Fire intensity regulates the short-term postfire response of the microbiome in Arctic tundra soil

Arctic tundra fires have been increasing in extent, frequency and intensity and are likely impacting both soil nitrogen (N) and phosphorus (P) cycling and, thus, permafrost ecosystem functioning. However, little is known on the underlying microbial mechanisms, and different fire intensities were neglected so far. To better understand immediate influences of different fire intensities on the soil microbiome involved in nutrient cycling in permafrost-affected soil, we deployed experimental fires with low and high intensity on an Arctic tundra soil on Disko Island, Greenland. Soil sampling took place three days postfire and included an unburned control. Using quantitative real-time PCR, copy numbers of 16S and ITS as well as of 17 genes coding for functional microbial groups catalyzing major steps of N and P turnover were assessed. We show that fires change the abundance of microbial groups already after three days with fire intensity as key mediating factor. Specifically, low-intensity fire significantly enhanced the abundance of chiA mineralizers and ammonia-oxidizing archaea, while other groups were not affected. On the contrary, high-intensity fire decreased the abundance of chiA mineralizers and of microbes that fix dinitrogen, indicating a dampening effect on N cycling. Only high-intensity fires enhanced ammonium concentrations (by an order of magnitude). This can be explained by burned plant material and the absence of plant uptake, together with impaired further N processing. Fire with high intensity also decreased nirK-type denitrifiers. In contrast, after fire with low intensity there was a trend for a decreased nosZ : (nirK+nirS) ratio, indicating – together with increased nitrate concentrations – an enhanced potential for nitric oxide and nitrous oxide emissions. Concerning P transformation, only gcd was affected in the short term which is important for P solubilization. Changes in gene numbers consistently showed the same contrasting pattern of elevated abundance with low fire intensity and decreased abundance with high fire intensity. Differentiating fire intensities is therefore crucial for further, longer-term studies of fire-induced changes in N and P transformations and potential nutrient-climate feedbacks of permafrost-affected soils

Dynamics of Bacterial Root Endophytes of Malus domestica Plants Grown in Field Soils Affected by Apple Replant Disease

Apple replant disease (ARD) is a worldwide problem for tree nurseries and orchards leading to reduced plant growth and fruit quality. The etiology of this complex phenomenon is poorly understood, but shifts of the bulk soil and rhizosphere microbiome seem to play an important role. Since roots are colonized by microbes from the rhizosphere, studies of the endophytic microbiome in relation to ARD are meaningful. In this study, culture-independent and culture-dependent approaches were used in order to unravel the endophytic root microbiome of apple plants 3, 7, and 12 months after planting in ARD-affected soil and ARD-unaffected control soil at two different field sites. Next to a high diversity of Pseudomonas in roots from all soils, molecular barcoding approaches revealed an increase in relative abundance of endophytic Actinobacteria over time in plants grown in ARD and control plots. Furthermore, several amplicon sequence variants (ASVs) linked to Streptomyces, which had been shown in a previous greenhouse ARD biotest to be negatively correlated to shoot length and fresh mass, were also detected in roots from both field sites. Especially in roots of apple plants from control soil, these Streptomyces ASVs increased in their relative abundance over time. The isolation of 150 bacterial strains in the culture-dependent approach revealed a high diversity of members of the genus Pseudomonas, confirming the data of the molecular barcoding approach. However, only partial overlaps were found between the two approaches, underlining the importance of combining these methods in order to better understand this complex disease and develop possible countermeasures. Overall, this study suggests a key role of Streptomyces in the etiology of ARD in the field. Copyright © 2022 Mahnkopp-Dirks, Radl, Kublik, Gschwendtner, Schloter and Winkelmann

Climate Change Induces Shifts in Abundance and Activity Pattern of Bacteria and Archaea Catalyzing Major Transformation Steps in Nitrogen Turnover in a Soil from a Mid-European Beech Forest

