| 1. |
- Buck, Moritz, et al.
(författare)
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16S rRNA gene sequences of Candidatus Methylumidiphilus (Methylococcales), a putative methanotrophic genus in lakes and ponds
- 2022
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Ingår i: Aquatic Microbial Ecology. - : Inter-Research Science Center. - 0948-3055 .- 1616-1564. ; 88, s. 25-30
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Tidskriftsartikel (refereegranskat)abstract
- A putative novel methanotrophic genus, Candidatus Methylumidiphilus (Methylococcales), was recently shown to be ubiquitous and one of the most abundant methanotrophic genera in water columns of oxygen-stratified lakes and ponds in boreal and subarctic areas. However, it has probably escaped detection in many previous studies that used 16S rRNA gene amplicon sequencing due to insufficient database coverage, as previously analysed metagenome-assembled genomes (MAGs) affiliated with Ca. Methylumidiphilus do not contain 16S rRNA genes. Therefore, we screened MAGs affiliated with the genus for their 16S rRNA gene sequences in a recently published lake and pond MAG data set. Among 66 MAGs classified as Ca. Methylumidiphilus (with completeness over 40% and contamination less than 5 %) originating from lakes in Finland, Sweden and Switzerland as well as from ponds in Canada, we found 5 MAGs, each containing one 1532 bp sequence spanning the V1-V9 regions of the 16S rRNA gene. After removal of sequence redundancy, this resulted in 2 unique 16S rRNA gene sequences. These sequences represented 2 different putative species: Ca. Methylumidiphilus alinenensis (GenBank accession OK236221) and another unnamed species of Ca. Methylumidiphilus (GenBank accession OK236220). We suggest that including these 2 sequences in reference databases will enhance 16S rRNA gene-based detection of members of this genus from environmental samples.
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| 2. |
- Florenza, Javier, et al.
(författare)
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Choice of methodology and surrogate prey are decisive for the quality of protistan bacterivory rate estimates
- 2023
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Ingår i: Aquatic Microbial Ecology. - : Inter-Research Science Publisher. - 0948-3055 .- 1616-1564. ; 89, s. 43-53
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Tidskriftsartikel (refereegranskat)abstract
- ABSTRACT: Microeukaryote predation on bacteria is a fundamental phenomenon to understand energy and nutrient dynamics at the base of the aquatic food web. To date, the most prevalent way to estimate grazing rates is by using epifluorescence microscopy to enumerate ingestion events of fluorescently labelled tracers (FLTs) after short-term incubation experiments. However, this approach can be sensitive to the type of FLT, requires skillful preparation of the samples and is limited to small sample sizes. We tested the susceptibility of rate estimates to the choice of prey and made a side-by-side comparison between microscopy and flow cytometry when recording ingestion by a bacterivorous flagellate. Short-term uptake experiments were established using 5 types of FLTs differing in quality (living, dead or inert) and size (large or small), with Ochromonas triangulata as a model flagellate. The experiments showed that (1) each of the different prey types yielded different clearing rates, ranging from 0.5 to 3.6 nl cell-1 h-1, with the largest differences (3-fold or higher) between small prey (lower rates) and large prey (higher rates); (2) the cytometry estimate differed significantly from the microscopy estimate in 3 out of 4 experimental configurations; and (3) the precision of the cytometric analysis was greater, with >3-fold higher uncertainty associated with microscopy counting. Our results validate that flow cytometry provides a more precise bacterivory estimate, and that the choice of FLT influences the grazing rate estimate to a high extent regardless of the analytical method used.
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| 3. |
- Guo, Junwen, 1982-, et al.
