Distribution of denitrifying bacterial communities in the stratified water column and sediment-water interface in two freshwater lakes and the Baltic Sea

We have studied the distribution and community composition of denitrifying bacteria in the stratified water column and at the sediment-water interface in lakes Plusee and Schohsee, and a near-shore site in the Baltic Sea in Germany. Although environmental changes induced by the stratification of the water column in marine environments are known to affect specific populations of denitrifying bacteria, little information is available for stratified freshwater lakes and brackish water. The aim of the present study was to fill this gap and to demonstrate specific distribution patterns of denitrifying bacteria in specific aquatic habitats using two functional markers for the nitrite reductase (nirK and nirS genes) as a proxy for the communities. The leading question to be answered was whether communities containing the genes nirK and nirS have similar, identical, or different distribution patterns, and occupy the same or different ecological niches. The genes nirK and nirS were analyzed by PCR amplification with specific primers followed by terminal restriction fragment length polymorphism (T-RFLP) and by cloning and sequence analysis. Overall, nirS-denitrifiers were more diverse than nirK-denitrifiers. Denitrifying communities in sediments were clearly different from those in the water column in all aquatic systems, regardless of the gene analyzed. A differential distribution of denitrifying assemblages was observed for each particular site. In the Baltic Sea and Lake Plusee, nirK-denitrifiers were more diverse throughout the water column, while nirS-denitrifiers were more diverse in the sediment. In Lake Schohsee, nirS-denitrifiers showed high diversity across the whole water body. Habitat-specific clusters of nirS sequences were observed for the freshwater lakes, while nirK sequences from both freshwater lakes and the Baltic Sea were found in common phylogenetic clusters. These results demonstrated differences in the distribution of bacteria containing nirS and those containing nirK indicating that both types of denitrifiers apparently occupy different ecological niches.

Benthic Biofilms in Glacier-Fed Streams from Scandinavia to the Himalayas Host Distinct Bacterial Communities Compared with the Streamwater

Tom Ian Battin, Massimo Bourquin, Jade Brandani, Susheel Bhanu Busi, Vincent Henri De Staercke, Leïla Ezzat, Stylianos Fodelianakis, Tyler Joe Kohler, Grégoire Marie Octave Edouard Michoud, Emmy Marie Oppliger, Hannes Markus Peter, Paraskevi Pramateftaki, Martina Andrea Schön, Michail Styllas, Virginia Tadei, Matteo Tolosano

Microbial life in glacier-fed streams (GFSs) is dominated by benthic biofilms which fulfill critical ecosystem processes. However, it remains unclear how the bacterial communities of these biofilms assemble in stream ecosystems characterized by rapid turnover of benthic habitats and high suspended sediment loads. Using16S rRNA gene amplicon sequence data collected from 54 GFSs across the Himalayas, European Alps, and Scandinavian Mountains, we found that benthic biofilms harbor bacterial communities that are distinct from the bacterial assemblages suspended in the streamwater. Our data showed a decrease in species richness in the benthic biofilms compared to the bacterial cells putatively free-living in the water. The benthic biofilms also differed from the suspended water fractions in terms of community composition. Differential abundance analyses highlighted bacterial families that were specific to the benthic biofilms and the suspended assemblages. Notably, source-sink models suggested that the benthic biofilm communities are not simply a subset of the suspended assemblages. Rather, we found evidence that deterministic processes (e.g., species sorting) shape the benthic biofilm communities. This is unexpected given the high vertical mixing of water and contained bacterial cells in GFSs and further highlights the benthic biofilm mode of life as one that is determined through niche-related processes. Our findings therefore reveal a "native" benthic biofilm community in an ecosystem that is currently threatened by climate-induced glacier shrinkage. IMPORTANCE Benthic biofilms represent the dominant form of life in glacier-fed streams. However, it remains unclear how bacterial communities within these biofilms assemble. Our findings from glacier-fed streams from three major mountain ranges across the Himalayas, the European Alps and the Scandinavian Mountains reveal a bacterial community associated with benthic biofilms that is distinct from the assemblage in the overlying streamwater. Our analyses suggest that selection is the underlying process to this differentiation. This is unexpected given that bacterial cells that are freely living or attached to the abundant sediment particles suspended in the water continuously mix with the benthic biofilms. The latter colonize loose sediments that are subject to high turnover owing to the forces of the water flow. Our research unravels the existence of a microbiome specific to benthic biofilms in glacier-fed streams, now under major threats due to global warming. Benthic biofilms represent the dominant form of life in glacier-fed streams. However, it remains unclear how bacterial communities within these biofilms assemble.

