| 1. |
- Liu, Haoyu, et al.
(författare)
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Distinct B cell subsets in Peyer's patches convey probiotic effects by Limosilactobacillus reuteri
- 2021
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Ingår i: Microbiome. - : Springer Nature. - 2049-2618. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Background: Intestinal Peyer's patches (PPs) form unique niches for bacteria-immune cell interactions that direct host immunity and shape the microbiome. Here we investigate how peroral administration of probiotic bacterium Limosilactobacillus reuteri R2LC affects B lymphocytes and IgA induction in the PPs, as well as the downstream consequences on intestinal microbiota and susceptibility to inflammation.Results: The B cells of PPs were separated by size to circumvent activation-dependent cell identification biases due to dynamic expression of markers, which resulted in two phenotypically, transcriptionally, and spatially distinct subsets: small IgD(+)/GL7(-)/S1PR1(+)/Bcl6, CCR6-expressing pre-germinal center (GC)-like B cells with innate-like functions located subepithelially, and large GL7(+)/S1PR1(-)/Ki67(+)/Bcl6, CD69-expressing B cells with strong metabolic activity found in the GC. Peroral L. reuteri administration expanded both B cell subsets and enhanced the innate-like properties of pre-GC-like B cells while retaining them in the sub-epithelial compartment by increased sphingosine-1-phosphate/S1PR1 signaling. Furthermore, L. reuteri promoted GC-like B cell differentiation, which involved expansion of the GC area and autocrine TGF beta-1 activation. Consequently, PD-1-T follicular helper cell-dependent IgA induction and production was increased by L. reuteri, which shifted the intestinal microbiome and protected against dextran-sulfate-sodium induced colitis and dysbiosis.Conclusions: The Peyer's patches sense, enhance and transmit probiotic signals by increasing the numbers and effector functions of distinct B cell subsets, resulting in increased IgA production, altered intestinal microbiota, and protection against inflammation.
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| 2. |
- Abrahamsson, Katarina, 1957, et al.
(författare)
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Variations of biochemical parameters along a transect in the Southern Ocean, with special emphasis on volatile halogenated organic compounds
- 2004
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Ingår i: Deep-sea research. Part II, Topical studies in oceanography. - : Elsevier BV. - 0967-0645. ; 51:22-24, s. 2745-2756
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Tidskriftsartikel (refereegranskat)abstract
- A number of parameters of biogeochemical interest were monitored along a north-southerly transect (S 43-S 63degrees) in the Atlantic Sector of the Southern Ocean from the 8th to the 20th of December 1997. Changes in total dissolved inorganic carbon (C-T) and total alkalinity (A(T)) were mostly dependent on temperature and salinity until the ice edge was reached. After this point only a weak correlation was seen between these. Highest mean values of C-T and A(T) were observed in the Winter Ice Edge (WIE) (2195 and 2319 mumol kg(-1), respectively). Lowest mean AT (2277 mumol kg(-1)) was observed in the Sub-Antarctic Front (SAF), whereas lowest mean CT concentration (2068 mumol kg(-1)) was associated with the Sub-Tropical Front (STF). The pH in situ varied between 8.060 and 8.156 where the highest values were observed in the southern part of the Antarctic Polar Front (APF) and in the Summer Ice Edge (SIE) Region. These peaks were associated with areas of high chlorophyll a (chl a) and tribromomethane values. In the other areas the pH in situ was mainly dependent on hydrography. Bacterial abundance decreased more than one order of magnitude when going from north to south. The decrease appeared to be strongly related to water temperature and there were no elevated abundances at frontal zones. Microphytoplankton dominated in the SAF and APF, whereas the nano- and picoplankton dominated outside these regions. Volatile halogenated compounds were found to vary both with regions, and with daylight. For the iodinated compounds, the highest concentrations were found north of the STF. Brominated hydrocarbons had high concentrations in the STF, but elevated concentrations were also found in the APF and SIE regions. No obvious correlation could be found between the occurrence of individual halocarbons and chl a. On some occasions trichloroethene and tribromomethane related to the presence of nano- and microplankton, respectively.
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| 3. |
- Ahmed Osman, Omneya, et al.
