Schauerella fraxinea gen. nov., sp. nov., a bacterial species that colonises ash trees tolerant to dieback caused by Hymenoscyphus fraxineus.

The tolerance of ash trees against the pathogen Hymenoscyphus fraxineus seems to be associated with the occurrence of specific microbial taxa on leaves. A group of bacterial isolates, primarily identified on tolerant trees, was investigated with regard to their taxonomic classification and their potential to suppress the ash dieback pathogen. Examination of OGRI values revealed a separate species position. A phylogenomic analysis, based on orthologous and marker genes, indicated a separate genus position along with the species Achromobacter aestuarii. Furthermore, analysis of the ratio of average nucleotide identities and genome alignment fractions demonstrated genomic dissimilarities typically observed for inter-genera comparisons within this family. As a result of these investigations, the strains are considered to represent a separate species within a new genus, for which the name Schauerella fraxinea gen. nov., sp. nov. is proposed, with the type strain B3P038T (=LMG 33092 T = DSM 115926 T). Additionally, a reclassification of the species Achromobacter aestuarii as Schauerella aestuarii comb. nov. is proposed. In a co-cultivation assay, the strains were able to inhibit the growth of a H. fraxineus strain. Accordingly, a functional analysis of the genome of S. fraxinea B3P038T revealed genes mediating the production of antifungal substances. This potential, combined with the prevalent presence in the phyllosphere of tolerant ash trees, makes this group interesting for an inoculation experiment with the aim of controlling the pathogen in an integrative approach. For future field trials, a strain-specific qPCR system was developed to establish an efficient method for monitoring the inoculation success.

Genomic Characterization of Aureimonas altamirensis C2P003-A Specific Member of the Microbiome of Fraxinus excelsior Trees Tolerant to Ash Dieback.

Some European ash trees show tolerance towards dieback caused by the invasive pathogen Hymenoscyphus fraxineus. The microbiome of these trees harbours a range of specific bacterial groups. One of these groups belonging to the species Aureimonas altamirensis was studied in detail by genome analysis and a plant inoculation trial. The strain group was shown to be phylogenetically distinct from clinical isolates by 16S rRNA analysis and phylogenomics. Genome analysis of a representative strain C2P003 resulted in a large number of unique gene sequences in comparison to other well-studied strains of the species. A functional analysis of the genome revealed features associated with the synthesis of exopolysaccharides, protein secretion and biofilm production as well as genes for stress adaptation, suggesting the ability of C2P003 to effectively colonize ash leaves. The inoculation of ash seedlings with C2P003 showed a significant positive effect on the plant health of the seedlings that were exposed to H. fraxineus infection. This effect was maintained over a period of three years and was accompanied by a significant shift in the bacterial microbiome composition one year after inoculation. Overall, the results indicate that C2P003 may suppress H. fraxineus in or on ash leaves via colonization resistance or indirectly by affecting the microbiome.

Consumption of N2O by Flavobacterium azooxidireducens sp. nov. Isolated from Decomposing Leaf Litter of Phragmites australis (Cav.).

Microorganisms acting as sinks for the greenhouse gas nitrous oxide (N2O) are gaining increasing attention in the development of strategies to control N2O emissions. Non-denitrifying N2O reducers are of particular interest because they can provide a real sink without contributing to N2O release. The bacterial strain under investigation (IGB 4-14T), isolated in a mesocosm experiment to study the litter decomposition of Phragmites australis (Cav.), is such an organism. It carries only a nos gene cluster with the sec-dependent Clade II nosZ and is able to consume significant amounts of N2O under anoxic conditions. However, consumption activity is considerably affected by the O2 level. The reduction of N2O was not associated with cell growth, suggesting that no energy is conserved by anaerobic respiration. Therefore, the N2O consumption of strain IGB 4-14T rather serves as an electron sink for metabolism to sustain viability during transient anoxia and/or to detoxify high N2O concentrations. Phylogenetic analysis of 16S rRNA gene similarity revealed that the strain belongs to the genus Flavobacterium. It shares a high similarity in the nos gene cluster composition and the amino acid similarity of the nosZ gene with various type strains of the genus. However, phylogenomic analysis and comparison of overall genome relatedness indices clearly demonstrated a novel species status of strain IGB 4-14T, with Flavobacterium lacus being the most closely related species. Various phenotypic differences supported a demarcation from this species. Based on these results, we proposed a novel species Flavobacterium azooxidireducens sp. nov. (type strain IGB 4-14T = LMG 29709T = DSM 103580T).

