| 1. |
- Beier, Sara, et al.
(author)
-
Global Phylogeography of Chitinase Genes in Aquatic Metagenomes
- 2011
-
In: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 77:3, s. 1101-1106
-
Journal article (peer-reviewed)abstract
- Phylogeny-based analysis of chitinase and 16S rRNA genes from metagenomic data suggests that salinity is a major driver for the distribution of both chitinolytic and total bacterial communities in aquatic systems. Additionally, more acidic chitinase proteins were observed with increasing salinity. Congruent habitat separation was further observed for both genes according to latitude and proximity to the coastline. However, comparison of chitinase and 16S rRNA genes extracted from different geographic locations showed little congruence in distribution. There was no indication that dispersal limited the global distribution of either gene.
|
|
| 2. |
- Ahmed Osman, Omneya, et al.
(author)
-
Interactions of Freshwater Cyanobacteria with Bacterial Antagonists
- 2017
-
In: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 83:7
-
Journal article (peer-reviewed)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.
|
|
| 3. |
|
|
| 4. |
- Ambrazaitis, Gilbert, 1979-, et al.
(author)
-
Do dialect-specific prosodic properties shape the path to contrastive focus? - Production and comprehension data from 3-5 year-old children acquiring Stockholm or Scania Swedish
- 2023
-
Conference paper (peer-reviewed)abstract
- Cuing information structure (IS) is a fundamental function of prosody in many languages. For instance, in English or Dutch, a contrastive focus on the color adjective in a phrase like ‘the green boat’ is marked by a pitch accent on GREEN and, crucially, a lack of post-focal accent on BOAT: ‘the GREEN boat’. Listeners infer from this prosodic structure that ‘boat’ represents already activated (given) information and that the color that is specially mentioned represents one out of a set of alternatives.According to research findings, children achieve proficiency in the production of prosodic IS encoding within the age range of 4 to 8 years, displaying considerable variability. This variability is suggested to result from structural prosodic differences between languages. For instance, Stockholm Swedish speaking children mark (non-contrastive) focus using the Swedish prominence cuing H(igh) tone in an adult-like manner already at 4-5 years, while Dutch speaking children handle Dutch intonational pitch accents only after the age of 7-8 years. One hypothesis is that this relates to the presence of lexical pitch accents in Swedish, which could make Swedish speaking children more sensitive to prosodic contrasts; in addition, the combination of lexical accent + prominence H results in a complex contour which is particularly salient. However, studies investigating this have usually had a strict focus on speech production.The few previous studies that have conducted parallel production and comprehension experiments have typically used offline methods to assess comprehension. More recent studies using online methods such as eye tracking have usually not included children younger than 6 years of age and have not been complemented by production data. In this study we combine production and comprehension experiments, using eye tracking, to study contrastive focus prosody in 3- to 5-year-old children speaking either Scanian or Stockholm Swedish. In Scanian, instead of adding the prominence H-tone for focus, phrase-level prominence is encoded through phonetic adjustments of the (lexical) HL accent patterns. By comparing these two Swedish varieties we can thus control for phonological features (incl. lexical tone), as well as grammar and lexicon, when exploring effects of prosodic-typological differences.In our production experiment we elicit adjective-noun phrases in three different focus conditions (broad, contrast on adjective, contrast on noun), using an interactive video/card game. Production data are analyzed acoustically and auditorily.As for comprehension, our visual-word eye-tracking experiment makes use of the same pictures of colored objects to investigate whether and how children rely on prosody for reference resolution (e.g., Where is the yellow boat? And where is the GREEN boat?). The time course of eye movements will be analyzed using growth curves. Both production and eye-tracking data will be analyzed as a function of dialect, age and standardized measures of language production and comprehension (The New Reynell Developmental Language Scales), as well as compared to data from adult controls. Data are currently being collected. A preliminary analysis of eye-tracking data from 24 Scanian children (ages 3-5 years collapsed) and a subset of adults from both dialects suggests similar comprehension of focus prosody as in adults (as a mismatched focus prosody in the adjective successfully elicits looks at the foil item in all groups), although processing appears to be slower, and anticipatory strategies differ slightly from those of adults (as the color of the first-mentioned adjective in a trial elicits looks at the color-matched distractor in adults, but not in children). An analysis contrasting comprehension data for both dialects, as well as a preliminary analysis of production data will be presented at the conference.
|
|
| 5. |
- Ambrazaitis, Gilbert, 1979-, et al.