(författare)
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Carbon-nitrogen association influences response of the microplankton food web to enrichment
- 2022
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Ingår i: Aquatic Microbial Ecology. - : Inter-Research Science Center. - 0948-3055 .- 1616-1564. ; 88, s. 187-199
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Tidskriftsartikel (refereegranskat)abstract
- In aquatic ecosystems, there are 2 major forms of N available at the base of the planktonic food web: dissolved organic N (DON) and dissolved inorganic N (DIN). In DON, N is associated with organic C, which may promote both heterotrophs and autotrophs. In environments where DIN nitrate is the prevailing N form and dissociated dissolved organic C (DOC) is available, heterotrophs may also be promoted, but they may compete with the autotrophs for DIN. The influence of associated or dissociated CN nutrient sources on the interaction between organisms and the food web function is poorly known and has not been studied before. To approach this question, we performed a microcosm experiment with a coastal microbial food web, where N and C nutrient sources were provided either associated in 1 molecular compound (DON), or dissociated in 2 separate molecular compounds (DIN and DOC). The results showed that association or dissociation of C and N input had marked effects on all trophic levels, most probably through its effect on bacteria-phytoplankton interaction, which switched between increased coupling and increased competition. The biomass of all components of the food web benefitted from the association of C and N in a single DON molecule. Our study indicated that the degree of association between C and N is an important factor affecting the productivity and efficiency of the microbial food web. Therefore, the C and N association should be considered when studying aquatic systems.
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| 4. |
- Sjöstedt, Johanna, 1982-, et al.
(författare)
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Substrate diversity affects carbon utilization rate and threshold concentration for uptake by natural bacterioplankton communities
- 2022
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Ingår i: Aquatic Microbial Ecology. - : Inter-Research Science Center. - 0948-3055 .- 1616-1564. ; 88
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Tidskriftsartikel (refereegranskat)abstract
- Persistence of dissolved organic matter (DOM) in aquatic environments may in part be explained by high diversity and low concentrations of carbon substrates. However, changes in dissolved substrate quality can modify aquatic bacterial community composition and rate of carbon uptake. The aim of this study was to test if the presence of multiple simple substrates affects the turnover of organic carbon. Natural bacterial communities were grown in continuous cultures supplied with either individual carbon substrates—salicylic acid (SA), tryptophan (Trp) or tyrosine (Tyr)—or a combination of the 3 substrates. Concentrations were tracked using fluorescence spectroscopy, and steady-state concentrations of a few nanomolar were reached. Bacterial growth efficiency was dependent on which carbon sources were present and reached an intermediate level in the combined treatment. The bacterial community maintained steady-state concentrations of Trp that were lower in the combined treatment than in the individual substrate treatment. In addition, steady-state concentrations were reached faster during growth on combined carbon substrates, although the maximum utilization rate of each individual compound was lower. However, the steady-state concentration of total carbon (sum of carbon content of SA, Trp and Tyr) was higher in the combined culture than in the individual substrate treatments, and seemed to be determined by the carbon substate for which the bacteria had the lowest affinity. The results from this study indicate that persistence of dissolved organic carbon can in part be explained by vast substrate diversity, which raises the threshold concentration for utilization by natural bacterial communities.
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| 5. |
- Sjöstedt, Johanna, et al.
(författare)
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Substrate diversity affects carbon utilization rate and threshold concentration for uptake by natural bacterioplankton communities
- 2022
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Ingår i: Aquatic Microbial Ecology. - 0948-3055. ; 88, s. 95-108
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Tidskriftsartikel (refereegranskat)abstract
- Persistence of dissolved organic matter (DOM) in aquatic environments may in part be explained by high diversity and low concentrations of carbon substrates. However, changes in dissolved substrate quality can modify aquatic bacterial community composition and rate of carbon uptake. The aim of this study was to test if the presence of multiple simple substrates affects the turnover of organic carbon. Natural bacterial communities were grown in continuous cultures supplied with either individual carbon substrates-salicylic acid (SA), tryptophan (Trp) or tyrosine (Tyr)-or a combination of the 3 substrates. Concentrations were tracked using fluorescence spectroscopy, and steady-state concentrations of a few nanomolar were reached. Bacterial growth efficiency was dependent on which carbon sources were present and reached an intermediate level in the combined treatment. The bacterial community maintained steady-state concentrations of Trp that were lower in the combined treatment than in the individual substrate treatment. In addition, steady-state concentrations were reached faster during growth on combined carbon substrates, although the maximum utilization rate of each individual compound was lower. However, the steady-state concentration of total carbon (sum of carbon content of SA, Trp and Tyr) was higher in the combined culture than in the individual substrate treatments, and seemed to be determined by the carbon substate for which the bacteria had the lowest affinity. The results from this study indicate that persistence of dissolved organic carbon can in part be explained by vast substrate diversity, which raises the threshold concentration for utilization by natural bacterial communities.
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