Physiological and genomic characterisation of Luteimonas fraxinea sp. nov., a bacterial species associated with trees tolerant to ash dieback.

A group of isolates of the genus Luteimonas was characterised, which represented a specific component of the healthy core microbiome of Fraxinus excelsior in forest districts with a high infection rate of H. fraxineus, the causal agent of ash dieback. Based on phylogenomic and phenotypic analyses, a clear differentiation from related Luteimonas species was shown. Comparisons of the overall genome relatedness indices with the closest phylogenetic neighbours resulted in values below the recommended species cut-off levels. In addition, differences in several physiological and chemotaxonomic traits allowed a clear demarcation from the type strains of closely related species. Conclusively, the strain group was considered to represent a novel species in the genus Luteimonas, for which the name Luteimonas fraxinea sp. nov. is proposed, with strain D4P002T (=DSM 113273T = LMG 32455T) as the type strain. A functional analysis of the genome revealed features particularly associated with attachment, biofilm production and motility, indicating the ability of D4P002T to effectively colonise ash leaves. In nursery trials, ash seedlings inoculated with this strain showed suppression of the pathogen over a period of three years. This effect was accompanied by a significant shift in the bacterial microbiome of the plants. Altogether, the exclusive occurrence in the microbiome of tolerant ash trees, the genetic background and the results of the inoculation experiment suggest that strain D4P002T may suppress the penetration and spreading of H. fraxineus in or on ash leaves via colonisation resistance or trigger a priming effect of plant defences against the pathogen.

Genomic evidence for two pathways of formaldehyde oxidation and denitrification capabilities of the species Paracoccus methylovorus sp. nov.

Three strains (H4-D09T, S2-D11 and S9-F39) of a member of the genus Paracoccus attributed to a novel species were isolated from topsoil of temperate grasslands. The genome sequence of the type strain H4-D09T exhibited a complete set of genes required for denitrification as well as methylotrophy. The genome of H4-D09T included genes for two alternative pathways of formaldehyde oxidation. Besides the genes for the canonical glutathione (GSH)-dependent formaldehyde oxidation pathway, all genes for the tetrahydrofolate-formaldehyde oxidation pathway were identified. The strain has the potential to utilize methanol and/or methylamine as a single carbon source as evidenced by the presence of methanol dehydrogenase (mxaFI) and methylamine dehydrogenase (mau) genes. Apart from dissimilatory denitrification genes (narA, nirS, norBC and nosZ), genes for assimilatory nitrate (nasA) and nitrite reductases (nirBD) were also identified. The results of phylogenetic analysis based on 16S rRNA genes coupled with riboprinting revealed that all three strains represented the same species of genus Paracoccus. Core genome phylogeny of the type strain H4-D09T indicated that Paracoccus thiocyanatus and Paracoccus denitrificans are the closest phylogenetic neighbours. The average nucleotide index (ANI) and digital DNA-DNA hybridization (dDDH) with the closest phylogenetic neighbours revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The major respiratory quinone is Q-10, and the predominant cellular fatty acids are C18 : 1ω7c, C19 : 0cyclo ω7c, and C16 : 0, which correspond to those detected in other members of the genus. The polar lipid profile consists of a diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), aminolipid (AL), glycolipid (GL) and an unidentified lipid (L).On the basis of our results, we concluded that the investigated isolates represent a novel species of the genus Paracoccus, for which the name Paracoccus methylovorus sp. nov. (type strain H4-D09T=LMG 31941T= DSM 111585T) is proposed.

Flooding Causes Dramatic Compositional Shifts and Depletion of Putative Beneficial Bacteria on the Spring Wheat Microbiota.