AMER SOC MICROBIOLOGY2022

Typologie des eaux souterraines de la molasse entre Chambéry et Linz (France, Suisse, Allemagne, Autriche)

The geochemical typology of natural subsurface waters of the Molasse basin is part of the AQUITYP project, initiated by the Geology Laboratory (GEOLEP) of the Swiss Federal Institute of Technology in Lausanne (EPFL). This study provides an overview of the variation in space of the hydrochemical parameters, especially of trace elements, in order to determine the geological origin of their aquifers. Our data base is mainly made up of two observation networks: a subsurface water network and a deep groundwater network. Complete analyses of all samples have been executed using standard methods for anions and silicium, and high resolution inductively coupled mass spectrometry (HR-ICP-MS) for major cations and trace elements down to the detection limit of about 0.2 µg/l. Subsurface water network It is the main observation network of this investigation and comprises 112 water samples from different springs, collected all over the Molasse basin between Chambéry (France) and Linz (Austria), but mainly in the Swiss Molasse basin. For this region, four groups are generally distinguished, according to the sediment deposition in a continental or marine environment, in ascending stratigraphic order: (1) the Lower Marine Molasse (UMM and North Helvetic "flysch" p.p.), (2) the Lower Freshwater Molasse (USM), (3) the Upper Marine Molasse (OMM) and (4) the Upper Freshwater Molasse (OSM). Our water samples originate from typical sedimentary deposits which we divided in about 30 different sub-type aquifers according to their geological origin and their depositional environment. They are defined on the basis of lithological and structural homogeneity. Therefore, only catchments that completely drain a single, lithologically homogenous, Molasse terrain unit are considered here. Spring catchments selected were generally not affected by runoff from towns, or paved roads. Agricultural activities have been avoided as well as possible. Such spring water should be free of major human influences and only in few cases contain a certain amount of fertilizer products (p.ex: nitrates). Leachate tests of crushed rocks and comparison with snow and soil water compositions allowed to decipher the geogene origin of the dissolved ions in natural groundwaters. The water withdrawn can be generally classified as a calcium-magnesium-hydrogenocarbonate (Ca-Mg-HCO3)-type water. The trace analyses allowed to distinguish several subtypes within this homogenous water type group. The general spacial distribution of the trace elements show, that spring waters in the Bavarian Molasse basin are caracterized by elements as lithium and uranium linked to acid rocks, while those of the Swiss Molasse basin are preferentially influenced by elements derived from mafic or ultramafic rocks, such as chromium and cobalt. The following elements show specific links between aquifer rock type and groundwater. Sulfates: Total mineralisation of spring waters issued from the gypse-bearing Molasse (USM) and the "Glimmersande" (OSM) are highly influenced by high sulfate contents. It can be demonstrated that sulfate ions are produced from two different sources within this two sub-type aquifers: from the dissolution of gypsum in water, producing high calcium contents as well, and from the oxydation of sulfurous ore minerals, especially pyrite, which are abundant in the "Glimmersande". The "Glimmersand" aquifers in NE Switzerland are furtheron caracterized by high lithium, molybdenum and uranium concentrations, reflecting the granitic composition of this sandstones. High barium contents (>150 µg/l) have been found in spring waters issued from aquifers with a dominant fissure permeability ("Grès de la Cornalle", "Gibloux-Delta" and "Rigi-Schüttung"). Its origin is supposed to be the mineral barite, which tends to precipitate in fractures. Therefore, high barium concentrations may indicate the presence of fracture flow within the aquifer. Considerably high silicon contents are linked to the quartzitic and fine grained aquifers of the brackish marine molasse in Bavaria. Both, petrographical composition and slow flow rate are favouring the water-rock interaction. Caracteristic lithium footprints are found in several waters, as in the aquifers composed of the "Glimmersande", the gypse-bearing molasse, the Rigi-conglomerates, the brackish and the estuarine marine molasse. Chromium strongly marks the waters originating from the Swiss marine Molasse aquifers. It is probably related to ophiolithic detritus derived from the flysch of the Prealpes. A couple of waters show weak anomalies of cobalt, which are nevertheless intimately linked to the presence of ophiolithic components in the sediments. Cobalt might be used as a hydrostratigraphical tool to identify greenstone inputs. Analysed colloidal aluminum may serve as a hydrodynamical parameter, indicating microturbidity within the aquifer. High amounts of aluminum varying in time, have been found in estuarin deposits of the OMM. Generally speaking, we propose three main origins of trace elements in the spring water of the Molasse basin: presence of certain petrographical components within the sediments such as basic and ultrabasic rocks, heavy minerals and evaporites. a small flow rate through interstitial porosity of fine grained sediments, favouring water-rock interaction. the abundance of colloidal material in the waters which depends on the petrographical composition of the aquifer and on sample treatment, e.g. filtration techniques. Deep groundwater network A second observation network composed of 21 borehole waters has been added for comparison. Compared to the subsurface waters, deep water chemistry might differ. The following reasons seem to be responsible: Long residence times of water in the underground favours slow reaction kinetics. Chemistry of very deep water can be influenced by mixing with older formation waters. Most of the deep boreholes in the Swiss Molasse basin are situated in the OMM and therefore represent a likely homogenous lithology. Borehole waters, because of different aquifer rock types and unknown surface and borehole influences, are least likely to represent typical Molasse water composition.

