International audience | Endophytic bacteria from roots and crude seed extracts of a Cu-tolerant population of Agrostis capillaris were inoculated to a sunflower metal-tolerant mutant line, and their influence on Cu tolerance and phytoextraction was assessed using a Cu-contaminated soil series. Ten endophytic bacterial strains isolated from surface-sterilized A. capillaris roots were mixed to prepare the root endophyte inoculant (RE). In parallel, surface-sterilized seeds of A. capillaris were crushed in MgSO4 to prepare a crude seed extract containing seed endophytes (SE). An aliquot of this seed extract was filtered at 0.2 μm to obtain a bacterial cell-free seed extract (SEF). After surface sterilization, germinated sunflower seeds were separately treated with one of five modalities: no treatment (C), immersion in MgSO4 (CMg) or SEF solutions and inoculation with RE or SE. All plants were cultivated on a Cu-contaminated soil series (13-1020 mg Cu kg(-1)). Cultivable RE strains were mostly members of the Pseudomonas genera, and one strain was closely related to Labrys sp. The cultivable SE strains belonged mainly to the Bacillus genera and some members of the Rhodococcus genera. The treatment effects depended on the soil Cu concentration. Both SE and SEF plants had a higher Cu tolerance in the 13-517 mg Cu kg(-1) soil range as reflected by increased shoot and root DW yields compared to control plants. This was accompanied by a slight decrease in shoot Cu concentration and increase in root Cu concentration. Shoot and root DW yields were more promoted by SE than SEF in the 13-114 mg Cu kg(-1) soil range, which could reflect the influence of seed-located bacterial endophytes. At intermediate soil Cu (416-818 mg Cu kg(-1) soil), the RE and CMg plants had lower shoot Cu concentrations than the control, SE and SEF plants. At high total soil Cu (617-1020 mg Cu kg(-1)), root DW yield of RE plants slightly increased and their root Cu concentration rose by up to 1.9-fold. In terms of phytoextraction efficiency, shoot Cu removal was increased for sunflower plants inoculated with crude and bacterial cell-free seed extracts by 1.3- to 2.2-fold in the 13-416 mg Cu kg(-1) soil range. Such increase was mainly driven by an enhanced shoot DW yield. The number and distribution of endophytic bacteria in the harvested sunflower tissues must be further examined.

Endophytic bacteria from roots and crude seed extracts of a Cu-tolerant population of Agrostis capillaris were inoculated to a sunflower metal-tolerant mutant line, and their influence on Cu tolerance and phytoextraction was assessed using a Cu-contaminated soil series. Ten endophytic bacterial strains isolated from surface-sterilized A. capillaris roots were mixed to prepare the root endophyte inoculant (RE). In parallel, surface-sterilized seeds of A. capillaris were crushed in MgSO₄to prepare a crude seed extract containing seed endophytes (SE). An aliquot of this seed extract was filtered at 0.2 μm to obtain a bacterial cell-free seed extract (SEF). After surface sterilization, germinated sunflower seeds were separately treated with one of five modalities: no treatment (C), immersion in MgSO₄(CMg) or SEF solutions and inoculation with RE or SE. All plants were cultivated on a Cu-contaminated soil series (13–1020 mg Cu kg⁻¹). Cultivable RE strains were mostly members of the Pseudomonas genera, and one strain was closely related to Labrys sp. The cultivable SE strains belonged mainly to the Bacillus genera and some members of the Rhodococcus genera. The treatment effects depended on the soil Cu concentration. Both SE and SEF plants had a higher Cu tolerance in the 13–517 mg Cu kg⁻¹soil range as reflected by increased shoot and root DW yields compared to control plants. This was accompanied by a slight decrease in shoot Cu concentration and increase in root Cu concentration. Shoot and root DW yields were more promoted by SE than SEF in the 13–114 mg Cu kg⁻¹soil range, which could reflect the influence of seed-located bacterial endophytes. At intermediate soil Cu (416–818 mg Cu kg⁻¹soil), the RE and CMg plants had lower shoot Cu concentrations than the control, SE and SEF plants. At high total soil Cu (617–1020 mg Cu kg⁻¹), root DW yield of RE plants slightly increased and their root Cu concentration rose by up to 1.9-fold. In terms of phytoextraction efficiency, shoot Cu removal was increased for sunflower plants inoculated with crude and bacterial cell-free seed extracts by 1.3- to 2.2-fold in the 13–416 mg Cu kg⁻¹soil range. Such increase was mainly driven by an enhanced shoot DW yield. The number and distribution of endophytic bacteria in the harvested sunflower tissues must be further examined.