Ongoing climate change will lead to more extreme weather events, including severe drought periods and intense drying rewetting cycles. This will directly influence microbial nitrogen (N) turnover rates in soil by changing the water content and the oxygen partial pressure. Therefore, a space for time climate change experiment was conducted by transferring intact beech seedling-soil mesocosms from a northwest (NW) exposed site, representing today’s climatic conditions, to a southwest (SW) exposed site, providing a model climate for future conditions with naturally occurring increased soil temperature (+0.8˚C in average). In addition, severe drought and intense rainfall was simulated by a rainout shelter at SW and manual rewetting after 39 days drought, respectively. Soil samples were taken in June, at the end of the drought period (August), 24 and 72 hours after rewetting (August) and after a regeneration period of four weeks (September). To follow dynamics of bacterial and archaeal communities involved in N turnover, abundance and activity of nitrifiers, denitrifiers, N2-fixing microbes and N-mineralizers was analyzed based on marker genes and the related transcripts by qPCR from DANN and RNA directly extracted from soil. Abundance of the transcripts was reduced under climate change with most pronounced effects for denitrification. Our results revealed that already a transfer from NW to SW without further treatment resulted in decreased cnor and nosZ transcripts, encoding for nitric oxide reductase and nitrous oxide reductase, respectively, while nirK transcripts, encoding for nitrite reductase, remained unaffected. Severe drought additionally led to reduced nirK and cnor transcripts at SW. After rewetting, nirK transcripts increased rapidly at both sites, while cnor and nosZ transcripts increased only at NW. Our data indicate that the climate change influences activity pattern of microbial communities involved in denitrification processes to a different extend, which may impact emission rates of the greenhouse gas N2O

N2 gas flushing alleviates the loss of bacterial diversity and inhibits psychrotrophic Pseudomonas during the cold storage of bovine raw milk

Peer reviewe

Early life determinants induce sustainable changes in the gut microbiome of six-year-old children

While the association between early life determinants and the development of the gut microbiome composition in infancy has been widely investigated, a potential persistent influence of early life determinants on the gut microbial community after its stabilization at later childhood remains largely unknown. Therefore, we aimed to identify the association between several early life determinants and the gut microbiome composition in six-year-old children from the LISA birth cohort. A total number of 166 fecal samples were analyzed using 16S rRNA gene-based barcoding to assess bacterial diversity pattern. The bacterial profiles were investigated for their association with maternal smoking during pregnancy, mode of delivery, breastfeeding, antibiotic treatment between one and two years of age, gender and socioeconomic status (SES). While alpha and beta diversity of the infants' gut microbiome remained unaffected, amplicon sequence variants (ASVs) annotated to Firmicutes and Actinobacteria responded to early life determinants, mostly to feeding practice and antibiotics use. ASVs associated to Bacteriodetes remained unaffected. Our findings indicate that early life determinants could have a long-term sustainable effect on the gut microflora of six-year-old children, however, associations with early life determinates are weaker than reported for infants

Seasonal Effects of Extreme Weather Events on Potential Extracellular Enzyme Activities in a Temperate Grassland Soil

Magnitude and timing of precipitation events within the growing season might be decisive for alterations in potential extracellular enzyme activity (PEEA), with consequences for nutrient cycle, and carbon storage in grassland ecosystems. Pattern of PEEA catalyzing major steps of the carbon cycle (β-glucosidase (β-gls), cellobiohydrolase (cel), glucuronidase (glr), and xylosidase (xyl), soil respiration rates and extractable organic carbon were analyzed in response to increased intra-annual precipitation variability in a European, mesic temperate grassland. The field experiment was carried out in three subsequent years by simulating recurrent drought events combined with heavy rainfall either early or late in the growing season (spring or summer) by rainout shelters and irrigation systems. Our data indicated comparable effects of the drought settings independent from the timing of the drought. Both for the simulated spring- and summer drought a decrease of enzymatic activities was observed compared to the control plots, with ß-gls activity after the summer drought being the only exception. However, response pattern toward rewetting differed depending on the seasonal timing of the drought being introduced. After spring drought, a fast recovery to control level was observed for PEEA of ß-gls and xyl, whereas cel and glr activity remained constantly lower. Rewetting after summer drought induced an increase of all enzymatic activities to values even higher compared to the controls. Overall, our data indicate a high resilience of PEEA toward drought and rewetting events in grassland soils, which is modulated by the seasonal timing of the extreme weather events

