Microbial communities in streambed sediments recovering from desiccation (original) (raw)
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PLoS ONE, 2013
Droughts are among the most important disturbance events for stream ecosystems; they not only affect stream hydrology but also the stream biota. Although desiccation of streams is common in Mediterranean regions, phases of dryness in headwaters have been observed more often and for longer periods in extended temperate regions, including Central Europe, reflecting global climate change and enhanced water withdrawal. The effects of desiccation and rewetting on the bacterial community composition and extracellular enzyme activity, a key process in the carbon flow of streams and rivers, were investigated in a typical Central European stream, the Breitenbach (Hesse, Germany). Wet streambed sediment is an important habitat in streams. It was sampled and exposed in the laboratory to different drying scenarios (fast, intermediate, slow) for 13 weeks, followed by rewetting of the sediment from the fast drying scenario via a sediment core perfusion technique for 2 weeks. Bacterial community structure was analyzed using CARD-FISH and TGGE, and extracellular enzyme activity was assessed using fluorogenic model substrates. During desiccation the bacterial community composition shifted toward composition in soil, exhibiting increasing proportions of Actinobacteria and Alphaproteobacteria and decreasing proportions of Bacteroidetes and Betaproteobacteria. Simultaneously the activities of extracellular enzymes decreased, most pronounced with aminopeptidases and less pronounced with enzymes involved in the degradation of polymeric carbohydrates. After rewetting, the general ecosystem functioning, with respect to extracellular enzyme activity, recovered after 10 to 14 days. However, the bacterial community composition had not yet achieved its original composition as in unaffected sediments within this time. Thus, whether the bacterial community eventually recovers completely after these events remains unknown. Perhaps this community undergoes permanent changes, especially after harsh desiccation, followed by loss of the specialized functions of specific groups of bacteria.
In the semiarid Mediterranean regions, water scarcity represents a common physiological stress for microbial communities residing in river sediments. However, the effect of drying has not yet adequately been evaluated when analyzing riverine microbiological processes. The bacterial community structure (abundance, biomass, composition) and functioning (carbon production, live cell percentage) were assessed during experimental desiccation in microcosms with sediments from different Mediterranean temporary rivers (Tagliamento, Krathis, Mulargia, Pardiela). Our results showed that the overall responses to drying of the bacterial community were independent from sediment origin and strictly related to water content. During desiccation, a prompt decline (up to 100%) of the initial bacterial carbon production was followed by a slower decrease in abundance and biomass, with an overall reduction of 74% and 78%, respectively. By the end of the experiment, live cells were still abundant but depressed in their main metabolic functions, thus resulting in a drastic increase in the community turnover time. Only 14% of the initial live cell biomass was available in dry sediments to immediately start the reactivation of the aquatic microbial food web after the arrival of new water. Community composition analysis showed a relative increase in alpha- and beta-Proteobacteria, when passing from wet to dry conditions. Our results suggest that the occurrence of drought events could affect carbon cycling through the freshwater microbial compartment, by temporarily limiting microbial mineralization and altering bacterial community structure.
Hydrobiologia, 2010
Temporary rivers are characterized by recurrent dry phases, and global warming will stress their hydrology by amplifying extreme events. Microbial degradation and transformation of organic matter (OM) in riverbed sediment are key processes with regard to carbon and nutrient fluxes. In this study, we describe structural and functional changes of benthic microbial communities in a riverine environment subject to hydrological fluctuation. Sampling was carried out in the outlet section of the Mulargia River (Sardinia, Italy) under various water regimes, including one flood event. Overall, sediments were characterized by low bacterial cell abundance (range 0.6-1.8 9 10 9 cell g -1 ) as a consequence of their low nutrient and OM concentrations. No major differences were found in the community composition. Alpha-Proteobacteria dominated during the whole year (range 21-30%) followed by Beta-Proteobacteria, Gamma-Proteobacteria, and Cytophaga-Flavobacteria which always contributed \18%. Planctomycetes and Firmicutes were found in smaller amounts (\7%). In spring, when the highest total organic carbon content was also detected (0.42% w/w), both bacterial abundance and C production (BCP, 170 nmol C h -1 g -1 ) reached relatively high values. During the flood event, an increase in BCP and the highest values of community respiration (CR, 74 nmol C h -1 g -1 ) were observed. Moreover, most of the extracellular enzyme activities (EEA) changed significantly during the flood. The variation of the water flow itself can explain part of these changes and other factors also come into play. The presence of different patterns of functional parameters could suggest that the quality of the OM could be the major driving force in nutrient flux.