International audience | Floods control greenhouse gas (GHG) emissions in floodplains; however, there is a lack of data on the impact of short-term events on emissions. We studied the short-term effect of changing groundwater (GW) depth on the emission of (GHG) carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) in two riparian grey alder (Alnus incana) stands of different age in Kambja, southern Estonia, using the opaque static chamber (five replicates in each site) and gas chromatography methods. The average carbon and total nitrogen content in the soil of the old alder (OA) stand was significantly higher than in the young alder (YA) stand. In both stands, one part was chosen for water table manipulation (Manip) and another remained unchanged with a stable and deeper GW table. Groundwater table manipulation (flooding) significantly increases CH4 emission (average: YA-Dry 468, YA-Manip 8,374, OA-Dry 468, OA-Manip 4,187 μg C m−2 h−1) and decreases both CO2 (average: OA-Dry 138, OA-Manip 80 mg C m−2 h−1) and N2O emissions (average: OA-Dry 23.1, OA-Manip 11.8 μg N m−2 h−1) in OA sites. There was no significant difference in CO2 and CH4 emissions between the OA and YA sites, whereas in OA sites with higher N concentration in the soil, the N2O emission was significantly higher than at the YA sites. The relative CO2 and CH4 emissions (the soil C stock-related share of gaseous losses) were higher in manipulated plots showing the highest values in the YA-Manip plot (0.03 and 0.0030 % C day−1, respectively). The soil N stock-related N2O emission was very low achieving 0.000019 % N day−1 in the OA-Dry plot. Methane emission shows a negative correlation with GW, whereas the 20 cm depth is a significant limit below which most of the produced CH4 is oxidized. In terms of CO2 and N2O, the deeper GW table significantly increases emission. In riparian zones of headwater streams, the short-term floods (e.g. those driven by extreme climate events) may significantly enhance methane emission whereas the long-term lowering of the groundwater table is a more important initiator of N2O fluxes from riparian gley soils than flood pulses.

Floods control greenhouse gas (GHG) emissions in floodplains; however, there is a lack of data on the impact of short-term events on emissions. We studied the short-term effect of changing groundwater (GW) depth on the emission of (GHG) carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O) in two riparian grey alder (Alnus incana) stands of different age in Kambja, southern Estonia, using the opaque static chamber (five replicates in each site) and gas chromatography methods. The average carbon and total nitrogen content in the soil of the old alder (OA) stand was significantly higher than in the young alder (YA) stand. In both stands, one part was chosen for water table manipulation (Manip) and another remained unchanged with a stable and deeper GW table. Groundwater table manipulation (flooding) significantly increases CH₄emission (average: YA-Dry 468, YA-Manip 8,374, OA-Dry 468, OA-Manip 4,187 μg C m⁻² h⁻¹) and decreases both CO₂(average: OA-Dry 138, OA-Manip 80 mg C m⁻² h⁻¹) and N₂O emissions (average: OA-Dry 23.1, OA-Manip 11.8 μg N m⁻² h⁻¹) in OA sites. There was no significant difference in CO₂and CH₄emissions between the OA and YA sites, whereas in OA sites with higher N concentration in the soil, the N₂O emission was significantly higher than at the YA sites. The relative CO₂and CH₄emissions (the soil C stock-related share of gaseous losses) were higher in manipulated plots showing the highest values in the YA-Manip plot (0.03 and 0.0030 % C day⁻¹, respectively). The soil N stock-related N₂O emission was very low achieving 0.000019 % N day⁻¹in the OA-Dry plot. Methane emission shows a negative correlation with GW, whereas the 20 cm depth is a significant limit below which most of the produced CH₄is oxidized. In terms of CO₂and N₂O, the deeper GW table significantly increases emission. In riparian zones of headwater streams, the short-term floods (e.g. those driven by extreme climate events) may significantly enhance methane emission whereas the long-term lowering of the groundwater table is a more important initiator of N₂O fluxes from riparian gley soils than flood pulses.

