How, not if, is the question mycologists should be asking about DNA-based typification

Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside the scope of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings chal-lenge the present stance of some in the mycological community - that the current situation is satisfactory and that no change is needed to "the code" - and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. The present authors hope for a revitalized and deepened discussion on DNA-based typification, because to us it seems harmful and counter-productive to intentionally deny the overwhelming majority of extant fungi a formal standing under the International Code of Nomenclature for algae, fungi, and plants

DNA Glycosylases Involved in Base Excision Repair May Be Associated with Cancer Risk in BRCA1 and BRCA2 Mutation Carriers

Peer reviewe

Exploring the taxonomic composition of two fungal communities on the Swedish west coast through metabarcoding

Fungi are heterotrophic, unicellular or filamentous organisms that exhibit a wide range of different lifestyles as, e.g., symbionts, parasites, and saprotrophs. Mycologists have traditionally considered fungi to be a nearly exclusively terrestrial group of organisms, but it is now known that fungi have a significant presence in aquatic environments as well. We know little about most fungi in limnic and marine systems, including aspects of their taxonomy, ecology, and geographic distribution. The present study seeks to improve our knowledge of fungi in the marine environment. The fungal communities of two coastal marine environments of the Kattegat sea, Sweden, were explored with metabarcoding techniques using the nuclear ribosomal internal transcribed spacer 2 (ITS2) metabarcode. Our data add new information to the current picture of fungal community composition in benthic and coastal habitats in Northern Europe. The dataset describes the number of operational taxonomic units (OTUs) and their taxonomic affiliations in two littoral gradients sampled on the Swedish west coast, Gothenburg municipality. Our data include basic diversity indices as well as chemical and edaphic sediment/soil parameters of the sampling sites. From the sites, 3470 and 4315 fungal OTUs, respectively, were recovered. The number of reads were 673,711 and 779,899, respectively, after quality filtering. Within the benthic sites, more than 80% of the sequences could not be classified taxonomically. The phylum composition of the classifiable sequences was dominated in both localities by Dikarya, which made up around 33% of the OTUs. Within Dikarya, Ascomycota was the dominant phylum. Guild assignment failed for more than half of the classifiable OTUs, with undefined saprotrophs being the most common resolved guild. This guild classification was slightly more common in the ocean sediment samples than in the terrestrial ones. Our metadata indicated that ocean sites contain organisms at a lower trophic level and that there are predominantly endophytic, parasitic, and pathogenic fungi in the marine environments. This hints at the presence of interesting and currently poorly understood fungus-driven ecological processes. It is also clear from our results that a very large number of marine fungi are in urgent need of taxonomic study and formal description

From the Mountain to the Valley - Drivers of Groundwater Prokaryotic Communities along an Alpine River Corridor

Rivers extend into the underlying groundwater which represents the unseen freshwater majority. Understanding microbial community composition and dynamics of shallow groundwater and lotic ecosystems is thus crucial, due to their potential impact on ecosystem processes and functioning.A 300 km section of the Mur river valley, from 2000 m.a.s.l. in the Austrian alps to the flats (200 m.a.s.l.) at the Slovenian border, was followed, analyzing river water from 14 stations and groundwater from 45 wells in early summer and late autumn. The active (RNA derived) and total prokaryotic communities were characterized using high-throughput gene amplicon sequencing. Key physico-chemical parameters and stress indicators were recorded. The groundwater microbiome is analyzed regarding its composition, change with land use, and difference to the river. Community composition and species turnover differed significantly. At high altitudes, dispersal limitation was the main driver of groundwater community assembly, whereas in the lowland, homogeneous selection explained the larger share. Land use was a key determinant of the groundwater microbiome composition. The alpine region was more diverse in prokaryotic taxa, with some early diverging archaeal lineages being highly abundant. This dataset shows a longitudinal change in prokaryotic communities that is dependent on regional differences affected by geomorphology and land use

Grundwasser / High-resolution monitoring of groundwater quality in unconsolidated aquifers using UV-Vis spectrometry