(författare)
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Interactions of Freshwater Cyanobacteria with Bacterial Antagonists
- 2017
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Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 83:7
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Tidskriftsartikel (refereegranskat)abstract
- Cyanobacterial and algal mass development, or blooms, have severe effects on freshwater and marine systems around the world. Many of these phototrophs produce a variety of potent toxins, contribute to oxygen depletion, and affect water quality in several ways. Coexisting antagonists, such as cyanolytic bacteria, hold the potential to suppress, or even terminate, such blooms, yet the nature of this interaction is not well studied. We isolated 31 cyanolytic bacteria affiliated with the genera Pseudomonas, Stenotrophomonas, Acinetobacter, and Delftia from three eutrophic freshwater lakes in Sweden and selected four phylogenetically diverse bacterial strains with strong-to-moderate lytic activity. To characterize their functional responses to the presence of cyanobacteria, we performed RNA sequencing (RNA-Seq) experiments on coculture incubations, with an initial predator-prey ratio of 1: 1. Genes involved in central cellular pathways, stress-related heat or cold shock proteins, and antitoxin genes were highly expressed in both heterotrophs and cyanobacteria. Heterotrophs in coculture expressed genes involved in cell motility, signal transduction, and putative lytic activity. L, D-Transpeptidase was the only significantly upregulated lytic gene in Stenotrophomonas rhizophila EK20. Heterotrophs also shifted their central metabolism from the tricarboxylic acid cycle to the glyoxylate shunt. Concurrently, cyanobacteria clearly show contrasting antagonistic interactions with the four tested heterotrophic strains, which is also reflected in the physical attachment to their cells. In conclusion, antagonistic interactions with cyanobacteria were initiated within 24 h, and expression profiles suggest varied responses for the different cyanobacteria and studied cyanolytes. IMPORTANCE Here, we present how gene expression profiles can be used to reveal interactions between bloom-forming freshwater cyanobacteria and antagonistic heterotrophic bacteria. Species-specific responses in both heterotrophs and cyanobacteria were identified. The study contributes to a better understanding of the interspecies cellular interactions underpinning the persistence and collapse of cyanobacterial blooms.
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| 4. |
- Ahrens, Lutz, et al.
(författare)
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Microcosm experiment to test bacterial responses to perfluorooctanoate exposure
- 2023
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 857
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Tidskriftsartikel (refereegranskat)abstract
- The impact of perfluoroalkyl and polyfluoroalkyl substances on microbial communities is challenging to investigate in situ because of the complexity and dynamics of natural ecosystems. In the present study, four microcosms were estab-lished to explore the impact of perfluorooctanoate (PFOA) on bacterial communities in riverine and marine settings. PFOA distribution between the aqueous and sedimentary phases fluctuated in both PFOA-amended and unamended control systems. PFOA was more rapidly partitioned into the sediment in marine than in riverine microcosms. Differ-ences in iron concentration and salinity may influence PFOA exchange between water and sediment. In marine micro-cosms, the alpha diversity of bacterial communities was significantly correlated to PFOA concentration. PFOA tended to correlate more strongly with bacterial community composition in water than in sediment. At the whole system level, Lefse's analysis indicated Algoriphagus halophilus as biomarkers for PFOA exposure in both riverine and marine systems, and the family Flavobacteriaceae were also more abundant in the exposed systems. In terms of temporal variation (comparison between three time points in the systems), metastat analysis showed great variability of potential PFOA-sensitive bacteria at the genus level. As such, most PFOA-sensitive genera were transitory and variable and existed for a short term in different systems (river, sea, blank, and experiment) and phases. Compared with other PFOA-sensitive genera, we suggest that further research is carried out to explore the use of Limnobacter as a bioindicator for temporal monitoring of PFOA pollution.
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| 5. |
- Alneberg, Johannes, et al.
(författare)
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Genomes from uncultivated prokaryotes : a comparison of metagenome-assembled and single-amplified genomes
- 2018
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Ingår i: Microbiome. - : BioMed Central. - 2049-2618. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Background: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms. Results: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77-99.84%) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs. Conclusions: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.
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| 6. |
- Alneberg, Johannes, et al.
(författare)
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Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Background: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms.Results: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (>98.7% identity) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs; the metagenome assembly was found to cause incompleteness to a higher degree than the binning procedure.Conclusions: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.
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| 7. |
- Alonso-Sáez, Laura, et al.
(författare)
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High archaeal diversity in Antarctic circumpolar deep waters
- 2011
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Ingår i: Environmental Microbiology Reports. - : Wiley. - 1758-2229 .- 1758-2229. ; 3:6, s. 689-697
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Tidskriftsartikel (refereegranskat)abstract
- Archaea are abundant in polar oceans but important ecological aspects of this group remain enigmatic, such as patterns of diversity and biogeography. Here, we provide the first high-throughput sequencing population study of Antarctic archaea based on 198 bp fragments of the 16S rRNA gene, targeting different water masses across the Amundsen and Ross Seas. Our results suggest that archaeal commu- nity composition is strongly shaped by hydrography and significantly influenced by environmental param- eters. Archaeal communities from cold continental shelf waters (SW) of the Ross Sea were similar over depth with a single thaumarchaeal phylotype domi- nating Antarctic surface waters (AASW) and deeper SW (contributing up to 80% of reads). However, this phylotype contributed less than 8% of reads in cir- cumpolar deep waters (CDW). A related thaumar- chaeon (98% identity) was almost absent in AASW, but contributed up to 30% of reads in CDW, suggest- ing ecological differentiation of closely related phylo- types. Significantly higher archaeal richness and evenness were observed in CDW, with Shannon indices (c. 2.5) twice as high as for AASW, and high contributions of Group II Euryarchaeota. Based on these results, we suggest that CDW is a hotspot of archaeal diversity and may play an important role in the dispersal of archaeal phylotypes to other oceanic water masses.
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| 8. |
- Alonso-Saez, Laura, et al.
