Fungal Community Shifts in Structure and Function across a Boreal Forest Fire Chronosequence

Forest fires are a common natural disturbance in forested ecosystems and have a large impact on the microbial communities in forest soils. The response of soil fungal communities to forest fire is poorly documented. Here, we investigated fungal community structure and function across a 152-year boreal forest fire chronosequence using high-throughput sequencing of the internal transcribed spacer 2 (ITS2) region and a functional gene array (GeoChip). Our results demonstrate that the boreal forest soil fungal community was most diverse soon after a fire disturbance and declined over time. The differences in the fungal communities were explained by changes in the abundance of basidiomycetes and ascomycetes. Ectomycorrhizal (ECM) fungi contributed to the increase in basidiomycete abundance over time, with the operational taxonomic units (OTUs) representing the genera Cortinarius and Piloderma dominating in abundance. Hierarchical cluster analysis by using gene signal intensity revealed that the sites with different fire histories formed separate clusters, suggesting differences in the potential to maintain essential biogeochemical soil processes. The site with the greatest biological diversity had also the most diverse genes. The genes involved in organic matter degradation in the mature forest, in which ECM fungi were the most abundant, were as common in the youngest site, in which saprotrophic fungi had a relatively higher abundance. This study provides insight into the impact of fire disturbance on soil fungal community dynamics.     

Climate‐induced warming imposes a threat to north European spring ecosystems

Interest in climate change effects on groundwater has increased dramatically during the last decade. The mechanisms of climate‐related groundwater depletion have been thoroughly reviewed, but the influence of global warming on groundwater‐dependent ecosystems (GDEs) remains poorly known. Here we report long‐term water temperature trends in 66 northern European cold‐water springs. A vast majority of the springs (82%) exhibited a significant increase in water temperature during 1968–2012. Mean spring water temperatures were closely related to regional air temperature and global radiative forcing of the corresponding year. Based on three alternative climate scenarios representing low (RCP2.6), intermediate (RCP6) and high‐emission scenarios (RCP8.5), we estimate that increase in mean spring water temperature in the region is likely to range from 0.67 °C (RCP2.6) to 5.94 °C (RCP8.5) by 2086. According to the worst‐case scenario, water temperature of these originally cold‐water ecosystems (regional mean in the late 1970s: 4.7 °C) may exceed 12 °C by the end of this century. We used bryophyte and macroinvertebrate species data from Finnish springs and spring‐fed streams to assess ecological impacts of the predicted warming. An increase in spring water temperature by several degrees will likely have substantial biodiversity impacts, causing regional extinction of native, cold‐stenothermal spring specialists, whereas species diversity of headwater generalists is likely to increase. Even a slight (by 1 °C) increase in water temperature may eliminate endemic spring species, thus altering bryophyte and macroinvertebrate assemblages of spring‐fed streams. Climate change‐induced warming of northern regions may thus alter species composition of the spring biota and cause regional homogenization of biodiversity in headwater ecosystems.     

Protein body formation in leaves of Nicotiana benthamiana: a concentration‐dependent mechanism influenced by the presence of fusion tags

Protein bodies (PBs) are endoplasmic reticulum (ER) derived organelles originally found in seeds whose function is to accumulate seed storage proteins. It has been shown that PB formation is not limited to seeds and green fluorescent protein (GFP) fused to either elastin‐like polypeptide (ELP) or hydrophobin (HFBI) fusion tags induce the formation of PBs in leaves of N. benthamiana. In this study, we compared the ELP‐ and HFBI‐induced PBs and showed that ELP‐induced PBs are larger than HFBI‐induced PBs. The size of ELP‐ and HFBI‐induced PBs increased over time along with the accumulation levels of their fused protein. Our results show that PB formation is a concentration‐dependent mechanism in which proteins accumulating at levels higher than 0.2% of total soluble protein are capable of inducing PBs in vivo. Our results show that the presence of fusion tags is not necessary for the formation of PBs, but affects the distribution pattern and size of PBs. This was confirmed by PBs induced by fluorescent proteins as well as fungal xylanases. We noticed that in the process of PB formation, secretory and ER‐resident molecules are passively sequestered into the lumen of PBs. We propose to use this property of PBs as a tool to increase the accumulation levels of erythropoietin and human interleukin‐10 by co‐expression with PB‐inducing proteins.     

