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Antibiotics are chemotherapeutic agents, which have been a very powerful tool in the clinical management of bacterial diseases since the 1940s. However, benefits offered by these magic bullets have been substantially lost in subsequent days following the widespread emergence and dissemination of antibiotic-resistant strains. While it is obvious that excessive and imprudent use of antibiotics significantly contributes to the emergence of resistant strains, antibiotic resistance is also observed in natural bacteria of remote places unlikely to be impacted by human intervention. Both antibiotic biosynthetic genes and resistance-conferring genes have been known to evolve billions of years ago, long before clinical use of antibiotics. Hence it appears that antibiotics and antibiotics resistance determinants have some other roles in nature, which often elude our attention because of overemphasis on the therapeutic importance of antibiotics and the crisis imposed by the antibiotic resistance in pathogens. In the natural milieu, antibiotics are often found to be present in sub-inhibitory concentrations acting as signaling molecules supporting the process of quorum sensing and biofilm formation. They also play an important role in the production of virulence factors and influence host-parasite interactions (e.g., phagocytosis, adherence to the target cell, and so on). The evolutionary and ecological aspects of antibiotics and antibiotic resistance in the naturally occurring microbial community are little understood. Therefore, the actual role of antibiotics in nature warrants in-depth investigations. Studies on such an intriguing behavior of the microorganisms promise insight into the intricacies of the microbial physiology and are likely to provide some lead in controlling the emergence and subsequent dissemination of antibiotic resistance. This article highlights some of the recent findings on the role of antibiotics and the genes that confer resistance to antibiotics in nature.
Internal waves (seiches) are well-studied physical processes in stratified lakes, but their effects on sediment porewater chemistry and microbiology are still largely unexplored. Due to pycnocline oscillations, sediments are exposed to recurrent changes between epilimnetic and hypolimnetic water. This results in strong differences of environmental conditions, which should be reflected in the responses of redox-sensitive biogeochemical processes at both, the sediment-water interface and deeper sediment layers. We tested in a series of mesocosm experiments the influence of seiche-induced redox changes on porewater chemistry and bacterial activity in the sediments under well controlled conditions. Thereby, we excluded effects of changes in current and temperature regimes. For a period of 10 days, intact sediment cores from oligotrophic Lake Stechlin were incubated under constant (either oxic or anoxic) or alternating redox conditions. Solute concentrations were measured as porewater profiles in the sediment, while microbial activity was determined in the upper 0.5 cm of sediment. Oxic and alternating redox conditions resulted in similar ammonium, phosphate, and methane porewater concentrations, while concentrations of each analyte were considerably higher in anoxic cores. Microbial activity was clearly lower in the anoxic cores than in the oxic and the alternating cores. In conclusion, cores with intermittent anoxic phases of up to 24 hours do not differ in biogeochemistry and microbial activities from static oxic sediments. However, due to various physical processes seiches cause oxygen to penetrate deeper into sediment layers, which affects sediment redox gradients and increase microbial activity in seiche-influenced sediments.
We studied bacterial associations with the green alga Desmodesmus armatus and the diatom Stephanodiscus minutulus under changing environmental conditions and bacterial source communities, to evaluate whether bacteriaalgae associations are species-specific or more generalized and determined by external factors. Axenic and xenic algae were incubated in situ with and without allelopathically active macrophytes, and in the laboratory with sterile and nonsterile lake water and an allelochemical, tannic acid (TA). Bacterial community composition (BCC) of algae-associated bacteria was analyzed by denaturing gradient gel electrophoresis (DGGE), nonmetric multidimensional scaling, cluster analyses, and sequencing of DGGE bands. BCC of xenic algal cultures of both species were not significantly affected by changes in their environment or bacterial source community, except in the case of TA additions. Species-specific interactions therefore appear to overrule the effects of environmental conditions and source communities. The BCC of xenic and axenic D.armatus cultures subjected to in situ bacterial colonization, however, had lower similarities (ca.55%), indicating that bacterial precolonization is a strong factor for bacteriaalgae associations irrespective of environmental conditions and source community. Our findings emphasize the ecological importance of species-specific bacteriaalgae associations with important repercussions for other processes, such as the remineralization of nutrients, and organic matter dynamics.