Flooding affects both above- and below-ground ecosystem processes, and it represents a substantial threat for crop and cereal productivity under climate change. Plant-associated microbiota play a crucial role in plant growth and fitness, but we still have a limited understanding of the response of the crop-microbiota complex under extreme weather events, such as flooding. Soil microbes are highly sensitive to abiotic disturbance, and shifts in microbial community composition, structure and functions are expected when soil conditions are altered due to flooding events (e.g., anoxia, pH alteration, changes in nutrient concentration). Here, we established a pot experiment to determine the effects of flooding stress on the spring wheat-microbiota complex. Since plant phenology could be an important factor in the response to hydrological stress, flooding was induced only once and at different plant growth stages (PGSs), such as tillering, booting and flowering. After each flooding event, we measured in the control and flooded pots several edaphic and plant properties and characterized the bacterial community associated to the rhizosphere and roots of wheat plant using a metabarcoding approach. In our study, flooding caused a significant reduction in plant development and we observed dramatic shifts in bacterial community composition at each PGS in which the hydrological stress was induced. However, a more pronounced disruption in community assembly was always shown in younger plants. Generally, flooding caused a (i) significant increase of bacterial taxa with anaerobic respiratory capabilities, such as members of Firmicutes and Desulfobacterota, (ii) a significant reduction in Actinobacteria and Proteobacteria, (iii) depletion of several putative plant-beneficial taxa, and (iv) increases of the abundance of potential detrimental bacteria. These significant differences in community composition between flooded and control samples were correlated with changes in soil conditions and plant properties caused by the hydrological stress, with pH and total N as the soil, and S, Na, Mn, and Ca concentrations as the root properties most influencing microbial assemblage in the wheat mircobiota under flooding stress. Collectively, our findings demonstrated the role of flooding on restructuring the spring wheat microbiota, and highlighted the detrimental effect of this hydrological stress on plant fitness and performance.

Crop host signatures reflected by co-association patterns of keystone Bacteria in the rhizosphere microbiota.

BACKGROUND: The native crop bacterial microbiota of the rhizosphere is envisioned to be engineered for sustainable agriculture. This requires the identification of keystone rhizosphere Bacteria and an understanding on how these govern crop-specific microbiome assembly from soils. We identified the metabolically active bacterial microbiota (SSU RNA) inhabiting two compartments of the rhizosphere of wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), rye (Secale cereale), and oilseed rape (Brassica napus L.) at different growth stages. RESULTS: Based on metabarcoding analysis the bacterial microbiota was shaped by the two rhizosphere compartments, i.e. close and distant. Thereby implying a different spatial extent of bacterial microbiota acquirement by the cereals species versus oilseed rape. We derived core microbiota of each crop species. Massilia (barley and wheat) and unclassified Chloroflexi of group 'KD4-96' (oilseed rape) were identified as keystone Bacteria by combining LEfSe biomarker and network analyses. Subsequently, differential associations between networks of each crop species' core microbiota revealed host plant-specific interconnections for specific genera, such as the unclassified Tepidisphaeraceae 'WD2101 soil group'. CONCLUSIONS: Our results provide keystone rhizosphere Bacteria derived from for crop hosts and revealed that cohort subnetworks and differential associations elucidated host species effect that was not evident from differential abundance of single bacterial genera enriched or unique to a specific plant host. Thus, we underline the importance of co-occurrence patterns within the rhizosphere microbiota that emerge in crop-specific microbiomes, which will be essential to modify native crop microbiomes for future agriculture and to develop effective bio-fertilizers.

Genomic Analysis of the Endophytic Stenotrophomonas Strain 169 Reveals Features Related to Plant-Growth Promotion and Stress Tolerance.