European Strategy for Accelerator-Based Neutrino Physics

Massive neutrinos reveal physics beyond the Standard Model, which could have deep consequences for our understanding of the Universe. Their study should therefore receive the highest level of priority in the European Strategy. The discovery and study of leptonic CP violation and precision studies of the transitions between neutrino flavours require high intensity, high precision, long baseline accelerator neutrino experiments. The community of European neutrino physicists involved in oscillation experiments is strong enough to support a major neutrino long baseline project in Europe, and has an ambitious, competitive and coherent vision to propose. Following the 2006 European Strategy for Particle Physics (ESPP) recommendations, two complementary design studies have been carried out: LAGUNA/LBNO, focused on deep underground detector sites, and EUROnu, focused on high intensity neutrino facilities. LAGUNA LBNO recommends, as first step, a conventional neutrino beam CN2PY from a CERN SPS North Area Neutrino Facility (NANF) aimed at the Pyhasalmi mine in Finland. A sterile neutrino search experiment which could also be situated in the CERN north area has been proposed (ICARUS-NESSIE) using a two detector set-up, allowing a definitive answer to the 20 year old question open by the LSND experiment. EUROnu concluded that a 10 GeV Neutrino Factory, aimed at a magnetized neutrino detector situated, also, at a baseline of around 2200 km (+-30%), would constitute the ultimate neutrino facility; it recommends that the next 5 years be devoted to the R&D, preparatory experiments and implementation study, in view of a proposal before the next ESPP update. The coherence and quality of this program calls for the continuation of neutrino beams at CERN after the CNGS, and for a high priority support from CERN and the member states to the experiments and R&D program.Comment: Prepared by the program committee of the Neutrino `town meeting', CERN, 14-16 May 2012 and submitted to the European Strategy For European Particle Physic

Climate Change Impairs Nitrogen Cycling in European Beech Forests

European beech forests growing on marginal calcareous soils have been proposed to be vulnerable to decreased soil water availability. This could result in a large-scale loss of ecological services and economical value in a changing climate. In order to evaluate the potential consequences of this drought-sensitivity, we investigated potential species range shifts for European beech forests on calcareous soil in the 21st century by statistical species range distribution modelling for present day and projected future climate conditions. We found a dramatic decline by 78% until 2080. Still the physiological or biogeochemical mechanisms underlying the drought sensitivity of European beech are largely unknown. Drought sensitivity of beech is commonly attributed to plant physiological constraints. Furthermore, it has also been proposed that reduced soil water availability could promote nitrogen (N) limitation of European beech due to impaired microbial N cycling in soil, but this hypothesis has not yet been tested. Hence we investigated the influence of simulated climate change (increased temperatures, reduced soil water availability) on soil gross microbial N turnover and plant N uptake in the beech-soil interface of a typical mountainous beech forest stocking on calcareous soil in SW Germany. For this purpose, triple 15N isotope labelling of intact beech seedling-soil-microbe systems was combined with a space-for-time climate change experiment. We found that nitrate was the dominant N source for beech natural regeneration. Reduced soil water content caused a persistent decline of ammonia oxidizing bacteria and therefore, a massive attenuation of gross nitrification rates and nitrate availability in the soil. Consequently, nitrate and total N uptake of beech seedlings were strongly reduced so that impaired growth of beech seedlings was observed already after one year of exposure to simulated climatic change. We conclude that the N cycle in this ecosystem and here specifically nitrification is vulnerable to reduced water availability, which can directly lead to nutritional limitations of beech seedlings. This tight link between reduced water availability, drought stress for nitrifiers, decreased gross nitrification rates and nitrate availability and finally nitrate uptake by beech seedlings could represent the Achilles’ heel for beech under climate change stresses

Molecular Barcoding Reveals the Genus Streptomyces as Associated Root Endophytes of Apple (Malus domestica) Plants Grown in Soils Affected by Apple Replant Disease

Apple replant disease (ARD) occurs when apple is repeatedly planted at the same site, leading to growth reductions and losses in fruit yield and quality. Up to now, the etiology has been poorly understood; however, soil (micro)biota are known to be involved. Because endophytes often colonize plants via the rhizosphere, this study aimed at comparing the bacterial endophytic root microbiome in plants growing in ARD-affected and unaffected soils from three different sites based on greenhouse biotests using a molecular barcoding approach. The initial endophytic microbiome of the starting material (in vitro propagated plants of the apple rootstock M26) did not significantly affect the overall richness and diversity of the endophytic community in plants after 8 weeks of growth in the respective soils but some genera of the initial microbiome managed to establish in apple roots. Proteobacteria was the dominant phylum in all samples. No differences in diversity or number of amplicon sequence variants (ASVs) between plants grown in ARD soil and unaffected soil was observed. However, several ASVs of high abundance uniquely found in plants grown in ARD-affected soils were Streptomyces spp. In soil from all three sites, these Streptomyces spp. were negatively correlated with plant growth parameters. Future inoculation experiments using selected Streptomyces isolates have to prove whether bacteria from this genus are opportunists or part of the ARD complex. For the first time, the bacterial endophytic community of apple roots grown in ARD-affected soils was characterized, which will help us to understand the etiology of ARD and develop countermeasures