Data Descriptor : A European Multi Lake Survey dataset of environmental variables, phytoplankton pigments and cyanotoxins

Under ongoing climate change and increasing anthropogenic activity, which continuously challenge ecosystem resilience, an in-depth understanding of ecological processes is urgently needed. Lakes, as providers of numerous ecosystem services, face multiple stressors that threaten their functioning. Harmful cyanobacterial blooms are a persistent problem resulting from nutrient pollution and climate-change induced stressors, like poor transparency, increased water temperature and enhanced stratification. Consistency in data collection and analysis methods is necessary to achieve fully comparable datasets and for statistical validity, avoiding issues linked to disparate data sources. The European Multi Lake Survey (EMLS) in summer 2015 was an initiative among scientists from 27 countries to collect and analyse lake physical, chemical and biological variables in a fully standardized manner. This database includes in-situ lake variables along with nutrient, pigment and cyanotoxin data of 369 lakes in Europe, which were centrally analysed in dedicated laboratories. Publishing the EMLS methods and dataset might inspire similar initiatives to study across large geographic areas that will contribute to better understanding lake responses in a changing environment.Peer reviewe

Reconstruction of the microbial phosphorus turnover in forest soils with different phosphorus stocks.

The main objective of this study was the identification of microbial traits and key players involved in mobilization of phosphorus (P) in forest soils. In the mineral topsoil, the strongest genetic potential was proven for P transporters, the solubilization of inorganic-P and P starvation-inducible genes. The P cycle associated microbial community was highly complex, though dominated by few dominant taxa. While the impact of the soil P content on community composition was insignificant, an adaptation of the microbial P nutrition strategy to the soil specific P characteristics was proven

The importance of C, N and P as driver for bacterial community structure in German beech dominated forest soils.

Among several environmental factors shaping soil microbial communities the impact of soil nutrients is of special interest. While continuous application mainly of N and P dramatically shifts community composition during fertilization, it remains unclear whether this effect is consistent in generic, unfertilized beech forest ecosystems of Germany, where differences in nutrient contents are mostly a result of the parental material and climatic conditions. We postulate that in such ecosystems nutrient effects are less pronounced due to the possibility of the soil microbiome to adapt to the corresponding conditions over decades and the vegetation acts as the major driver. To test this hypothesis, we investigated the bacterial community composition in five different German beech dominated forest soils, representing a natural gradient of total- and easily available mineral-P. A community fingerprinting approach was performed using terminal-Restriction Fragment Length Polymorphism analysis of the 16S rRNA gene, while abundance of bacteria was measured applying quantitative real-time PCR. Bacterial communities at the five forest sites were distinctly separated, with strongest differences between the end-members of the P-gradient. However the majority of identified microbial groups (43%) were present at all sites, forming a core microbiome independent from the differences in soil chemical properties. Especially in the P-deficient soil the abundance of unique bacterial groups was highly increased, indicating a special adaption of the community to P limitation at this site. In this regard Correspondence Analysis elucidated that exclusively soil pH significantly affected community composition at the investigated sites. In contrast soil C, N and P contents did mainly affect the overall abundance of bacteria

qPCR zur quantitativen Validierung von Metagenomdaten.

Microorganisms are essential to maintain ecosystem functions and health as they catalyze most keystone processes. Formerly the quantification of key functions was performed by broad ranged primers, which were mainly based on genomes of cultivated microbes. To take advantage of the enormous development of next generation sequencing technologies, we propose to use metagenomic data for the design of new primer systems. Here we describe a two-phasic approach for a targeted and site specific primer design for qPCR

Phosphorus depletion in forest soils shapes bacterial communities towards phosphorus recycling systems.