Plant-associated Stenotrophomonas isolates have great potential for plant growth promotion, especially under stress conditions, due to their ability to promote tolerance to abiotic stresses such as salinity or drought. The endophytic strain Stenotrophomonas sp. 169, isolated from a field-grown poplar, increased the growth of inoculated in vitro plants, with a particular effect on root development, and was able to stimulate the rooting of poplar cuttings in the greenhouse. The strain produced high amounts of the plant growth-stimulating hormone auxin under in vitro conditions. The comparison of the 16S rRNA gene sequences and the phylogenetic analysis of the core genomes showed a close relationship to Stenotrophomonas chelatiphaga and a clear separation from Stenotrophomonas maltophilia. Whole genome sequence analysis revealed functional genes potentially associated with attachment and plant colonization, growth promotion, and stress protection. In detail, an extensive set of genes for twitching motility, chemotaxis, flagella biosynthesis, and the ability to form biofilms, which are connected with host plant colonization, could be identified in the genome of strain 169. The production of indole-3-acetic acid and the presence of genes for auxin biosynthesis pathways and the spermidine pathway could explain the ability to promote plant growth. Furthermore, the genome contained genes encoding for features related to the production of different osmoprotective molecules and enzymes mediating the regulation of stress tolerance and the ability of bacteria to quickly adapt to changing environments. Overall, the results of physiological tests and genome analysis demonstrated the capability of endophytic strain 169 to promote plant growth. In contrast to related species, strain 169 can be considered non-pathogenic and suitable for biotechnology applications.

Pseudomonas campi sp. nov., a nitrate-reducing bacterium isolated from grassland soil.

A novel strain was isolated from grassland soil that has the potential to assimilate ammonium by the reduction of nitrate in the presence of oxygen. Whole genome sequence analysis revealed the presence of an assimilatory cytoplasmic nitrate reductase gene nasA and the assimilatory nitrite reductase genes nirBD which are involved in the sequential reduction of nitrate to nitrite and further to ammonium, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate represents a member of the genus Pseudomonas. The closest phylogenetic neighbours based on 16S rRNA gene sequence analysis are the type strains of Pseudomonas peli (98.17%) and Pseudomonas guineae (98.03%). In contrast, phylogenomic analysis revealed a close relationship to Pseudomonas alcaligenes. Computation of the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) with the closest phylogenetic neighbours of S1-A32-2T revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. On the basis of these results, it was concluded that the soil isolate represents a novel species of the genus Pseudomonas, for which the name Pseudomonas campi sp. nov. (type strain S1-A32-2T=LMG 31521T=DSM 110222T) is proposed.

Analyzing Ash Leaf-Colonizing Fungal Communities for Their Biological Control of Hymenoscyphus fraxineus.

The invasive ascomycete Hymenoscyphus fraxineus has been threatening Fraxinus excelsior populations throughout Europe for over two decades. Since the infection and first colonization by the pathogen occurs in leaves, leaf-colonizing microorganisms have been discussed as a barrier and as possible biocontrol agents against the disease. To identify fungal groups with health-supporting potential, we compared the fungal microbiota of compound leaves from susceptible and tolerant ash trees in four ash stands with high H. fraxineus exposure. The fungal communities were analyzed both culture-independently by ITS2 amplicon sequencing and by the taxonomic classification of 1,704 isolates using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) or sequencing of the entire ITS region. The fungal community structure did not show significant differences depending on the health status. However, for several OTUs and a MALDI group, a significantly higher abundance was found in tolerant ash trees. Thus, the yeast Papiliotrema flavescens was significantly increased and accounted for 12.3% of the mycobiome of tolerant ashes (OTU0003), and it had also a distinctly higher abundance among the isolates. The filamentous ascomycete Sarocladium strictum was increased 24-fold among the isolates of tolerant trees, but its abundance was comparably low. An in vitro screening for the growth inhibition of the pathogen via cocultivation resulted in 28 yeast-like isolates and 79 filamentous fungi with antagonistic activity. A statistical cocultivation test on two H. fraxineus strains confirmed six of the yeast-like isolates that suppressed H. fraxineus significantly, from 39-50%, two of them through a fungicidal effect. The highest inhibition rates among the yeasts were found for three isolates belonging to Aureobasidium pullulans and P. flavescens. The cocultivation test of the filamentous isolates revealed higher effects compared to the yeasts. Four isolates showed significant inhibition of both H. fraxineus strains with a rate of 72-100%, and five further isolates inhibited only one H. fraxineus strain significantly. The most effective isolates were members of the genus Cladosporium. During the next step, in planta tests will be necessary to verify the efficacy of the antagonistic isolates and to assess their suitability as biocontrol agents.