(author)
-
Språkutveckling och prosodisk typologi: Produktion och perception av den dialektspecifika fokusmarkeringen hos 3- till 5-åriga barn från Stockholm och Skåne
- 2023
-
Conference paper (other academic/artistic)abstract
- Att lägga satsbetoningen på ordet som bör fokuseras utifrån en given informationsstruktur är något som barn enligt tidigare internationell forskning verkar bemästra relativt sent i utvecklingen av sitt förstaspråk. Förmågan att uppfatta och tolka satsbetoning verkar barn enligt vissa studier utveckla ännu senare, men få tidigare studier har genomfört parallella produktions- och perceptionstest, och få perceptionsstudier har i detta sammanhang använt sig av online metoder (så som ögonrörelsemätning) med barn yngre än sex år. En del tidigare studier har påvisat typologiska skillnader; till exempel verkar svenska barn kunna producera en vuxenlik fokusbetoning tidigare än nederländska barn.Med vår studie ämnar vi bidra till en bättre förståelse av hur barn utvecklar sin förmåga att producera och uppfatta kontrastiva fokusbetoningar (t. ex. en röd BIL, en RÖD bil), hur produktionen och perceptionen hänger ihop, och vilken roll prosodisk språktypologi kan spela i sammanhanget. Vi undersöker dessa förmågor hos (totalt ca 120) förskolebarn med stockholmsvenska respektive skånska som förstaspråk – två dialekter som representerar motpoler i en prosodisk typologi när det gäller hur satsbetoning kodas intonationsfonologiskt. I vår produktionsstudie eliciterar vi adjektiv-substantiv fraser med varierad kontrastiv fokus, och i perceptionsstudien mäter vi barnens bearbetning av prosodin i liknande fraser med hjälp av ögonrörelsemätning. Datainsamling pågår i skrivande stund, och prelimära resultat kommer att presenteras på workshopen.
|
|
| 6. |
- Beier, Sara, et al.
(author)
-
Bacterial chitin degradation : mechanisms and ecophysiological strategies
- 2013
-
In: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 4, s. 149-
-
Research review (peer-reviewed)abstract
- Chitin is one the most abundant polymers in nature and interacts with both carbon and nitrogen cycles. Processes controlling chitin degradation are summarized in reviews published some 20 years ago, but the recent use of culture-independent molecular methods has led to a revised understanding of the ecology and biochemistry of this process and the organisms involved. This review summarizes different mechanisms and the principal steps involved in chitin degradation at a molecular level while also discussing the coupling of community composition to measured chitin hydrolysis activities and substrate uptake. Ecological consequences are then highlighted and discussed with a focus on the cross feeding associated with the different habitats that arise because of the need for extracellular hydrolysis of the chitin polymer prior to metabolic use. Principal environmental drivers of chitin degradation are identified which are likely to influence both community composition of chitin degrading bacteria and measured chitin hydrolysis activities.