(författare)
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High bicarbonate assimilation in the dark by Arctic bacteria
- 2010
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Ingår i: ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 4:12, s. 1581-1590
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Tidskriftsartikel (refereegranskat)abstract
- Although both autotrophic and heterotrophic microorganisms incorporate CO2 in the dark through different metabolic pathways, this process has usually been disregarded in oxic marine environments. We studied the significance and mediators of dark bicarbonate assimilation in dilution cultures inoculated with winter Arctic seawater. At stationary phase, bicarbonate incorporation rates were high (0.5-2.5 mu gC L-1 d(-1)) and correlated with rates of bacterial heterotrophic production, suggesting that most of the incorporation was due to heterotrophs. Accordingly, very few typically chemoautotrophic bacteria were detected by 16S rRNA gene cloning. The genetic analysis of the biotin carboxylase gene accC putatively involved in archaeal CO2 fixation did not yield any archaeal sequence, but amplified a variety of bacterial carboxylases involved in fatty acids biosynthesis, anaplerotic pathways and leucine catabolism. Gammaproteobacteria dominated the seawater cultures (40-70% of cell counts), followed by Betaproteobacteria and Flavobacteria as shown by catalyzed reporter deposition fluorescence in situ hybridization (CARDFISH). Both Beta-and Gammaproteobacteria were active in leucine and bicarbonate uptake, while Flavobacteria did not take up bicarbonate, as measured by microautoradiography combined with CARDFISH. Within Gammaproteobacteria, Pseudoalteromonas-Colwellia and Oleispira were very active in bicarbonate uptake (ca. 30 and 70% of active cells, respectively), while the group Arctic96B-16 did not take up bicarbonate. Our results suggest that, potentially, the incorporation of CO2 can be relevant for the metabolism of specific Arctic heterotrophic phylotypes, promoting the maintenance of their cell activity and/or longer survival under resource depleted conditions.
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| 9. |
- Alonso-Sáez, Laura, et al.
(författare)
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Role for urea in nitrification by polar marine Archaea
- 2012
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 109:44, s. 17989-17994
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Tidskriftsartikel (refereegranskat)abstract
- Despite the high abundance of Archaea in the global ocean, their metabolism and biogeochemical roles remain largely unresolved. We investigated the population dynamics and metabolic activity of Thaumarchaeota in polar environments, where these microorganisms are particularly abundant and exhibit seasonal growth. Thaumarchaeota were more abundant in deep Arctic and Antarctic waters and grew throughout the winter at surface and deeper Arctic halocline waters. However, in situ single-cell activity measurements revealed a low activity of this group in the uptake of both leucine and bicarbonate (<5% Thaumarchaeota cells active), which is inconsistent with known heterotrophic and autotrophic thaumarchaeal lifestyles. These results suggested the existence of alternative sources of carbon and energy. Our analysis of an environmental metagenome from the Arctic winter revealed that Thaumarchaeota had pathways for ammonia oxidation and, unexpectedly, an abundance of genes involved in urea transport and degradation. Quantitative PCR analysis confirmed that most polar Thaumarchaeota had the potential to oxidize ammonia, and a large fraction of them had urease genes, enabling the use of urea to fuel nitrification. Thaumarchaeota from Arctic deep waters had a higher abundance of urease genes than those near the surface suggesting genetic differences between closely related archaeal populations. In situ measurements of urea uptake and concentration in Arctic waters showed that small-sized prokaryotes incorporated the carbon from urea, and the availability of urea was often higher than that of ammonium. Therefore, the degradation of urea may be a relevant pathway for Thaumarchaeota and other microorganisms exposed to the low-energy conditions of dark polar waters.
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| 10. |
- Alonso-Saez, Laura, et al.
(författare)
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Winter bloom of a rare betaproteobacteriurn in the Arctic Ocean
- 2014
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 5, s. 425-
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Tidskriftsartikel (refereegranskat)abstract
- Extremely low abundance microorganisms (members of the "rare biosphere") are believed to include dormant taxa, which can sporadically become abundant following environmental triggers. Yet, microbial transitions from rare to abundant have seldom been captured in situ, and it is uncertain how widespread these transitions are. A bloom of a single ribotype (>= 99% similarity in the 16S ribosomal RNA gene) of a widespread betaproteobacterium (Janthinobacterium sp.) occurred over 2 weeks in Arctic marine waters. The Janthinobactenum population was not detected microscopically in situ in January and early February, but suddenly appeared in the water column thereafter, eventually accounting for up to 20% of bacterial cells in mid February. During the bloom, this bacterium was detected at open water sites up to 50 km apart, being abundant down to more than 300 m. This event is one of the largest monospecific bacterial blooms reported in polar oceans. It is also remarkable because Betaproteobacteria are typically found only in low abundance in marine environments. In particular, Janthinobacterium were known from non-marine habitats and had previously been detected only in the rare biosphere of seawater samples, including the polar oceans. The Arctic Janthinobacterium formed mucilagenous monolayer aggregates after short (ca. 8 h) incubations, suggesting that biofilm formation may play a role in maintaining rare bacteria in pelagic marine environments. The spontaneous mass occurrence of this opportunistic rare taxon in polar waters during the energy-limited season extends current knowledge of how and when microbial transitions between rare and abundant occur in the ocean.
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