A Comparative Analysis of Ash Leaf-Colonizing Bacterial Communities Identifies Putative Antagonists of Hymenoscyphus fraxineus.

In the last few years, the alarming spread of Hymenoscyphus fraxineus, the causal agent of ash dieback, has resulted in a substantial threat to native ash stands in central and northern Europe. Since leaves and leaf petioles are the primary infection sites, phyllosphere microorganisms are presumed to interact with the pathogen and are discussed as a source of biocontrol agents. We studied compound leaves from susceptible and visible infection-free trees in four ash stands with a high likelihood of infection to assess a possible variation in the bacterial microbiota, depending on the health status of the trees. The bacterial community was analyzed by culture-independent 16S rRNA gene amplicon sequencing and through the isolation and taxonomic classification of 2,589 isolates using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The bacterial community structure did not show significant differences. However, a set of amplicon sequence variants (ASVs) and MALDI groups belonging to Luteimonas, Aureimonas, Pseudomonas, Bacillus, and Paenibacillus were distinctly increased in tolerant trees, which may be associated with the ability of the tree to resist the pathogen. The most obvious differences were observed for Luteimonas, a genus that is also exclusively present in the healthy core microbiome. In a first in vitro screen of antagonists, approximately 11% of total isolates suppressed the growth of H. fraxineus, but a statistical test with two different H. fraxineus strains confirmed only the antagonistic activity of 8% of these isolates. The antagonistic isolates were assigned to Bacillus velezensis, Pantoea vagans, and Pseudomonas caspiana. Overall, our study provides a set of isolates or phylogenetic groups that might be involved in the process that prevents the penetration and spread of H. fraxineus. In the next step, in planta experiments are required with a longer period of exposure to H. fraxineus to evaluate effective isolates or consortia of isolates acting through direct antagonism or competition or indirectly by inducing resistance.

Systemic sclerosis in sub-Saharan Africa: a systematic review.

Systematic studies on connective tissue disorders are scarce in sub-Saharan Africa. Our aim was to analyse the published clinical data on systemic sclerosis (SSc) in sub-Saharan Africa. A systematic review was carried out in accordance with the PRISMA guidelines. We screened the Embase, PubMed and African Health Sciences databases for literature published until March 2018. Searches produced 1210 publications. After abstract and full-text screenings, 91 publications were analysed, and epidemiological information and clinical features extracted. Publications were mostly publications case reports (36%), cross-sectional studies (26%) and case series (23%) and came predominantly from South Africa (45%), Nigeria (15%) and Senegal (14%). A total of 1884 patients were reported, 66% of patients came from South Africa. The patients were between 4 and 77 years old; 83% of patients were female. Overall, 72% had diffuse SSc. Raynaud´s phenomenon was reported in 78% and skin ulcerations in 42% of patients. Focal skin hypopigmentation was common and telangiectasia not frequent. Interstitial lung involvement was reported in 50%, pulmonary hypertension in 30%, heart involvement in 28% of patients. Oesophageal reflux was observed in 70% and dysphagia in 37% of patients. Antinuclear antibodies were positive in 65% of patients. Anti-centromere autoantibodies (9.2%) and RNA polymerase 3 antibodies (7.1%) were rare and anti-fibrillarin most frequent (16.5%). SSc presentations in sub-Saharan Africa differ from those reported in Europe and America by a frequent diffuse skin involvement, focal skin hypopigmentation and a high prevalence of anti-fibrillarin autoantibodies.

Genome-based phylogeny of the genera Proteus and Cosenzaea and description of Proteus terrae subsp. terrae subsp. nov. and Proteus terrae subsp. cibarius subsp. nov.

