The Toxic Effects of Antibiotics on Freshwater and Marine Photosynthetic Microorganisms: State of the Art

Antibiotic residues have been commonly detected worldwide in freshwater, estuarine, and marine ecosystems. The review summarizes the up-to-date information about the toxic effects of over 60 antibiotics on nontarget autotrophic microorganisms with a particular focus on marine microalgae. A comprehensive overview of the available reports led to the identification of significant knowledge gaps. The data on just one species of freshwater green algae (Raphidocelis subcapitata) constitute 60% of the total information on the toxicity of antibiotics, while data on marine species account for less than 14% of the reports. Moreover, there is a clear knowledge gap regarding the chronic effects of antibiotic exposure (only 9% of studies represent exposition time values longer than 7 days). The review summarizes the information on different physiological endpoints, including processes involved in photosynthesis, photoprotective and antioxidant mechanisms. Currently, the hazard assessment is mostly based on the results of the evaluation of individual chemicals and acute toxicity tests of freshwater organisms. Future research trends should involve chronic effect studies incorporating sensitive endpoints with the application of environmentally relevant concentrations, as well as studies on the mixture effects and combined environmental factors influencing toxicity.

Bioelectrochemical nitrogen removal as a polishing mechanism for domestic wastewater treated effluents

Addition of an external carbon source is usually necessary to guarantee a sufficiently high C/N ratio and enable denitrification in wastewater treatment plants (WWTPs). Alternatively, denitrification processes using autotrophic microorganisms have been proposed i.e., with the use of H2 as electron donor or with the use of cathodic denitrification in bioelectrochemical systems (BES), in which electrons are transferred directly to a denitrifying biofilm. The aim of this work was to investigate and demonstrate the feasibility of applying an easy-to-operate BES as a polishing mechanism for treated secondary clarified effluent from a municipal WWTP, containing low levels of organic matter, buffer capacity and low concentrations of remaining nitrate. In the proposed system, nitrogen removal rates (0.018–0.121 Kg N m−3 d−1) increased with the nitrogen loading rates, suggesting that biofilm kinetics were not rate limiting. The lowest energy consumption for denitrification was 12.7 kWh Kg N−1, equivalent to 0.021 kWh m−3 and could be further reduced by 14% by adding recirculation circuits within both the anode and cathode.

Proteomic and Mutant Analysis of the CO2 Concentrating Mechanism of Hydrothermal Vent Chemolithoautotroph Thiomicrospira crunogena

ABSTRACT Many autotrophic microorganisms are likely to adapt to scarcity in dissolved inorganic carbon (DIC; CO2 + HCO3 − + CO3 2−) with CO2 concentrating mechanisms (CCM) that actively transport DIC across the cell membrane to facilitate carbon fixation. Surprisingly, DIC transport has been well studied among cyanobacteria and microalgae only. The deep-sea vent gammaproteobacterial chemolithoautotroph Thiomicrospira crunogena has a low-DIC inducible CCM, though the mechanism for uptake is unclear, as homologs to cyanobacterial transporters are absent. To identify the components of this CCM, proteomes of T. crunogena cultivated under low- and high-DIC conditions were compared. Fourteen proteins, including those comprising carboxysomes, were at least 4-fold more abundant under low-DIC conditions. One of these proteins was encoded by Tcr_0854; strains carrying mutated copies of this gene, as well as the adjacent Tcr_0853, required elevated DIC for growth. Strains carrying mutated copies of Tcr_0853 and Tcr_0854 overexpressed carboxysomes and had diminished ability to accumulate intracellular DIC. Based on reverse transcription (RT)-PCR, Tcr_0853 and Tcr_0854 were cotranscribed and upregulated under low-DIC conditions. The Tcr_0853-encoded protein was predicted to have 13 transmembrane helices. Given the mutant phenotypes described above, Tcr_0853 and Tcr_0854 may encode a two-subunit DIC transporter that belongs to a previously undescribed transporter family, though it is widespread among autotrophs from multiple phyla. IMPORTANCE DIC uptake and fixation by autotrophs are the primary input of inorganic carbon into the biosphere. The mechanism for dissolved inorganic carbon uptake has been characterized only for cyanobacteria despite the importance of DIC uptake by autotrophic microorganisms from many phyla among the Bacteria and Archaea. In this work, proteins necessary for dissolved inorganic carbon utilization in the deep-sea vent chemolithoautotroph T. crunogena were identified, and two of these may be able to form a novel transporter. Homologs of these proteins are present in 14 phyla in Bacteria and also in one phylum of Archaea, the Euryarchaeota. Many organisms carrying these homologs are autotrophs, suggesting a role in facilitating dissolved inorganic carbon uptake and fixation well beyond the genus Thiomicrospira.