Die Grundwasserqualit\ue4t wird in vielen L\ue4ndern routinem\ue4 fig im Rahmen einer Jahres- oder Quartalsbeprobung \ufcberwacht. Diese Beprobungsfrequenz kann allerdings in manchen F\ue4llen nicht gen\ufcgen, um die zeitliche Dynamik der Grundwasserqualit\ue4t, wie zum Beispiel saisonale Schwankungen oder die Reaktion auf Extremereignisse, zu erfassen. Ein L\uf6sungsansatz ist es, vor-Ort Messsysteme, wie zum Beispiel UV-Vis Spektrometer zu nutzen. Anhand von Nitrat als h\ue4ufigem Schadstoff im Grundwasser wurde die Eignung dieser Sensoren f\ufcr eine zeitlich hochaufgel\uf6ste Grundwasser\ufcberwachung in oberfl\ue4chennahen Lockergesteinsaquiferen untersucht. Die In-Situ-Nitratmessungen in den vier ausgew\ue4hlten Pegeln zeigten eine weitestgehend gute cbereinstimmung mit den Labormessungen aus bepumpten Proben. Unsere Ergebnisse zeigen jahreszeitliche \uc4nderungen und, an zwei der vier Standorte, ausgepr\ue4gte kurzzeitige Schwankungen im Nitratgehalt, einhergehend mit Niederschlagsereignissen, \uc4nderungen im Grundwasserspiegel und der Grundwassertemperatur. Diese kurzzeitigen Schwankungen, und somit die urs\ue4chlichen Zusammenh\ue4nge mit hydrologischen Ereignissen und Landnutzung, werden bei konventionellen Probennahmeprogrammen \ufcbersehen und bergen das Risiko von nicht repr\ue4sentativen Datenreihen bei einer ung\ufcnstig getakteten, konventionellen Beprobung. Weiterhin geben wir praktische Hinweise f\ufcr den Einsatz des Sensors.In many countries, groundwater quality is routinely monitored in yearly or quarterly intervals. Such frequencies, however, may not be sufficient for investigations into the temporal dynamics of water quality, due to seasonal variability or responses to extreme events. One approach to overcome this limitation is the use of in-situ sensors, such as UV-Vis spectrometers. With a focus on nitrate as an abundant groundwater contaminant, we explored the suitability of these sensors for high-resolution groundwater monitoring in shallow unconsolidated oxic aquifers. In-situ nitrate measurements in four selected wells compared well with values from lab analyses determined in pumped groundwater samples. Most importantly, our results revealed distinct seasonal patterns and, at two sites, pronounced short-term fluctuations in nitrate concentrations concomitant to patterns observed in precipitation, hydraulic head and groundwater temperature. Such dynamics in water quality, and thus the causal relationship with hydrological events and land use, will unfortunately be overlooked when following conventional sampling schemes with the risk of non-representative time series if routine sampling is timed unfavorably. Finally, we provide practical advice for deployment of the sensor.Version of recor

Microorganisms / From the Mountain to the Valley: Drivers of Groundwater Prokaryotic Communities along an Alpine River Corridor

Rivers are the \u201ctip of the iceberg\u201d, with the underlying groundwater being the unseen freshwater majority. Microbial community composition and the dynamics of shallow groundwater ecosystems are thus crucial, due to their potential impact on ecosystem processes and functioning. In early summer and late autumn, samples of river water from 14 stations and groundwater from 45 wells were analyzed along a 300 km transect of the Mur River valley, from the Austrian alps to the flats at the Slovenian border. The active and total prokaryotic communities were characterized using high-throughput gene amplicon sequencing. Key physico-chemical parameters and stress indicators were recorded. The dataset was used to challenge ecological concepts and assembly processes in shallow aquifers. The groundwater microbiome is analyzed regarding its composition, change with land use, and difference to the river. Community composition and species turnover differed significantly. At high altitudes, dispersal limitation was the main driver of groundwater community assembly, whereas in the lowland, homogeneous selection explained the larger share. Land use was a key determinant of the groundwater microbiome composition. The alpine region was more diverse and richer in prokaryotic taxa, with some early diverging archaeal lineages being highly abundant. This dataset shows a longitudinal change in prokaryotic communities that is dependent on regional differences affected by geomorphology and land use.Version of recor