Studies investigating the effect of increasing CO2 levels on the phosphorus cycle in natural waters are lacking although phosphorus often controls phytoplankton development in many aquatic systems. The aim of our study was to analyse effects of elevated CO2 levels on phosphorus pool sizes and uptake. The phosphorus dynamic was followed in a CO2-manipulation mesocosm experiment in the Storfjarden (western Gulf of Finland, Baltic Sea) in summer 2012 and was also studied in the surrounding fjord water. In all mesocosms as well as in surface waters of Storfjarden, dissolved organic phosphorus (DOP) concentrations of 0.26aEuro-+/- aEuro-0.03 and 0.23aEuro-+/- aEuro-0.04aEuro-A mu molaEuro-L-1, respectively, formed the main fraction of the total P-pool (TP), whereas phosphate (PO4) constituted the lowest fraction with mean concentration of 0.15aEuro-A +/- aEuro-0.02 in the mesocosms and 0.17aEuro-A +/- aEuro-0.07aEuro-A mu molaEuro-L-1 in the fjord. Transformation of PO4 into DOP appeared to be the main pathway of PO4 turnover. About 82aEuro-% of PO4 was converted into DOP whereby only 18aEuro-% of PO4 was transformed into particulate phosphorus (PP). PO4 uptake rates measured in the mesocosms ranged between 0.6 and 3.9aEuro-nmolaEuro-L(-1)aEuro-h(-1). About 86aEuro-% of them was realized by the size fraction < aEuro-3aEuro-A mu m. Adenosine triphosphate (ATP) uptake revealed that additional P was supplied from organic compounds accounting for 25-27aEuro-% of P provided by PO4 only. CO2 additions did not cause significant changes in phosphorus (P) pool sizes, DOP composition, and uptake of PO4 and ATP when the whole study period was taken into account. However, significant short-term effects were observed for PO4 and PP pool sizes in CO2 treatments > aEuro-1000aEuro-A mu atm during periods when phytoplankton biomass increased. In addition, we found significant relationships (e.g., between PP and Chl a) in the untreated mesocosms which were not observed under high fCO(2) conditions. Consequently, it can be hypothesized that the relationship between PP formation and phytoplankton growth changed with CO2 elevation. It can be deduced from the results, that visible effects of CO2 on P pools are coupled to phytoplankton growth when the transformation of PO4 into POP was stimulated. The transformation of PO4 into DOP on the other hand does not seem to be affected. Additionally, there were some indications that cellular mechanisms of P regulation might be modified under CO2 elevation changing the relationship between cellular constituents.
The sum of benthic autotrophic and bacterial production often exceeds the sum of pelagic autotrophic and bacterial production, and hence may contribute substantially to whole-lake carbon fluxes, especially in shallow lakes. Furthermore, both benthic and pelagic autotrophic and bacterial production are highly edible and of sufficient nutritional quality for animal consumers. We thus hypothesised that pelagic and benthic transfer efficiencies (ratios of production at adjacent trophic levels) in shallow lakes should be similar. We performed whole ecosystem studies in two shallow lakes (3.5ha, mean depth 2m), one with and one without submerged macrophytes, and quantified pelagic and benthic biomass, production and transfer efficiencies for bacteria, phytoplankton, epipelon, epiphyton, macrophytes, zooplankton, macrozoobenthos and fish. We expected higher transfer efficiencies in the lake with macrophytes, because these provide shelter and food for macrozoobenthos and may thus enable a more efficient conversion of basal production to consumer production. In both lakes, the majority of the whole-lake autotrophic and bacterial production was provided by benthic organisms, but whole-lake primary consumer production mostly relied on pelagic autotrophic and bacterial production. Consequently, transfer efficiency of benthic autotrophic and bacterial production to macrozoobenthos production was an order of magnitude lower than the transfer efficiency of pelagic autotrophic and bacterial production to rotifer and crustacean production. Between-lake differences in transfer efficiencies were minor. We discuss several aspects potentially causing the unexpectedly low benthic transfer efficiencies, such as the food quality of producers, pelagic-benthic links, oxygen concentrations in the deeper lake areas and additional unaccounted consumer production by pelagic and benthic protozoa and meiobenthos at intermediate or top trophic levels. None of these processes convincingly explain the large differences between benthic and pelagic transfer efficiencies. Our data indicate that shallow eutrophic lakes, even with a major share of autotrophic and bacterial production in the benthic zone, can function as pelagic systems with respect to primary consumer production. We suggest that the benthic autotrophic production was mostly transferred to benthic bacterial production, which remained in the sediments, potentially cycling internally in a similar way to what has previously been described for the microbial loop in pelagic habitats. Understanding the energetics of whole-lake food webs, including the fate of the substantial benthic bacterial production, which is either mineralised at the sediment surface or permanently buried, has important implications for regional and global carbon cycling.