Autotrophic fixation of geogenic CO₂ by microorganisms contributes to soil organic matter formation and alters isotope signatures in a wetland mofette

To quantify the contribution of autotrophic microorganisms to organic matter (OM) formation in soils, we investigated natural CO2 vents (mofettes) situated in a wetland in northwest Bohemia (Czech Republic). Mofette soils had higher soil organic matter (SOM) concentrations than reference soils due to restricted decomposition under high CO2 levels. We used radiocarbon (Δ14C) and stable carbon (δ13C) isotope ratios to characterize SOM and its sources in two mofettes and compared it with respective reference soils, which were not influenced by geogenic CO2. The geogenic CO2 emitted at these sites is free of radiocarbon and enriched in 13C compared to atmospheric CO2. Together, these isotopic signals allow us to distinguish C fixed by plants from C fixed by autotrophic microorganisms using their differences in 13C discrimination. We can then estimate that up to 27 % of soil organic matter in the 0–10 cm layer of these soils was derived from microbially assimilated CO2. Isotope values of bulk SOM were shifted towards more positive δ13C and more negative Δ14C values in mofettes compared to reference soils, suggesting that geogenic CO2 emitted from the soil atmosphere is incorporated into SOM. To distinguish whether geogenic CO2 was fixed by plants or by CO2 assimilating microorganisms, we first used the proportional differences in radiocarbon and δ13C values to indicate the magnitude of discrimination of the stable isotopes in living plants. Deviation from this relationship was taken to indicate the presence of microbial CO2 fixation, as microbial discrimination should differ from that of plants. 13CO2-labelling experiments confirmed high activity of CO2 assimilating microbes in the top 10 cm, where δ13C values of SOM were shifted up to 2 ‰ towards more negative values. Uptake rates of microbial CO2 fixation ranged up to 1.59 ± 0.16 μg gdw−1 d−1. We inferred that the negative δ13C shift was caused by the activity of autotrophic microorganisms using the Calvin–Benson–Bassham (CBB) cycle, as indicated from quantification of cbbL/cbbM marker genes encoding for RubisCO by quantitative polymerase chain reaction (qPCR) and by acetogenic and methanogenic microorganisms, shown present in the mofettes by previous studies. Combined Δ14C and δ13C isotope mass balances indicated that microbially derived carbon accounted for 8–27 % of bulk SOM in this soil layer. The findings imply that autotrophic microorganisms can recycle significant amounts of carbon in wetland soils and might contribute to observed radiocarbon reservoir effects influencing Δ14C signatures in peat deposits.

Autotrophic fixation of geogenic CO₂ by microorganisms contributes to soil organic matter formation and alters isotope signatures in a wetland mofette