Mitogenome rearrangement in the cold-water scleractinian coral Lophelia pertusa (Cnidaria, Anthozoa) involves a long-term evolving group I intron

Group I introns are genetic insertion elements that invade host genomes in a wide range of organisms. In metazoans, however, group I introns are extremely rare, so far only identified within mitogenomes of hexacorals and some sponges. We sequenced the complete mitogenome of the cold-water scleractinian coral Lophelia pertusa, the dominating deep sea reef-building coral species in the North Atlantic Ocean. The mitogenome (16,150 bp) has the same gene content but organized in a unique gene order compared to that of other known scleractinian corals. A complex group I intron (6460 bp) inserted in the ND5 gene (position 717) was found to host seven essential mitochondrial protein genes and one ribosomal RNA gene. Phylogenetic analysis supports a vertical inheritance pattern of the ND5-717 intron among hexacoral mitogenomes with no examples of intron loss. Structural assessments of the Lophelia intron revealed an unusual organization that lacks the universally conserved ωG at the 3′ end, as well as a highly compact RNA core structure with overlapping ribozyme and protein coding capacities. Based on phylogenetic and structural analyses we reconstructed the evolutionary history of ND5-717, from its ancestral protist origin, through intron loss in some early metazoan lineages, and into a compulsory feature with functional implications in hexacorals.     

Fine root foraging strategies in Norway spruce forests across a European climate gradient

Fine root acclimation to different environmental conditions is crucial for growth and sustainability of forest trees. Relatively small changes in fine root standing biomass (FRB), morphology or mycorrhizal symbiosis may result in a large change in forest carbon, nutrient and water cycles. We elucidated the changes in fine root traits and associated ectomycorrhizal (EcM) fungi in 12 Norway spruce stands across a climatic and N deposition gradient from subarctic‐boreal to temperate regions in Europe (68°N–48°N). We analysed the standing FRB and the ectomycorrhizal root tip biomass (EcMB, g m^?2) simultaneously with measurements of the EcM root morphological traits (e.g. mean root length, root tissue density (RTD), N% in EcM roots) and frequency of dominating EcM fungi in different stands in relation to climate, soil and site characteristics. Latitude and N deposition explained the greatest proportion of variation in fine root traits. EcMB per stand basal area (BA) increased exponentially with latitude: by about 12.7 kg m^?2 with an increase of 10° latitude from southern Germany to Estonia and southern Finland and by about 44.7 kg m^?2 with next latitudinal 10° from southern to northern Finland. Boreal Norway spruce forests had 4.5 to 11 times more EcM root tips per stand BA, and the tips were 2.1 times longer, with 1.5 times higher RTD and about 1/3 lower N concentration. There was 19% higher proportion of root tips colonized by long‐distance exploration type forming EcM fungi in the southern forests indicating importance of EcM symbiont foraging strategy in fine root nutrient acquisition. In the boreal zone, we predict ca. 50% decrease in EcMB per stand BA with an increase of 2 °C annual mean temperature. Different fine root foraging strategies in boreal and temperate forests highlight the importance of complex studies on respective regulatory mechanisms in changing climate.     

Human biodistribution and dosimetry of ¹¹C-CUMI-101, an agonist radioligand for serotonin-1a receptors in brain

As a reported agonist,¹¹C-CUMI-101 is believed to selectively bind the G-protein-coupled state of the serotonin-1A (5-HT_1A) receptor, thereby providing a measure of the active subset of all 5-HT_1A receptors in brain. Although ¹¹C-CUMI-101 has been successfully used to quantify 5-HT_1A receptors in human and monkey brain, its radiation exposure has not previously been reported. The purpose of this study was to calculate the radiation exposure to organs of the body based on serial whole-body imaging with positron emission tomography (PET) in human subjects.

Methods

Nine healthy volunteers were injected with 428±84 MBq (mean ± SD) ¹¹C-CUMI-101 and then imaged with a PET-only device for two hours from head to mid-thigh. Eleven source organs (brain, heart, liver, pancreas, stomach, spleen, lungs, kidneys, lumbar spine L1-5, thyroid, and urinary bladder) were identified on whole body images and used to calculate radiation doses using the software program OLINDA/EXM 1.1. To confirm that we had correctly identified the pancreas, a tenth subject was imaged on a PET/CT device.