EPFL1995

Horizontal distribution patterns of testate amoebae (Protozoa) in a Sphagnum magellanicum carpet

Daniel Borcard, Alexandre Buttler, Jean-Michel Gobat, Edward Mitchell

The distribution of soil microorganisms is generally believed to be patchy and to reflect habitat heterogeneity. Despite this general rule, the amount of existing data oil species distribution patterns is scarce. Testate amoebae (Protozoa; Rhizopoda) are an important component of soil microbial communities and are increasingly used in ecological and paleoecological studies of Sphagnum-dominated peatlands, but data on the spatial structure of communities are completely lacking. This is an important aspect since quantitative models used for paleoecological reconstruction and monitoring are based on species assemblages. We explored the distribution patterns of testate amoebae distribution in a macroscopically homogeneous Sphagnum carpet, down to a scale of several centimeters. Distributions maps of the species and spatially constrained sample groups were produced. Multivariate and individual spatial autocorrelations were calculated. The importance of spatial structure was quantified by canonical correspondence analysis. Our ultimate goal is to find the finest resolution of environmental monitoring using testate amoebae. The distribution patterns differed among species, resulting in a complex spatial structure of the species assemblage in a whole. Spatial structure accounted for 36% of the total variation of species abundance in a canonical correspondence analysis constrained by spatial variables. This structure was partly correlated to altitude (microtopography) at a very fine scale. These results confirmed the existence of significant broad-and fine-scale spatial structures within restate amoebae communities that could in parr be interpreted as effects of ecological gradients. This shows that, on a surface area of 0.25 m(2), ecological conditions which look uniform from a macroscopic point of view are not perceived as such by Sphagnum-inhabiting organisms. Therefore, restate amoebae could prove very useful to monitor fine-scale ecological processes or disturbances. Studies of the species' spatial distribution patterns in combination with autoecological studies are needed and should be included in the toolbox of biomonitoring itself.

2000