To quantify the contribution of autotrophic microorganisms to organic matter formation (OM) in soils, we investigated natural CO2 vents (mofettes) situated in a wetland in NW Bohemia (Czech Republic). Mofette soils had higher SOM concentrations than reference soils due to restricted decomposition under high CO2 levels. We used radiocarbon (Δ14C) and stable carbon isotope ratios (δ13C) to characterize SOM and its sources in two moffetes and compared it with respective reference soils, which were not influenced by geogenic CO2. The geogenic CO2 emitted at these sites is free of radiocarbon and enriched in δ13C compared to atmospheric CO2. Together, these isotopic signals allow us to distinguish C fixed by plants from C fixed by autotrophic microorganisms using their differences in δ13C discrimination. We can then estimate that up to 27 % of soil organic matter in the 0–10 cm layer of these soils was derived from microbially assimilated CO2. Isotope values of bulk SOM were shifted towards more positive δ13C and more negative Δ14C values in mofettes compared to reference soils, suggesting that geogenic CO2 emitted from the soil atmosphere is incorporated into SOM. To distinguish whether geogenic CO2 was fixed by plants or by CO2 assimilating microorganisms, we first used the proportional differences in radiocarbon and δ13C values to indicate the magnitude of discrimination of the stable isotopes in living plants. Deviation from this relationship was taken to indicate the presence of microbial CO2 fixation, as microbial discrimination should differ from that of plants. 13CO2-labelling experiments confirmed high activity of CO2 assimilating microbes in the top 10 cm, where δ13C values of SOM were shifted up to 2 ‰ towards more negative values. Uptake rates of microbial CO2 fixation ranged up to 1.59 ± 0.16 μg gdw−1 d−1. We inferred that the negative δ13C shift was caused by the activity of chemo-lithoautotrophic microorganisms, as indicated from quantification of cbbL/cbbM marker genes encoding for RubisCO by quantitative polymerase chain reaction (qPCR) and by acetogenic and methanogenic microorganisms, shown present in the moffettes by previous studies. Combined Δ14C and δ13C isotope mass balances indicated that microbially derived carbon accounted for 8 to 27 % of bulk SOM in this soil layer. The findings imply that autotrophic organisms can recycle significant amounts of carbon in wetland soils and might contribute to observed reservoir effects influencing radiocarbon signatures in peat deposits.

Significant Role for Microbial Autotrophy in the Sequestration of Soil Carbon

ABSTRACTSoils were incubated for 80 days in a continuously labeled14CO2atmosphere to measure the amount of labeled C incorporated into the microbial biomass. Microbial assimilation of14C differed between soils and accounted for 0.12% to 0.59% of soil organic carbon (SOC). Assuming a terrestrial area of 1.4 × 108km2, this represents a potential global sequestration of 0.6 to 4.9 Pg C year−1. Estimated global C sequestration rates suggest a “missing sink” for carbon of between 2 and 3 Pg C year−1. To determine whether14CO2incorporation was mediated by autotrophic microorganisms, the diversity and abundance of CO2-fixing bacteria and algae were investigated using clone library sequencing, terminal restriction fragment length polymorphism (T-RFLP), and quantitative PCR (qPCR) of the ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) gene (cbbL). Phylogenetic analysis showed that the dominantcbbL-containing bacteria wereAzospirillum lipoferum,Rhodopseudomonas palustris,Bradyrhizobium japonicum,Ralstonia eutropha, andcbbL-containing chromophytic algae of the generaXanthophytaandBacillariophyta. Multivariate analyses of T-RFLP profiles revealed significant differences incbbL-containing microbial communities between soils. Differences incbbLgene diversity were shown to be correlated with differences in SOC content. Bacterial and algalcbbLgene abundances were between 106and 108and 103to 105copies g−1soil, respectively. BacterialcbbLabundance was shown to be positively correlated with RubisCO activity (r= 0.853;P< 0.05), and bothcbbLabundance and RubisCO activity were significantly related to the synthesis rates of [14C]SOC (r= 0.967 and 0.946, respectively;P< 0.01). These data offer new insights into the importance of microbial autotrophy in terrestrial C cycling.

Cultivation of Anaerobic and Facultatively Anaerobic Bacteria from Spacecraft-Associated Clean Rooms

ABSTRACT In the course of this biodiversity study, the cultivable microbial community of European spacecraft-associated clean rooms and the Herschel Space Observatory located therein were analyzed during routine assembly operations. Here, we focused on microorganisms capable of growing without oxygen. Anaerobes play a significant role in planetary protection considerations since extraterrestrial environments like Mars probably do not provide enough oxygen for fully aerobic microbial growth. A broad assortment of anaerobic media was used in our cultivation strategies, which focused on microorganisms with special metabolic skills. The majority of the isolated strains grew on anaerobic, complex, nutrient-rich media. Autotrophic microorganisms or microbes capable of fixing nitrogen were also cultivated. A broad range of facultatively anaerobic bacteria was detected during this study and also, for the first time, some strictly anaerobic bacteria (Clostridium and Propionibacterium) were isolated from spacecraft-associated clean rooms. The multiassay cultivation approach was the basis for the detection of several bacteria that had not been cultivated from these special environments before and also led to the discovery of two novel microbial species of Pseudomonas and Paenibacillus.