The genera Proteus and Cosenzaea are closely related members of the family Morganellaceae. The genus Cosenzaea consists of the species Cosenzaea myxofaciens originally separated from the genus Proteus by rpoB gene analysis. Due to the high similarity of the 16S rRNA genes between species of both genera, the taxonomic status is here re-evaluated by a genome-based approach. Based on a core genome phylogeny and genome relatedness indices, it is shown that the taxonomy and nomenclature given for the basonym Proteus myxofaciens is more appropriate. Therefore, we propose to use this name in preference. Furthermore, the species status of Proteus terrae and Proteus cibarius was reassessed. Both species are related at subspecies level by digital DNA-DNA hybridization (dDDH) analysis. Additionally, average amino acid identity (AAI) and average nucleotide identity (ANI) do not support a separate species status, and therefore it is proposed to classify P. cibarius as a subspecies of P. terrae. Consequently, both species are being renamed Proteus terrae subsp. cibarius subsp. nov. and Proteus terrae subsp. terrae subsp. nov., respectively. The genome relatedness indices revealed a close relationship of the Proteus genomospecies 5 with P. terrae subsp. terrae. Thus, it has been assigned to the same subspecies.

Environmental Control on Microbial Turnover of Leaf Carbon in Streams - Ecological Function of Phototrophic-Heterotrophic Interactions.

In aquatic ecosystems, light availability can significantly influence microbial turnover of terrestrial organic matter through associated metabolic interactions between phototrophic and heterotrophic communities. However, particularly in streams, microbial functions vary significantly with the structure of the streambed, that is the distribution and spatial arrangement of sediment grains in the streambed. It is therefore essential to elucidate how environmental factors synergistically define the microbial turnover of terrestrial organic matter in order to better understand the ecological role of photo-heterotrophic interactions in stream ecosystem processes. In outdoor experimental streams, we examined how the structure of streambeds modifies the influence of light availability on microbial turnover of leaf carbon (C). Furthermore, we investigated whether the studied relationships of microbial leaf C turnover to environmental conditions are affected by flow intermittency commonly occurring in streams. We applied leaves enriched with a 13C-stable isotope tracer and combined quantitative and isotope analyses. We thereby elucidated whether treatment induced changes in C turnover were associated with altered use of leaf C within the microbial food web. Moreover, isotope analyses were combined with measurements of microbial community composition to determine whether changes in community function were associated with a change in community composition. In this study, we present evidence, that environmental factors interactively determine how phototrophs and heterotrophs contribute to leaf C turnover. Light availability promoted the utilization of leaf C within the microbial food web, which was likely associated with a promoted availability of highly bioavailable metabolites of phototrophic origin. However, our results additionally confirm that the structure of the streambed modifies light-related changes in microbial C turnover. From our observations, we conclude that the streambed structure influences the strength of photo-heterotrophic interactions by defining the spatial availability of algal metabolites in the streambed and the composition of microbial communities. Collectively, our multifactorial approach provides valuable insights into environmental controls on the functioning of stream ecosystems.

Dry-wet cycles of kettle hole sediments leave a microbial and biogeochemical legacy.

Understanding interrelations between an environment's hydrological past and its current biogeochemistry is necessary for the assessment of biogeochemical and microbial responses to changing hydrological conditions. The question how previous dry-wet events determine the contemporary microbial and biogeochemical state is addressed in this study. Therefore, sediments exposed to the atmosphere of areas with a different hydrological past within one kettle hole, i.e. (1) the predominantly inundated pond center, (2) the pond margin frequently desiccated for longer periods and (3) an intermediate zone, were incubated with the same rewetting treatment. Physicochemical and textural characteristics were related to structural microbial parameters regarding carbon and nitrogen turnover, i.e. abundance of bacteria and fungi, denitrifiers (targeted by the nirK und nirS functional genes) and nitrate ammonifiers (targeted by the nrfA functional gene). Our study reveals that, in combination with varying sediment texture, the hydrological history creates distinct microbial habitats with defined boundary conditions within the kettle hole, mainly driven by redox conditions, pH and organic matter (OM) composition. OM mineralization, as indicated by CO2-outgassing, was most efficient in exposed sediments with a less stable hydrological past. The potential for nitrogen retention via nitrate ammonification was highest in the hydrologically rather stable pond center, counteracting nitrogen loss due to denitrification. Therefore, the degree of hydrological stability is an important factor leaving a microbial and biogeochemical legacy, which determines carbon and nitrogen losses from small lentic freshwater systems in the long term run.