River and stream biofilms in mediterranean fluvial ecosystems face both extreme seasonality as well as arrhythmic fluctuations. The hydrological extremes (droughts and floods) impose direct changes in water availability but also in the quantity and quality of organic matter and nutrients that sustain the microbial growth. This review analyzes how these ecological pulses might determine unique properties of biofilms developing in mediterranean streams. The paper brings together data from heterotrophic and autotrophic community structure, and extracellular enzyme activities in biofilms in mediterranean streams. Mediterranean stream biofilms show higher use of peptides during the favorable period for epilithic algae development (spring), and preferential use of cellulose and hemicellulose in autumn as a response to allochthonous input. The drying process causes the reduction in bacterial production and chlorophyll biomass, but the rapid recovery of both autotrophs and heterotrophs with rewetting indicates their adaptability to fluctuations. Bacteria surviving the drought are mainly associated with sediment and leaf litter which serve as ''humid refuges''. Some algae and cyanobacteria show resistant strategies to cope with the drought stress. The resistance to these fluctuations is strongly linked to the streambed characteristics (e.g., sediment grain size, organic matter accumulation, nutrient content).
Scientific Reports, 2019
Stream microbes that occur in the Mediterranean Basin have been shown to possess heightened sensitivity to intensified water stress attributed to climate change. Here, we investigate the effects of long-term drought (150 days), storms and rewetting (7 days) on the diversity and composition of archaea, bacteria and fungi inhabiting intermittent streambed sediment (surface and hyporheic) and buried leaves. Hydrological alterations modified the archaeal community composition more than the bacterial community composition, whereas fungi were the least affected. Throughout the experiment, archaeal communities colonizing sediments showed greater phylogenetic distances compared to those of bacteria and fungi, suggesting considerable adaptation to severe hydrological disturbances. The increase in the class abundances, such as those of Thermoplasmata within archaea and of Actinobacteria and Bacilli within bacteria, revealed signs of transitioning to a drought-favoured and soil-like community ...
Limnology and Oceanography
Heterotrophic bacteria play a key role in the degradation of organic matter and carbon cycling in river sediments. These bacterial communities are directly influenced by environmental variables that differ spatially and temporally in rivers. Here, we studied the longitudinal patterns of sediment bacterial community composition and dissolved organic matter utilization under base flow and drought conditions in a Mediterranean river. Our results indicated that sediment microbial communities were affected by dissolved organic matter quality and origin along the river continuum. In headwaters the potential degradation of cellulose and hemicellulose was greater (i.e., higher b-glucosidase and b-xylosidase activities), suggesting higher microbial utilization of allochthonous detritus from terrestrial origin. Conversely, the accumulation and transport of more recalcitrant compounds (i.e., decrease in the recalcitrant index) became potentially relevant downstream. Furthermore, discharge fluctuations had clear effects on bacterial community composition and dissolved organic matter use. The hydrological fragmentation of the river continuum during drought period generated sediment microhabitats dominated by gamma and delta-Proteobacteria, with a greater potential capacity to degrade a wide range of compounds, particularly nitrogen containing moieties. During base flow conditions, we observed a higher occurrence of alpha-Proteobacteria and a greater potential use of more recalcitrant carbon compounds, mostly of terrestrial origin. Overall, our findings suggest an upstreamdownstream longitudinal transition of sediment microbial communities that rely on allochthonous to autochthonous dissolved organic matter, and a shift toward autochthonous dissolved organic matter reliance during drought.
FEMS Microbiology Ecology, 2013
In a context of global change, alterations in the water cycle may impact the structure and function of terrestrial and aquatic ecosystems. Wetlands are particularly at risk because hydrological regime has a major influence on microbially mediated biogeochemical processes in sediments. While the influence of water availability on wetland biogeochemical processes has been comprehensively studied, the influence of hydrological regime on microbial community structure has been overlooked. We tested for the effect of hydrological regime on the structure and functions of microbial communities by comparing sediments collected at multiple sites in the Ain d epartement (Eastern France). Each site consisted of two plots, one permanently and one seasonally inundated. At the time of sampling, all plots were continuously inundated for more than 6 months but still harboured distinct bacterial communities. This change in community structure was not associated with marked modifications in the rates of microbial activities involved in the C and N cycles. These results suggest that the observed structural change could be related to bacterial taxa responding to the environmental variations associated with different hydrological regimes, but not strongly associated with the biogeochemical processes monitored here.