Results

Brain had high uptake (∼11% of injected activity (IA)) at 10 min. Although liver had the highest uptake (∼35% IA at 120 min), excretion of this activity was not visible in gall bladder or intestine during the scanning session. Organs which received the highest doses (microSv/MBq) were pancreas (32.0), liver (18.4), and spleen (14.5). The effective dose of ¹¹C-CUMI-101 was 5.3±0.5 microSv/MBq.

Conclusion

The peak brain uptake (∼11% IA) of ¹¹C-CUMI-101 is the highest among more than twenty ¹¹C-labeled ligands reported in the literature and provides good counting statistics from relatively low injected activities. Similar to that of other ¹¹C-labeled ligands for brain imaging, the effective dose of ¹¹C-CUMI-101 is 5.3±0.5 microSv/MBq, a value that can now be used to estimate the radiation risks in future research studies.     

Spontaneous hemodynamic oscillations during human sleep and sleep stage transitions characterized with near-infrared spectroscopy

Understanding the interaction between the nervous system and cerebral vasculature is fundamental to forming a complete picture of the neurophysiology of sleep and its role in maintaining physiological homeostasis. However, the intrinsic hemodynamics of slow-wave sleep (SWS) are still poorly known. We carried out 30 all-night sleep measurements with combined near-infrared spectroscopy (NIRS) and polysomnography to investigate spontaneous hemodynamic behavior in SWS compared to light (LS) and rapid-eye-movement sleep (REM). In particular, we concentrated on slow oscillations (3-150 mHz) in oxy- and deoxyhemoglobin concentrations, heart rate, arterial oxygen saturation, and the pulsation amplitude of the photoplethysmographic signal. We also analyzed the behavior of these variables during sleep stage transitions. The results indicate that slow spontaneous cortical and systemic hemodynamic activity is reduced in SWS compared to LS, REM, and wakefulness. This behavior may be explained by neuronal synchronization observed in electrophysiological studies of SWS and a reduction in autonomic nervous system activity. Also, sleep stage transitions are asymmetric, so that the SWS-to-LS and LS-to-REM transitions, which are associated with an increase in the complexity of cortical electrophysiological activity, are characterized by more dramatic hemodynamic changes than the opposite transitions. Thus, it appears that while the onset of SWS and termination of REM occur only as gradual processes over time, the termination of SWS and onset of REM may be triggered more abruptly by a particular physiological event or condition. The results suggest that scalp hemodynamic changes should be considered alongside cortical hemodynamic changes in NIRS sleep studies to assess the interaction between the autonomic and central nervous systems.     

Quantification of bacteria in human feces using 16S rRNA-hybridization, DNA-staining and flow cytometry

Hybridization of bacteria with fluorescent probes targeting 16S rRNA and inspection of hybridized bacteria with fluorescence microscopy (microscopy-FISH, i.e. fluorescence in situ hybridization) have constituted an accessible method for the analysis of mixed bacterial samples such as feces. However, microscopy-FISH is a slow method and prone to errors. Flow cytometry (FCM) enables analysis of bacteria more rapidly, accurately and reliably than microscopy. In this study, a FCM method for the analysis of 16S rRNA-hybridized and DNA-stained fecal bacteria was developed. The results of FCM-FISH were comparable to those of microscopy-FISH, and the coefficients of variation of the FCM analyses were extraordinarily low. In previous FCM-FISH studies, the Eub 338 probe, which is supposed to hybridize all bacteria, has been used to detect all bacteria present in the sample. We found that Eub 338 did not bind to all bacteria, which could be detected by DNA-staining; while SYTOX Orange DNA-stain detected all bacterial species tested and produced high fluorescence intensities enabling clear separation of bacteria from non-bacterial material. Thus, DNA-staining is a method of choice for the detection of all bacteria in FCM-FISH. We conclude that FCM of 16S rRNA-hybridized and DNA-stained bacteria is a rapid and reliable method for the analysis of mixed bacterial samples including feces.