A Conceptual Framework for Understanding the Biogeochemistry of Dry Riverbeds Through the Lens of Soil Science

Intermittent rivers and ephemeral streams (IRES) encompass fluvial ecosystems that eventually stop flowing and run dry at some point in space and time. During the dry phase, channels of IRES consist mainly of dry riverbeds (DRBs), prevalent yet widely unexplored ecotones between dry and wet phases that can strongly influence the biogeochemistry of fluvial networks. DRBs are often overlooked because they do not strictly belong to either domain of soil or freshwater science. Due to this dual character of DRBs, we suggest that concepts and knowledge from soil science can be used to expand the understanding of IRES biogeochemistry. Based on this idea, we propose that DRBs can be conceptually understood as early stage soils exhibiting many similarities with soils through two main forces: i) time since last sediment transport event, and ii) the development status of stabilizing structures (e.g. soil crusts and/or vascular plants). Our analysis suggests that while DRBs and soils may differ in master physical attributes (e.g. soil horizons vs fluvial sedimentary facies), they become rapidly comparable in terms of microbial communities and biogeochemical processes. We further propose that drivers of DRBs biogeochemistry are similar to those of soils and, hence, concepts and methods used in soil science are transferable to DRBs research. Finally, our paper presents future research directions to advance the knowledge of DRBs and to understand their role in the biogeochemistry of intermittent fluvial networks

DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work

Effective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requires reliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and content quality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are particularly important if molecular identification tools are to be implemented in biomonitoring and reports in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). We analysed gaps in the two most important reference databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a focus on the taxa most frequently used in WFD and MSFD. Our analyses show that coverage varies strongly among taxonomic groups, and among geographic regions. In general, groups that were actively targeted in barcode projects (e.g. fish, true bugs, caddisflies and vascular plants) are well represented in the barcode libraries, while others have fewer records (e.g. marine molluscs, ascidians, and freshwater diatoms). We also found that species monitored in several countries often are represented by barcodes in reference libraries, while species monitored in a single country frequently lack sequence records. A large proportion of species (up to 50%) in several taxonomic groups are only represented by private data in BOLD. Our results have implications for the future strategy to fill existing gaps in barcode libraries, especially if DNA metabarcoding is to be used in the monitoring of European aquatic biota under the WFD and MSFD. For example, missing species relevant to monitoring in multiple countries should be prioritized for future collaborative programs. We also discuss why a strategy for quality control and quality assurance of barcode reference libraries is needed and recommend future steps to ensure full utilisation of metabarcoding in aquatic biomonitoring.This paper is a deliverable of the European Cooperation in Science and Technology (COST) Action DNAqua-Net (CA15219) Working Group 1, led by Torbjørn Ekrem and Fedor Čiampor. Thanks to the University of Minho and University of Pécs for hosting workshops and working group meetings. We also thank staff at National Environment Agencies and others that provided national checklists of taxa used in biomonitoring, and otherwise assisted with checklist proof-reading: Jarmila Makovinská and Emília Mišíková Elexová (Slovakia); Steinar Sandøy and Dag Rosland (Norway); Mišel Jelič (Croatia); Marlen Vasquez (Cyprus); Adam Petrusek (Czech Republic); Kristel Panksep (Estonia); Panagiotis Kaspiditis (Greece); Matteo Montagna (Italy); Marija Katarzyte (Lithuania); Ana Rotter (Slovenia); Rosa Trabajo (Spain); Florian Altermatt (Switzerland); Kristian Meissner (Finland), Rigers Bakiu (Albania), Valentina Stamenkovic and Jelena Hinic (Macedonia); Patricia Mergen (Belgium); Gael Denys & the French Biodiversity Agency (France); Mary Kelly-Quinn (Ireland); Piotr Panek and Andrzej Zawal (Poland); Cesare Mario Puzzi (Italy); Carole Fitzpatrick (United Kingdom); Simon Vitecek (Austria); Ana Filipa Filipe (Portugal); Peter Anton Stæhr & Anne Winding (Denmark); Michael Monaghan (Germany); Alain Dohet, Lionel L'Hoste, Nora Welschbillig & Luc Ector (Luxembourg), Lujza Keresztes, (Romania). The authors also want to thank Dirk Steinke for providing the original European ERMS list for marine taxa and Florian Malard for comments on the manuscript. The preparation of the AMBI checklist was carried out in the scope of a Short-term Scientific Mission (ECOST-STSM-CA15219-150217- 082111) granted to SD visiting AZTI, Spain. ZC was supported by grants EFOP-3.6.1.-16-2016-00004 and 20765-3/2018/FEKUTSTRAT. TE was supported by the NorBOL-grant (226134/F50) from the Research Coun cil of Norway. BR, FL and MFG contributed through support from the GBOL project, which is generously funded by the German Federal Min istry of Education and Research (FKZ 01LI1101 and 01LI1501). MG contributed through support of the Polish National Science Centre, grants N N303 5794 39 and 2014/15/B/NZ8/00266. SF was funded by the project PORBIOTA - Portuguese E-Infrastructure for Information and Research on Biodiversity (POCI-01-0145-FEDER-022127), supported by Operational Thematic Program for Competitiveness and Internationalization (POCI), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (FEDER)