Organic matter availability during pre- and post-drought periods in a Mediterranean stream
Hydrobiologia, 2010
Mediterranean streams are characterized by water flow changes caused by floods and droughts. When intermittency occurs in river ecosystems, hydrologic connectivity is interrupted and this affects benthic, hyporheic and flowing water compartments. Organic matter use and transport can be particularly affected during the transition from wet to dry and dry to wet conditions. In order to characterize the changes in benthic organic matter quantity and quality throughout a drying and rewetting process, organic matter, and enzyme activities were analyzed in the benthic accumulated material (biofilms growing on rocks and cobbles, leaves, and sand) and in flowing water (dissolved and particulate fractions). The total polysaccharide, amino acid, and lipid content in the benthic organic matter were on average higher in the drying period than in the rewetting period. However, during the drying period, peptide availability decreased, as indicated by decreases in leucine aminopeptidase activity, as well as amino acid content in the water and benthic material, except leaves; while polysaccharides were actively used, as indicated by an increase in b-glucosidase activity in the benthic substrata and an increase in polysaccharide content of the particulate water fraction and in leaf material. During this process, microbial heterotrophs were constrained to use the organic matter source of the lowest quality (polysaccharides, providing only C), since peptides (providing N and C) were no longer available. During the flow recovery phase, the microbial community rapidly recovered, suggesting the use of refuges and/or adaptation to desiccation during the previous drought period. The scouring during rewetting was responsible for the mobilization of the streambed and loss of benthic material, and the increase in high quality organic matter in transport (at that moment, polysaccharides and amino acids accounted for 30% of the total DOC). The dynamics of progressive and gradual drought effects, as well as the fast recovery after rewetting, might be affected by the interaction of the individual dynamics of each benthic substratum: sand sediments and leaves providing refuge for microorganisms and organic matter storage, while on cobbles, an active bacterial community is developed in the rewetting. Since global climate change may favor a higher intensity and frequency of droughts in
Complexity of Bacterial Communities in a River-Floodplain System (Danube, Austria)
Applied and Environmental Microbiology, 2005
Natural floodplains play an essential role in the processing and decomposition of organic matter and in the self-purification ability of rivers, largely due to the activity of bacteria. Knowledge about the composition of bacterial communities and its impact on organic-matter cycling is crucial for the understanding of ecological processes in river-floodplain systems. Particle-associated and free-living bacterial assemblages from the Danube River and various floodplain pools with different hydrological characteristics were investigated using terminal restriction fragment length polymorphism analysis. The particle-associated bacterial community exhibited a higher number of operational taxonomic units (OTUs) and was more heterogeneous in time and space than the free-living community. The temporal dynamics of the community structure were generally higher in isolated floodplain pools. The community structures of the river and the various floodplain pools, as well as those of the particle-associated and free-living bacteria, differed significantly. The compositional dynamics of the planktonic bacterial communities were related to changes in the algal biomass, temperature, and concentrations of organic and inorganic nutrients. The OTU richness of the free-living community was correlated with the concentration and origin of organic matter and the concentration of inorganic nutrients, while no correlation with the OTU richness of the particle-associated assemblage was found. Our results demonstrate the importance of the river-floodplain interactions and the influence of damming and regulation on the bacterial-community composition.
Applied Sciences, 2021
Lake Alboraj, located in southeast Spain, was declared natural Microreserve and included into European Natura-2000 Network due to its contribution to environmental heritage. Unfortunately, the ecological status of the lake has changed dramatically, mainly due to the lowering of water table caused by groundwater abstractions for irrigation. It is a permanent small karstic lake whose surface has reduced in the last decades to nearly the third part of its historical water level. The water column shows a marked seasonal oxycline, that splits an aerobic upper layer (epilimnion) from an anaerobic layer below (hypolimnion). Sequencing 16S rRNA gene amplicons and applying chemical tools at epilimnion, hypolimnion and sediment, showed a clear gradient in the bacterial community structure, which support the co-existence of assimilatory and dissimilatory microbial mediated reactions. Results allows to infer that microbial stratification could provide various physical and chemical environments ...