Phosphorus (P) is an important macronutrient for all biota on earth but similarly a finite resource. Microorganisms play on both sides of the fence as they effectively mineralize organic and solubilize precipitated forms of soil phosphorus, but conversely also take up and immobilize P. Therefore, we analyzed the role of microbes in two beech forest soils with high and low P content by direct sequencing of metagenomic DNA. For inorganic P solubilization, a significantly higher microbial potential was detected in the P-rich soil. This trait especially referred to Candidatus Solibacter usiatus, likewise one of the dominating species in the datasets. A higher microbial potential for efficient phosphate uptake systems (pstSCAB) was detected in the P-depleted soil. Genes involved in P starvation response regulation (phoB, phoR) were prevalent in both soils. This underlines the importance of effective phosphate (Pho) regulon control for microorganisms to use alternative P sources during phosphate limitation. Predicted genes were primarily harbored by Rhizobiales, Actinomycetales and Acidobacteriales

Novel oligonucleotide primers reveal a high diversity of microbes which drive phosphorous turnover in soil.

Phosphorus (P) is of central importance for cellular life but likewise a limiting macronutrient in numerous environments. Certainly microorganisms have proven their ability to increase the phosphorus bioavailability by mineralization of organic-P and solubilization of inorganic-P. On the other hand they efficiently take up P and compete with other biotas for phosphorus. However the actual microbial community that is associated to the turnover of this crucial macronutrient in different ecosystems remains largely anonymous especially in taking effects of seasonality and spatial heterogeneity into account. In this study seven oligonucleotide primers are presented which target genes coding for microbial acid and alkaline phosphatases (phoN, phoD), phytases (appA), phosphonatases (phnX) as well as the quinoprotein glucose dehydrogenase (gcd) and different P transporters (pitA, pstS). Illumina amplicon sequencing of soil genomic DNA underlined the high rate of primer specificity towards the respective target gene which usually ranged between 98% and 100% (phoN: 87%). As expected the primers amplified genes from a broad diversity of distinct microorganisms. Using DNA from a beech dominated forest soil, the highest microbial diversity was detected for the alkaline phosphatase (phoD) gene which was amplified from 15 distinct phyla respectively 81 families. Noteworthy the primers also allowed amplification of phoD from 6 fungal orders. The genes coding for acid phosphatase (phoN) and the quinoprotein glucose dehydrogenase (gcd) were amplified from 20 respectively 17 different microbial orders. In comparison the phytase and phosphonatase (appA, phnX) primers covered 13 bacterial orders from 2 different phyla respectively. Although the amplified microbial diversity was apparently limited to both primers that reliably detected all orders that contributed to the P turnover in the investigated soil as revealed by a previous metagenomic approach. Genes that code for microbial P transporter (pitA, pstS) were amplified from 13 respectively 9 distinct microbial orders. Accordingly the introduced primers represent a valuable tool for further analysis of the microbial community involved in the turnover of phosphorus in soils but most likely also in other environments

Temporal variations of phosphorus uptake by soil microbial biomass and young beech trees in two forest soils with contrasting phosphorus stocks.

The objective of this study was to determine temporal variations of phosphorus (P) uptake by young beech trees (Fagus sylvatica L.) and soil microorganisms in two forests with contrasting P stocks with the aim to better understand P dynamics in forest ecosystems. For this purpose, we conducted a mesocosm experiment and determined P uptake by F. sylvatica, total soil microbial biomass (SMB) and ectomycorrhizal fungi (EMF) at the root tip based on P-33 labeling at five times during the year. Furthermore, we measured EMF community composition, potential acid phosphatase activity (APA), and abundance of bacterial acid phosphatase (phoN) genes. The results showed that plant P uptake was elevated in summer and autumn in the mesocosms from the P-poor site, while it was elevated only in autumn in the mesocosms from the P-rich site. P uptake by SMB was higher in the organic layer at the P-poor site than in the organic layer at the P-rich site throughout the year, underlining the importance of the microbial P pool in the organic layer of P-poor forests. The finding shows that the SMB was able to compensate for the lower P availability in the soil of the P-poor site. The EMF community composition was very variable over the year, and plant P uptake seemed to be independent of EMF community composition. Despite the high species turnover in the EMF community, the potential APA was high throughout the year, indicating functional redundancy of the microbial community with respect to P mineralization. Taken together, our results show important differences in temporal patterns of P uptake by F. sylvatica and the SMB as well as in the total partitioning of P between the SMB and F. sylvatica across the sites. Moreover, decreasing P availability in forests would not only change the size of P stocks and of P cycling rates, but would also affect temporal dynamics of P uptake and the overall partitioning of P between different biotic compartments