|
|
| 7. |
- Beier, Sara
(author)
-
Bacterial Degradation and Use of Chitin in Aquatic Habitats
- 2010
-
Doctoral thesis (other academic/artistic)abstract
- Chitin belongs to the most abundant biopolymers on earth where it has an important role as a structural element in crustaceans, insects, fungi and some phytoplankton. Missing evidence for long-term accumulation of chitin in nature implies fast turnover and as chitin is composed of aminosugar subunits it holds central roles in both carbon and nitrogen cycles. The aim of this thesis was to contribute to a better understanding of organic matter cycling by learning more about the diversity, function and ecology of bacteria that degrade chitin. A metagenome-enabled study of the spatial distribution of chitinolytic bacteria in aquatic ecosystems identified salinity as the major environmental factor for shaping their community composition. To address the role of alternative environmental variables controlling chitinolytic communities, a temporally resolved study was completed in a dimictic freshwater lake. Pronounced seasonal change in the indigenous chitinolytic community was observed and parallel measured environmental parameters pointed to the availability and crystalline form of chitin as significant controlling factors. The different ecological niches occupied by microbes that utilize chitin for growth were studied in an experimental study. Single-cell quantification of chitinolytic cells and cells incorporating chitin hydrolysis products suggested that commensal use of chitin hydrolysis products without simultaneous chitinase activity could be an important ecological strategy in freshwater bacterioplankton communities. Members of the ubiquitous and often quantitatively dominant group of freshwater Actinobacteria Ac1 were identified as particularly active in this “cheater” lifestyle. Further experiments based on artificially created gradients in bacterial diversity demonstrated the importance of specific bacterial populations and community composition rather than overall community richness in controlling more specific functions such as chitin and cellulose degradation. To conclude, results of this thesis provide insight into the biogeography, niche-separation and species interactions of the functional community of chitin degraders and the influence of general bacterial diversity to the respective system functioning.
|
|
| 8. |
- Beier, Sara, et al.
(author)
-
Betaproteobacterial ammonia oxidizers in root zones of aquatic macrophytes
- 2010
-
In: Fundamental and Applied Limnology. - : Schweizerbart. - 1863-9135. ; 177:4, s. 241-255
-
Journal article (peer-reviewed)abstract
- Enhanced nitrification and coupled denitrification in macrophyte root zones may contribute to the depletion of nitrogen from the rhizosphere and are both critical processes for agriculture and rhizoremediation. We examined one factor likely to affect these processes: the ammonia oxidizing betaproteobacterial community composition, and whether or not it is influenced by plant species (Eleocharis acicularis, Eleocharis palustris, Typha angustifolia) or sediment characteristics. Genes coding for ammonia monooxygenase (amoA) and 16S rRNA of betaproteobacterial ammonia oxidizers were targeted. The betaproteobacterial ammonia oxidizing community in root surface biofilms was distinct from the surrounding rhizosphere sediment. In contrast, communities in rhizosphere and bulk sediment samples were very similar. Our results showed the occurrence of Nitrosomonas europaea-like bacteria nearly exclusively in the rhizoplane biofilms, while sequences affiliated with the Nitrosomonas oligotropha, Nitrosomonas communis and Nitrosospira-lineages were more frequently detected in the surrounding sediment. Our results further suggest that the presence of N. europaea on macrophyte roots depends on the sampling site rather than on the studied macrophyte species. We propose that the rhizoplane of aquatic macrophytes is a natural habitat for N. europaea.
|
|
| 9. |
|
|
| 10. |
- Beier, Sara, et al.
(author)
-
Pronounced seasonal dynamics of freshwater chitinase genes and chitin processing
- 2012
-
In: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 14:9, s. 2467-2479
-
Journal article (peer-reviewed)abstract
- Seasonal variation in activity of enzymes involved in polymer degradation, including chitinases, has been observed previously in freshwater environments. However, it is not known whether the seasonal dynamics are due to shifts in the activity of bacteria already present, or shifts in community structure towards emergence or disappearance of chitinolytic organisms. We traced seasonal shifts in the chitinase gene assemblage in a temperate lake and linked these communities to variation in chitinase activity. Chitinase genes from 20 samples collected over a full yearly cycle were characterized by pyrosequencing. Pronounced temporal shifts in composition of the chitinase gene pool (beta diversity) occurred along with distinct shifts in richness (alpha diversity) as well as chitin processing. Changes in the chitinase gene pool correlated mainly with temperature, abundance of crustacean zooplankton and phytoplankton blooms. Also changes in the physical structure of the lake, e.g. stratification and mixing were associated with changes in the chitinolytic community, while differences were minor between surface and suboxic hypolimnetic water. The lake characteristics influencing the chitinolytic community are all linked to changes in organic particles and we suggest that seasonal changes in particle quality and availability foster microbial communities adapted to efficiently degrade them.
|
|