Biotic and abiotic particles shape the microspatial architecture that defines the microbial aquatic habitat, being particles highly variable in size and quality along oceanic horizontal and vertical gradients. We analysed the prokaryotic (bacterial and archaeal) diversity and community composition present in six distinct particle size classes ranging from the pico-to the microscale (0.2 to 200 lm). Further, we studied their variations along oceanographic horizontal (from the coast to open oceanic waters) and vertical (from the ocean surface into the meso-and bathypelagic ocean) gradients. In general, prokaryotic community composition was more variable with depth than in the transition from the coast to the open ocean. Comparing the six size-fractions, distinct prokaryotic communities were detected in each size-fraction, and whereas bacteria were more diverse in the larger size-fractions, archaea were more diverse in the smaller size-fractions. Comparison of prokaryotic community composition among particle size-fractions showed that most, but not all, taxonomic groups have a preference for a certain size-fraction sustained with depth. Species sorting, or the presence of diverse ecotypes with distinct size-fraction preferences, may explain why this trend is not conserved in all taxa.
We investigated changes in quality and quantity of extracellular and biomass-derived organic matter (OM) from three axenic algae (genera Rhodomonas, Chlamydomonas, Coelastrum) during growth of Limnohabitans parvus, Limnohabitans planktonicus and Polynucleobacter acidiphobus representing important clusters of freshwater planktonic Betaproteobacteria. Total extracellular and biomass-derived OM concentrations from each alga were approximately 20 mg l(-1) and 1 mg l(-1) respectively, from which up to 9% could be identified as free carbohydrates, polyamines, or free and combined amino acids. Carbohydrates represented 54%-61% of identified compounds of the extracellular OM from each alga. In biomass-derived OM of Rhodomonas and Chlamydomonas 71%-77% were amino acids and polyamines, while in that of Coelastrum 85% were carbohydrates. All bacteria grew on alga-derived OM of Coelastrum, whereas only Limnohabitans strains grew on OM from Rhodomonas and Chlamydomonas. Bacteria consumed 24%-76% and 38%-82% of all identified extracellular and biomass-derived OM compounds respectively, and their consumption was proportional to the concentration of each OM compound in the different treatments. The bacterial biomass yield was higher than the total identifiable OM consumption indicating that bacteria also utilized other unidentified alga-derived OM compounds. Bacteria, however, also produced specific OM compounds suggesting enzymatic polymer degradation or de novo exudation.
The importance of ciliates as herbivores and in biogeochemical cycles is increasingly recognized. An opportunity to observe the potential consequences of zooplankton dominated by ciliates arose when winter fish kills resulted in strong suppression of crustaceans by young planktivorous fish in two shallow lakes. On an annual average, ciliates made up 38-76% of the total zooplankton biomass in both lakes during two subsequent years. Consequently, ciliate biomass and their estimated grazing potential were extremely high compared with other lakes of various trophic states and depths. Grazing estimates based on abundance and size suggest that ciliates should have cleared the water column of small (<5 mu m) and intermediate (5-50 mu m) sized phytoplankton more than once a day. Especially, small feeders within the ciliates were important, likely exerting a strong top-down control on small phytoplankton. Particle-attached bacteria were presumably strongly suppressed by intermediate-sized ciliate feeders. In contrast to other lakes, large phytoplankton was proportionately very abundant. The phytoplankton community had a high evenness, which may be attributed to the feeding by numerous fast growing and selective ciliate species. Our study highlights ciliates as an important trophic link and adds to the growing awareness of the role of winter processes for plankton dynamics.
Sediment resuspension represents a key process in all natural aquatic systems, owing to its role in nutrient cycling and transport of potential contaminants. Although suspended solids are generally accepted as an important quality parameter, current monitoring programs cover quantitative aspects only. Established methodologies do not provide information on origin, fate, and risks associated with uncontrolled inputs of solids in waters. Here we discuss the analytical approaches to assess the occurrence and ecological relevance of resuspended particulate matter in freshwaters, with a focus on the dynamics of associated contaminants and microorganisms. Triggered by the identification of specific physical-chemical traits and community structure of particle-associated microorganisms, recent findings suggest that a quantitative determination of microorganisms can be reasonably used to trace the origin of particulate matter by means of nucleic acid-based assays in different aquatic systems.