed by 1.6-fold higher bacterial abundances and 10-fold higher cell-specific α-and β-gluco sidase activities in the +DOM treatment than in the control throughout the experimental period. Analysis of diversity as determined by tag pyrosequencing of 16S rRNA genes after 3 and 5 bacterial generations showed that the bacterial communities in the +DOM treatment were more similar to each other than to communities in the control. Diversity indices such as richness and phylogenetic distance were higher in the DOM-amended cultures than in the control. Gammaproteobacteria dominated the communities selected in our cultures, representing between 87 and 99% of the sequences. The addition of DOM led to a higher relative abundance of several bacterial groups, in particular Alphaproteobacteria, Bacteroidetes, and Verrucomicrobia, which accounted for up to 14% of the sequences, compared to the control in which they represented < 5% of the sequences. Our results demonstrate that in this experimental context, an increased supply of bioavailable DOM sustained a higher bacterial diversity. KEY WORDS: Bacterial diversity · Dissolved organic matter · Continuous cultures · 454 pyrosequencingResale or republication not permitted without written consent of the publisher

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Section: Introductionmentioning

confidence: 84%

Changes in bacterial diversity in response to dissolved organic matter supply in a continuous culture experiment

Landa¹,

Cottrell²,

Kirchman³

et al. 2013

Aquat. Microb. Ecol.

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“…Samples without reverse transcriptase and with MilliQ water instead of target RNA served as negative controls. The hypervariable regions V3 and V4 of the bacterial 16S rRNA gene were PCR amplified using the barcoded forward primer 341F (5=-CCTACGGGNGGCWGCAG-3=) and the reverse primer 805R (5=-GACTACHVGGGTATCTAATCC-3=) (27). For each sample, two different bar codes were used to reduce bar code-specific bias (28).…”

Section: Methodsmentioning

confidence: 99%

Functional and Structural Responses of Hyporheic Biofilms to Varying Sources of Dissolved Organic Matter

Wagner

Bengtsson

Besemer

et al. 2014

Appl Environ Microbiol

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Headwater streams are tightly connected with the terrestrial milieu from which they receive deliveries of organic matter, often through the hyporheic zone, the transition between groundwater and streamwater. Dissolved organic matter (DOM) from terrestrial sources (that is, allochthonous) enters the hyporheic zone, where it may mix with DOM from in situ production (that is, autochthonous) and where most of the microbial activity takes place. Allochthonous DOM is typically considered resistant to microbial metabolism compared to autochthonous DOM. The composition and functioning of microbial biofilm communities in the hyporheic zone may therefore be controlled by the relative availability of allochthonous and autochthonous DOM, which can have implications for organic matter processing in stream ecosystems. Experimenting with hyporheic biofilms exposed to model allochthonous and autochthonous DOM and using 454 pyrosequencing of the 16S rRNA (targeting the "active" community composition) and of the 16S rRNA gene (targeting the "bulk" community composition), we found that allochthonous DOM may drive shifts in community composition whereas autochthonous DOM seems to affect community composition only transiently. Our results suggest that priority effects based on resource-driven stochasticity shape the community composition in the hyporheic zone. Furthermore, measurements of extracellular enzymatic activities suggest that the additions of allochthonous and autochthonous DOM had no clear effect on the function of the hyporheic biofilms, indicative of functional redundancy. Our findings unravel possible microbial mechanisms that underlie the buffering capacity of the hyporheic zone and that may confer stability to stream ecosystems.

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“…Each PCR reaction included a negative control. Primers used for amplification of the 16S rRNA gene were the bacterial 341F 5′-CCTACGG GNGGCWGCAG-3′ and 805R 5′-GACTACHVGGGTA TCTAATCC-3′, containing the 454 Titanium A and B adaptors, respectively (Logue et al, 2011). For each sample, two different sample-specific barcodes contained in the forward primer were used to reduce barcode-specific bias (Berry et al, 2011).…”

Section: Pcr Amplification and 454 Pyrosequencingmentioning

confidence: 99%

Altitudinal patterns of diversity and functional traits of metabolically active microorganisms in stream biofilms

et al. 2015

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Resources structure ecological communities and potentially link biodiversity to energy flow. It is commonly believed that functional traits (generalists versus specialists) involved in the exploitation of resources depend on resource availability and environmental fluctuations. The longitudinal nature of stream ecosystems provides changing resources to stream biota with yet unknown effects on microbial functional traits and community structure. We investigated the impact of autochthonous (algal extract) and allochthonous (spruce extract) resources, as they change along alpine streams from above to below the treeline, on microbial diversity, community composition and functions of benthic biofilms. Combining bromodeoxyuridine labelling and 454 pyrosequencing, we showed that diversity was lower upstream than downstream of the treeline and that community composition changed along the altitudinal gradient. We also found that, especially for allochthonous resources, specialisation by biofilm bacteria increased along that same gradient. Our results suggest that in streams below the treeline biofilm diversity, specialisation and functioning are associated with increasing niche differentiation as potentially modulated by divers allochthonous and autochthonous constituents contributing to resources. These findings expand our current understanding on biofilm structure and function in alpine streams.

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Freshwater bacterioplankton richness in oligotrophic lakes depends on nutrient availability rather than on species–area relationships

Cited by 94 publications

References 59 publications

Changes in bacterial diversity in response to dissolved organic matter supply in a continuous culture experiment

Changes in bacterial diversity in response to dissolved organic matter supply in a continuous culture experiment

Functional and Structural Responses of Hyporheic Biofilms to Varying Sources of Dissolved Organic Matter

Altitudinal patterns of diversity and functional traits of metabolically active microorganisms in stream biofilms

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