Characterization of the N2O-producing soil bacterium Rhizobium azooxidifex sp. nov.

In the context of studying the bacterial community involved in nitrogen transformation processes in arable soils exposed to different extents of erosion and sedimentation in a long-term experiment (CarboZALF), a strain was isolated that reduced nitrate to nitrous oxide without formation of molecular nitrogen. The presence of the functional gene nirK, encoding the respiratory copper-containing nitrite reductase, and the absence of the nitrous oxide reductase gene nosZ indicated a truncated denitrification pathway and that this bacterium may contribute significantly to the formation of the important greenhouse gas N2O. Phylogenetic analysis based on the 16S rRNA gene sequence and the housekeeping genes recA and atpD demonstrated that the investigated soil isolate belongs to the genus Rhizobium. The closest phylogenetic neighbours were the type strains of Rhizobium. subbaraonis and Rhizobium. halophytocola. The close relationship with R. subbaraonis was reflected by similarity analysis of the recA and atpD genes and their amino acid positions. DNA-DNA hybridization studies revealed genetic differences at the species level, which were substantiated by analysis of the whole-cell fatty acid profile and several distinct physiological characteristics. Based on these results, it was concluded that the soil isolate represents a novel species of the genus Rhizobium, for which the name Rhizobium azooxidifex sp. nov. (type strain Po 20/26T=DSM 100211T=LMG 28788T) is proposed.

Forest understory plant and soil microbial response to an experimentally induced drought and heat-pulse event: the importance of maintaining the continuum.

Drought duration and intensity are expected to increase with global climate change. How changes in water availability and temperature affect the combined plant-soil-microorganism response remains uncertain. We excavated soil monoliths from a beech (Fagus sylvatica L.) forest, thus keeping the understory plant-microbe communities intact, imposed an extreme climate event, consisting of drought and/or a single heat-pulse event, and followed microbial community dynamics over a time period of 28 days. During the treatment, we labeled the canopy with (13) CO2 with the goal of (i) determining the strength of plant-microbe carbon linkages under control, drought, heat and heat-drought treatments and (ii) characterizing microbial groups that are tightly linked to the plant-soil carbon continuum based on (13) C-labeled PLFAs. Additionally, we used 16S rRNA sequencing of bacteria from the Ah horizon to determine the short-term changes in the active microbial community. The treatments did not sever within-plant transport over the experiment, and carbon sinks belowground were still active. Based on the relative distribution of labeled carbon to roots and microbial PLFAs, we determined that soil microbes appear to have a stronger carbon sink strength during environmental stress. High-throughput sequencing of the 16S rRNA revealed multiple trajectories in microbial community shifts within the different treatments. Heat in combination with drought had a clear negative effect on microbial diversity and resulted in a distinct shift in the microbial community structure that also corresponded to the lowest level of label found in the PLFAs. Hence, the strongest changes in microbial abundances occurred in the heat-drought treatment where plants were most severely affected. Our study suggests that many of the shifts in the microbial communities that we might expect from extreme environmental stress will result from the plant-soil-microbial dynamics rather than from direct effects of drought and heat on soil microbes alone.

Water level changes affect carbon turnover and microbial community composition in lake sediments.