Effects of Different Water Management and Fertilizer Applications on CO2 Fluxes from a Selected Myanmar Rice (Oryza sativa L.) Cultivar

The application of nitrogen fertilizer and the water management practices are important to optimize potential yields in rice cultivation. Moreover, they may affect the emissions patterns of methane (CH4) and carbon dioxide (CO2) emission. Compared to methane, knowledge about the combined effects of different fertilizer rates together with different water management practices on CO2 fluxes are scarce. Therefore, this study aims to assess CO2 fluxes of a selected rice cultivar in response to different fertilizer applications and water management practices. The treatments included two different applications of inorganic fertilizer (recommended rate and farmer’s practice), organic manure application and water management practices; continuous flooding (CF) and alternate wetting and drying (AWD). Mean total CO2 flux in CF was -30.82 g CO2 m-2 d-1 during daytime and 29.64 g CO2 m-2 d-1 during nighttime. Surprisingly, the average net CO2 fluxes were negative under both CF (-49 mg CO2 m-2h-1) and AWD practices (-127 mg CO2 m-2h-1), indicating a net CO2 uptake by the rice plants. Inorganic fertilizer applications led to considerably higher net CO2 emissions compared to the control under both CF and AWD. Conversely, CO2 emission fluxes in the treatment with organic manure showed negative net CO2 fluxes under both water management practices and while revealing the same fresh biomass as observed in other treatments (inorganic fertilizer and control). Taken together, modifications of current cultivation systems toward using organic manure, that emit less CO2, could effectively mitigate CO2 impacts regardless of the selected water management practice

Methane Dynamics in a Large River - a Case Study of the Elbe River

We conducted multiple small (2011–2012) and one large sampling campaign (2013) at selected profiles along the Elbe River. With the data we were able to outline spatial and temporal variability of methane concentration, oxidation and emissions in one of the major rivers of Central Europe. The highest methane concentrations were found in human-altered riverine habitats, i.e., in a harbor (1,888 nmol L−1), in a lock and weirs (1409 ± 1545 nmol L−1), and in general in the whole “impounded” river segment (383 ± 215 nmol L−1). On the other hand, the lowest methane concentrations were found in the “lowland” river segment (86 ± 56 nmol L−1). The methane oxidation rate was more efficient in the “natural” segment (71 ± 113 nmol L−1day−1, which means a turnover time of 49 ± 83 day−1) than in the “lowland” segment (4 ± 3 nmol L−1day−1, which means a turnover time of 39 ± 45 day−1). Methane emissions from the surface water into the atmosphere ranged from 0.4 to 11.9 mg m−2 day−1 (mean 2.1 ± 0.6 mg m−2 day−1) with the highest CH4 emissions at the Meissen harbor (94 kg CH4 year−1). Such human-altered riverine habitats (i.e., harbors and similar) have not been taken into consideration in the CH4 budget before, despite them being part of the river ecosystems, they may be significant CH4 hot-spots. The total CH4 diffusive flux from the whole Elbe was estimated to be approximately 97 t CH4 year−1

Towards a DNA Barcode Reference Database for Spiders and Harvestmen of Germany

<div><p>As part of the German Barcode of Life campaign, over 3500 arachnid specimens have been collected and analyzed: ca. 3300 Araneae and 200 Opiliones, belonging to almost 600 species (median: 4 individuals/species). This covers about 60% of the spider fauna and more than 70% of the harvestmen fauna recorded for Germany. The overwhelming majority of species could be readily identified through DNA barcoding: median distances between closest species lay around 9% in spiders and 13% in harvestmen, while in 95% of the cases, intraspecific distances were below 2.5% and 8% respectively, with intraspecific medians at 0.3% and 0.2%. However, almost 20 spider species, most notably in the family Lycosidae, could not be separated through DNA barcoding (although many of them present discrete morphological differences). Conspicuously high interspecific distances were found in even more cases, hinting at cryptic species in some instances. A new program is presented: DiStats calculates the statistics needed to meet DNA barcode release criteria. Furthermore, new generic COI primers useful for a wide range of taxa (also other than arachnids) are introduced.</p></div

Statistics for closest species pairs and most distant congeneric pairs.

<p>Statistics for closest species pairs and most distant congeneric pairs.</p

Number of species sampled per family (excluding families represented only by 1 or 2 species in this study).

<p>Numbers above bars are percentages showing species coverage for Germany, as derived from the checklists mentioned in the text. Family names prefixed with "O." belong to Opiliones, all others are spider families.</p

List of primers used for amplification and sequencing of the 5' part of the mitochondrial COI gene.

<p>List of primers used for amplification and sequencing of the 5' part of the mitochondrial COI gene.</p