Macrosystem community change in lake phytoplankton and its implications for diversity and function

Aim

We use lake phytoplankton community data to quantify the spatio-temporal and scale-dependent impacts of eutrophication, land-use and climate change on species niches and community assembly processes while accounting for species traits and phylogenetic constraints.

Location

Finland.

Time period

1977–2017.

Major taxa

Phytoplankton.

Methods

We use hierarchical modelling of species communities (HMSC) to model metacommunity trajectories at 853 lakes over four decades of environmental change, including a hierarchical spatial structure to account for scale-dependent processes. Using a “region of common profile” approach, we evaluate compositional changes of species communities and trait profiles and investigate their temporal development.

Results

We demonstrate the emergence of novel and widespread community composition clusters in previously more compositionally homogeneous communities, with cluster-specific community trait profiles, indicating functional differences. A strong phylogenetic signal of species responses to the environment implies similar responses among closely related taxa. Community cluster-specific species prevalence indicates lower taxonomic dispersion within the current dominant clusters compared with the historically dominant cluster and an overall higher prevalence of smaller species sizes within communities. Our findings denote profound spatio-temporal structuring of species co-occurrence patterns and highlight functional differences of lake phytoplankton communities.

Main conclusions

Diverging community trajectories have led to a nationwide reshuffling of lake phytoplankton communities. At regional and national scales, lakes are not single entities but metacommunity hubs in an interconnected waterscape. The assembly mechanisms of phytoplankton communities are strongly structured by spatio-temporal dynamics, which have led to novel community types, but only a minor part of this reshuffling could be linked to temporal environmental change.     

Shiga toxin-producing Escherichia coli O100:H⁻: stx2e in drinking water contaminated by waste water in Finland

In November 2007, 450 m³ of treated wastewater leaked into the drinking water distribution system contaminating the drinking water of over 10,000 inhabitants of Nokia, Southern Finland. Nearly 1,000 people visited the health centre because of gastroenteritis during the following 5 weeks. A wide range of enteric pathogens was found in the patients. The authors used the 16-plex PCR to investigate whether the five major diarrheagenic Escherichia coli pathotypes (EPEC, ETEC, STEC, EIEC or EAEC) were present in the contaminated drinking water and in the patients’ stool samples. The contaminated drinking water was positive for genes characteristic of various E. coli pathotypes: pic, invE, hlyA, ent, escV, eae, aggR, stx ₂ , estIa and astA. These genes, except stx ₂ , hlyA and invE, were also detected in the stool samples of the patients linked to this outbreak. A sorbitol positive, streptomycin resistant STEC strain was isolated from the drinking water, and belonged to the serotype O100:H ^– , produced Stx2 toxin (titre 1:8 by reversed-passive latex agglutination method), and carried the genes stx _2e, estIa and irp2.     

Tendency toward eveningness is associated with unhealthy dietary habits

Subjects with higher preference for evening hours in daily activities (eveningness) have been repeatedly shown to practice adverse health behaviors as compared to those preferring morning hours (morningness). However, associations between chronotype and dietary intake have not been explored intensively. The authors explored whether the human chronotype is associated with food and nutrient intakes in a random sample of the population aged 25 to 74 yrs. The cross-sectional study included 4493 subjects from the National FINRISK 2007 Study. Chronotype was assessed using a shortened version of Horne and ?stberg's Morningness-Eveningness Questionnaire. Diet was assessed using a validated food frequency questionnaire. Associations between morningness-eveningness (ME) score and dietary intakes were analyzed by linear regression and difference between lowest (eveningness) and highest (morningness) ME score quintiles by Tukey's test. In the multivariable model, intakes of whole grain, rye, potatoes, and vegetables and roots decreased, whereas those of wine and chocolate increased with lower ME scores. Participants in the lowest ME score quintile consumed less fish (p 相似文献   

Control of immune responses by trafficking cell surface proteins, vesicles and lipid rafts to and from the immunological synapse

Supramolecular clusters at the immunological synapse provide a mechanism for structuring complex communication networks between cells of the immune system. Regulating intra- and intercellular trafficking of proteins and lipids to and from the immunological synapse provides an additional level of complexity in determining the functional outcome of immune cell interactions. An emergent principle is that molecules requiring tightly regulated cell surface expression, e.g. negative regulators of cell activation or molecules promoting cytotoxicity, are trafficked to the immunological synapse from intracellular secretory as required lysosomes. Many molecules required for the early stages of the intercellular communication are already present at the cell surface, sometimes in lipid rafts, and are rapidly translocated laterally to the intercellular contact. Our understanding of these events critically depends on utilizing appropriate technologies for probing supramolecular recognition in live cells. Thus, we also present here a critical discussion of the technologies used to study lipid rafts and, more broadly, a map of the spatial and temporal dimensions covered by current live cell physical techniques, highlighting where advances are needed to exceed current spatial and temporal boundaries.     