How, not if, is the question mycologists should be asking about DNA-based typification

Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside the scope of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings chal-lenge the present stance of some in the mycological community - that the current situation is satisfactory and that no change is needed to "the code" - and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. The present authors hope for a revitalized and deepened discussion on DNA-based typification, because to us it seems harmful and counter-productive to intentionally deny the overwhelming majority of extant fungi a formal standing under the International Code of Nomenclature for algae, fungi, and plants.ISSN:1314-4049ISSN:1314-405

DNA Glycosylases Involved in Base Excision Repair May Be Associated with Cancer Risk in BRCA1 and BRCA2 Mutation Carriers

Single Nucleotide Polymorphisms (SNPs) in genes involved in the DNA Base Excision Repair (BER) pathway could be associated with cancer risk in carriers of mutations in the high-penetrance susceptibility genes BRCA1 and BRCA2, given the relation of synthetic lethality that exists between one of the components of the BER pathway, PARP1 (poly ADP ribose polymerase), and both BRCA1 and BRCA2. In the present study, we have performed a comprehensive analysis of 18 genes involved in BER using a tagging SNP approach in a large series of BRCA1 and BRCA2 mutation carriers. 144 SNPs were analyzed in a two stage study involving 23,463 carriers from the CIMBA consortium (the Consortium of Investigators of Modifiers of BRCA1 and BRCA2). Eleven SNPs showed evidence of association with breast and/or ovarian cancer at p<0.05 in the combined analysis. Four of the five genes for which strongest evidence of association was observed were DNA glycosylases. The strongest evidence was for rs1466785 in the NEIL2 (endonuclease VIII-like 2) gene (HR: 1.09, 95% CI (1.03-1.16), p = 2.7×10 −3) for association with breast cancer risk in BRCA2 mutation carriers, and rs2304277 in the OGG1 (8-guanine DNA glycosylase) gene, with ovarian cancer risk in BRCA1 mutation carriers (HR: 1.12 95%CI: 1.03-1.21, p = 4.8×10 −3). DNA glycosylases involved in the first steps of the BER pathway may be associated with cancer risk in BRCA1/2 mutation carriers and should be more comprehensively studied. Women harboring a germ-line mutation in the BRCA1 or BRCA2 genes have a high lifetime risk to develop breast and/or ovarian cancer. However, not all carriers develop cancer and high variability exists regarding age of onset of the disease and type of tumor. One of the causes of this variability lies in other genetic factors that modulate the phenotype, the so-called modifier genes. Identification of these genes might have important implications for risk assessment and decision making regarding prevention of the disease. Given that BRCA1 and BRCA2 participate in the repair of DNA double strand breaks, here we have investigated whether variations, Single Nucleotide Polymorphisms (SNPs), in genes participating in other DNA repair pathway may be associated with cancer risk in BRCA carriers. We have selected the Base Excision Repair pathway because BRCA defective cells are extremely sensitive to the inhibition of one of its components, PARP1. Thanks to a large international collaborative effort, we have been able to identify at least two SNPs that are associated with increased cancer risk in BRCA1 and BRCA2 mutation carriers respectively. These findings could have implications not only for risk assessment, but also for treatment of BRCA1/2 mutation carriers with PARP inhibitors

p-values of association (−log10 scale) with breast cancer risk in <i>BRCA2</i> carriers for genotyped and imputed SNPs in the <i>NEIL2</i> gene.

<p>SNP rs1466785 is indicated with a purple arrow and the best causal imputed SNPs, rs804276 and rs804271 are indicated with a red arrow. Colors represent the pariwise r². Plot generated with LocusZoom <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004256#pgen.1004256-Pruim1" target="_blank">[42]</a> (<a href="http://csg.sph.umich.edu/locuszoom/" target="_blank">http://csg.sph.umich.edu/locuszoom/</a>).</p