International audience | Microbes are phylogenetically (Archaea, Bacteria, Eukarya, and viruses) and functionally diverse. They colonize highly varied environments and rapidly respond to and evolve as a response to local and global environmental changes, including those induced by pollutants resulting from human activities. This review exemplifies the Microbial Ecology EC2CO consortium’s efforts to explore the biology, ecology, diversity, and roles of microbes in aquatic and continental ecosystems.

Microbes are phylogenetically (Archaea, Bacteria, Eukarya, and viruses) and functionally diverse. They colonize highly varied environments and rapidly respond to and evolve as a response to local and global environmental changes, including those induced by pollutants resulting from human activities. This review exemplifies the Microbial Ecology EC2CO consortium’s efforts to explore the biology, ecology, diversity, and roles of microbes in aquatic and continental ecosystems.

Microbes are phylogenetically (Archaea, Bacteria, Eukarya, and viruses) and functionally diverse. They colonize highly varied environments and rapidly respond to and evolve as a response to local and global environmental changes, including those induced by pollutants resulting from human activities. This review exemplifies the Microbial Ecology EC2CO consortium’s efforts to explore the biology, ecology, diversity, and roles of microbes in aquatic and continental ecosystems.

International audience | Antibiotics and antibiotic resistance genes have shown to be omnipresent in the environment. In this study, we investigated the effect of vancomycin (VA) on denitrifying bacteria in river sediments of a Waste Water Treatment Plant, receiving both domestic and hospital waste. We exposed these sediments continuously in flow-through reactors to different VA concentrations under denitrifying conditions (nitrate addition and anoxia) in order to determine potential nitrate reduction rates and changes in sedimentary microbial community structures. The presence of VA had no effect on sedimentary nitrate reduction rates at environmental concentrations, whereas a change in bacterial (16S rDNA) and denitrifying (nosZ) community structures was observed (determined by polymerase chain reaction-denaturing gradient gel electrophoresis). The bacterial and denitrifying community structure within the sediment changed upon VA exposure indicating a selection of a non-susceptible VA population.

International audience | Antibiotics and antibiotic resistance genes have shown to be omnipresent in the environment. In this study, we investigated the effect of vancomycin (VA) on denitrifying bacteria in river sediments of a Waste Water Treatment Plant, receiving both domestic and hospital waste. We exposed these sediments continuously in flow-through reactors to different VA concentrations under denitrifying conditions (nitrate addition and anoxia) in order to determine potential nitrate reduction rates and changes in sedimentary microbial community structures. The presence of VA had no effect on sedimentary nitrate reduction rates at environmental concentrations, whereas a change in bacterial (16S rDNA) and denitrifying (nosZ) community structures was observed (determined by polymerase chain reaction-denaturing gradient gel electrophoresis). The bacterial and denitrifying community structure within the sediment changed upon VA exposure indicating a selection of a non-susceptible VA population.

Antibiotics and antibiotic resistance genes have shown to be omnipresent in the environment. In this study, we investigated the effect of vancomycin (VA) on denitrifying bacteria in river sediments of a Waste Water Treatment Plant, receiving both domestic and hospital waste. We exposed these sediments continuously in flow-through reactors to different VA concentrations under denitrifying conditions (nitrate addition and anoxia) in order to determine potential nitrate reduction rates and changes in sedimentary microbial community structures. The presence of VA had no effect on sedimentary nitrate reduction rates at environmental concentrations, whereas a change in bacterial (16S rDNA) and denitrifying (nosZ) community structures was observed (determined by polymerase chain reaction–denaturing gradient gel electrophoresis). The bacterial and denitrifying community structure within the sediment changed upon VA exposure indicating a selection of a non-susceptible VA population.