Significance of woodland key habitats for polypore diversity and red-listed species in boreal forests

Preservation of woodland key habitats has become an integral part of biodiversity-oriented forest management in northern Europe. In Finland, brook-side spruce forests constitute the most important key-habitat type in terms of total area and timber volume. Our aim was to compare polypore diversity and the occurrence of red-listed species between brook-side key habitats and comparable sites of managed forest as controls. Furthermore, we assessed the importance of stand structural features to polypore communities, and contrasted regions with different land-use history. Altogether 69 key habitats and 70 controls were inventoried in four regions across southern Finland. A total of 28,023 surveyed dead-wood units had 3,307 occurrences of 114 species of which 25 species were red-listed. Key habitats hosted on average 28% (about two species) more polypore species (mainly deciduous-specialists) than controls because of a larger average volume of dead wood and a higher proportion of dead deciduous wood. However, the average number of red-listed species was low and did not differ between the two forest categories. We detected a landscape effect connected with the intensity and length of forest management history, with the highest numbers of all and red-listed species per site in eastern Finland. Volume and diversity of dead wood were the most important variables explaining variation in species richness. Presently, key habitats in managed forests appear to contribute only little to the conservation of red-listed polypore species.     

Comparison between the preservation of chloroplast structure in the dark and the turnover rate of chlorophyll-protein complexes in a moss and two varieties of pea

The senescence and preservation of the structure of the chloroplastin the dark was studied in the protonema of Ceratodon purpureusand in two varieties of pea, a tall variety "Dippe Maj" anda dwarf variety "Early low". The latter variety is better ableto survive in darkness, probably because of the larger amountof starch in its chloroplasts. The integrity of the chloroplastswas better preserved in the moss than in the peas. During isolationof the chlorophyll-protein complexes, there was no decreasein the specific activity of the total lamellar extract in anyof the dark-grown materials. This contrasts with the turnoverof chlorophyll-protein complex (CP) II in the dark-grown moss.In the light, CP II had a half life of two weeks in both themoss and the higher plants, whereas no turnover was evidentin CP I. The lack of turnover for CP I is connected with itsdecrease in senescence. ¹Present address: Department of Botany, University of Turku,20500 Turku 50, Finland. (Received July 13, 1979; )     

Long-term forest composition and its drivers in taiga forest in NW Russia

Understanding the processes behind long-term boreal forest dynamics can provide information that assists in predicting future boreal vegetation under changing environmental conditions. Here, we examine Holocene stand-scale vegetation dynamics and its drivers at the western boundary of the Russian taiga forest in NW Russia. Fossil pollen and conifer stomata records from four small hollow sites and two lake sites are used to reconstruct local vegetation dynamics during the Holocene. Variation partitioning is used to assess the relative importance of the potential drivers (temperature, forest fires and growing site wetness) to the long-term stand-scale dynamics in taiga forest. All the main tree taxa, including the boreal keystone species Picea abies (Norway spruce) and Larix sibirica (Siberian larch), have been locally present since 10,000 cal yr bp. The constant Holocene presence of L. sibirica at three small hollow sites suggests a fast postglacial immigration of the species in northern Europe. Picea was present but not dominant at all study sites until its expansion between 8,000 and 7,000 cal yr bp markedly changed the forest structure through the suppression of Betula (birch), Pinus (pine) and Larix. Our results demonstrate that in general, the Holocene forest dynamics in our study region have been driven by temperature, but during short intervals the role of local factors, especially forest fires, has been prominent. The comparison between sites reveals the importance of local factors in stand-scale dynamics in taiga forests. Therefore, the future responses of taiga forest to climate change will be predominantly modulated by the local characteristics at the site.     

Signal enrichment with strain-level resolution in metagenomes using topological data analysis

Background

A metagenome is a collection of genomes, usually in a micro-environment, and sequencing a metagenomic sample en masse is a powerful means for investigating the community of the constituent microorganisms. One of the challenges is in distinguishing between similar organisms due to rampant multiple possible assignments of sequencing reads, resulting in false positive identifications. We map the problem to a topological data analysis (TDA) framework that extracts information from the geometric structure of data. Here the structure is defined by multi-way relationships between the sequencing reads using a reference database.

Results

Based primarily on the patterns of co-mapping of the reads to multiple organisms in the reference database, we use two models: one a subcomplex of a Barycentric subdivision complex and the other a Čech complex. The Barycentric subcomplex allows a natural mapping of the reads along with their coverage of organisms while the Čech complex takes simply the number of reads into account to map the problem to homology computation. Using simulated genome mixtures we show not just enrichment of signal but also microbe identification with strain-level resolution.

Conclusions

In particular, in the most refractory of cases where alternative algorithms that exploit unique reads (i.e., mapped to unique organisms) fail, we show that the TDA approach continues to show consistent performance. The Čech model that uses less information is equally effective, suggesting that even partial information when augmented with the appropriate structure is quite powerful.