Due to climate change, many lakes in Europe will be subject to higher variability of hydrological characteristics in their littoral zones. These different hydrological regimes might affect the use of allochthonous and autochthonous carbon sources. We used sandy sediment microcosms to examine the effects of different hydrological regimes (wet, desiccating, and wet-desiccation cycles) on carbon turnover. (13)C-labelled particulate organic carbon was used to trace and estimate carbon uptake into bacterial biomass (via phospholipid fatty acids) and respiration. Microbial community changes were monitored by combining DNA- and RNA-based real-time PCR quantification and terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA. The shifting hydrological regimes in the sediment primarily caused two linked microbial effects: changes in the use of available organic carbon and community composition changes. Drying sediments yielded the highest CO2 emission rates, whereas hydrological shifts increased the uptake of allochthonous organic carbon for respiration. T-RFLP patterns demonstrated that only the most extreme hydrological changes induced a significant shift in the active and total bacterial communities. As current scenarios of climate change predict an increase of drought events, frequent variations of the hydrological regimes of many lake littoral zones in central Europe are anticipated. Based on the results of our study, this phenomenon may increase the intensity and amplitude in rates of allochthonous organic carbon uptake and CO2 emissions.

Reference values for digital X-ray radiogrammetry parameters in children and adolescents in comparison to estimates in patients with distal radius fractures.

The first objective of this study was to determine normative digital X-ray radiogrammetry (DXR) values, based on original digital images, in a pediatric population (aged 6-18 years). The second aim was to compare these reference data with patients suffering from distal radius fractures, whereas both cohorts originated from the same geographical region and were evaluated using the same technical parameters as well as inclusion and exclusion criteria. DXR-BMD and DXR-MCI of the metacarpal bones II-IV were assessed on standardized digital hand radiographs, without printing or scanning procedures. DXR parameters were estimated separately by gender and among six age groups; values in the fracture group were compared to age- and gender-matched normative data using Student's t tests and Z scores. In the reference cohort (150 boys, 138 girls), gender differences were found in bone mineral density (DXR-BMD), with higher values for girls from 11 to 14 years and for boys from 15 to 18 years (p < 0.05). Girls had higher normative metacarpal index (DXR-MCI) values than boys, with significant differences at 11-14 years (p < 0.05). In the case-control investigation, the fracture group (95 boys, 69 girls) presented lower DXR-BMD at 15-18 years in boys and 13-16 years in girls vs. the reference cohort (p < 0.05); DXR-MCI was lower at 11-18 years in boys and 11-16 years in girls (p < 0.05). Mean Z scores in the fracture group for DXR-BMD were -0.42 (boys) and -0.46 (girls), and for DXR-MCI were -0.51 (boys) and -0.53 (girls). These findings indicate that the fully digital DXR technique can be accurately applied in pediatric populations ≥ 6 years of age. The lower DXR-BMD and DXR-MCI values in the fracture group suggest promising early identification of individuals with increased fracture risk, without the need for additional radiation exposure, enabling the initiation of prevention strategies to possibly reduce the incidence of osteoporosis later in life.

Conjugative transfer of a derivative of the IncP-1α plasmid RP4 and establishment of transconjugants in the indigenous bacterial community of poplar plants.

The persistence of traits introduced into the indigenous bacterial community of poplar plants was investigated using bioluminescence mediated by the luc gene. Three endophytic bacterial strains provided with the IncP-1α plasmid RP4-Tn-luc were used to inoculate poplar cuttings at different phenological stages. Screening of isolates by bioluminescence and real-time PCR detection of the luc gene revealed stable persistence for at least 10 weeks. Although the inoculated strains became established with a high population density after inoculation at leaf development (April) and senescence (October), the strains were suppressed by the indigenous bacteria at stem elongation (June). Transconjugants could be detected only at this phenological stage. Indigenous bacteria harbouring RP4-Tn-luc became established with densities ranging from 2 × 10(5) to 9 × 10(6) CFU g(-1) fresh weight 3 and 10 weeks after inoculation. The increased colonization of the cuttings by indigenous bacteria at stem elongation seemed to strongly compete with the introduced strains. Otherwise, the phenological stage of the plants as well as the density of the indigenous recipients could serve as the driver for a more frequent conjugative plasmid transfer. A phylogenetic assignment of transconjugants indicated the transfer of RP4-Tn-luc into six genera of Proteobacteria, mainly Sphingomonas, Stenotrophomonas and Xanthomonas.