Convergent Evolution of a Promiscuous 3-Hydroxypropionyl-CoA Dehydratase/Crotonyl-CoA Hydratase in Crenarchaeota and Thaumarchaeota.

The autotrophic 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) cycle functions in thermoacidophilic, (micro)aerobic, hydrogen-oxidizing Crenarchaeota of the order Sulfolobales as well as in mesophilic, aerobic, ammonia-oxidizing Thaumarchaeota. Notably, the HP/HB cycle evolved independently in these two archaeal lineages, and crenarchaeal and thaumarchaeal versions differ regarding their enzyme properties and phylogeny. These differences result in altered energetic efficiencies between the variants. Compared to the crenarchaeal HP/HB cycle, the thaumarchaeal variant saves two ATP equivalents per turn, rendering it the most energy-efficient aerobic pathway for carbon fixation. Characteristically, the HP/HB cycle includes two enoyl coenzyme A (CoA) hydratase reactions: the 3-hydroxypropionyl-CoA dehydratase reaction and the crotonyl-CoA hydratase reaction. In this study, we show that both reactions are catalyzed in the aforementioned archaeal groups by a promiscuous 3-hydroxypropionyl-CoA dehydratase/crotonyl-CoA hydratase (Msed_2001 in crenarchaeon Metallosphaera sedula and Nmar_1308 in thaumarchaeon Nitrosopumilus maritimus). Although these two enzymes are homologous, they are closely related to bacterial enoyl-CoA hydratases and were retrieved independently from the same enzyme pool by the ancestors of Crenarchaeota and Thaumarchaeota, despite the existence of multiple alternatives. This striking similarity in the emergence of enzymes involved in inorganic carbon fixation from two independently evolved pathways highlights that convergent evolution of autotrophy could be much more widespread than anticipated.IMPORTANCE Inorganic carbon fixation is the most important biosynthetic process on Earth and the oldest type of metabolism. The autotrophic HP/HB cycle functions in Crenarchaeota of the order Sulfolobales and in ammonia-oxidizing Archaea of the phylum Thaumarchaeota that are highly abundant in marine, terrestrial, and geothermal environments. Bioinformatic prediction of the autotrophic potential of microorganisms or microbial communities requires identification of enzymes involved in autotrophy. However, many microorganisms possess several isoenzymes that may potentially catalyze the reactions of the cycle. Here, we studied the enzymes catalyzing 3-hydroxypropionyl-CoA dehydration and crotonyl-CoA hydration in Nitrosopumilus maritimus (Thaumarchaeota) as well as in Metallosphaera sedula (Crenarchaeota). We showed that both reactions were catalyzed by homologous promiscuous enzymes, which evolved independently from each other from their bacterial homologs. Furthermore, the HP/HB cycle is of applied value, and knowledge of its enzymes is necessary to transfer them to a heterologous host for synthesis of various value-added products.

Decay of elevated antibiotic resistance genes in natural river sediments after sedimentation of wastewater particles.

Large-scale wastewater treatment plants (WWTPs) discharge hundreds of tons of total suspended solids (TSS) into surface waters every year. Additionally, a comparable amount is released by sewer overflows during heavy rain events in case of combined sewer systems. Along with sedimentation, particle-attached microorganisms and their antibiotic resistance genes (ARGs) are herewith transported to the riverbed of the receiving water. To better understand the dynamics of this process, a particulate wastewater fraction was added into batch reactors, which were previously filled with natural river sediments and tap water. In parallel, antibiotics (ABs) (erythromycin, tetracycline, ciprofloxacin, roxithromycin, penicillin V, and sulfamethoxazole) were spiked to investigate their capability to select for resistance. The abundance of six ARGs (ermB, tetM, blaTEM, sul1, CTX-M-32, and qnrS) as well as total bacteria (16S rDNA) was monitored in waters and in sediments for a duration of two months using quantitative PCR. Despite a continuous exposure to ABs (5 µg/L each), the abundance of ARGs remained unaffected. Addition of wastewater particles resulted in a sudden and strong increase of ARGs in waters (3-5 log units) and sediments (1-4 log units), however, elevated ARGs underwent a particular and complete decay. Our results indicate that the increased ARG abundances in receiving rivers are the result of a continuous import of ARGs from WWTP discharges or sewer overflow events. They further imply that elevated ARGs do not persist in receiving rivers, if this continuous import is removed. This seems to be the case merely for ARGs introduced by wastewater, given that a stable background concentration of ARGs was observed for the native population.

Impact of the particulate matter from wastewater discharge on the abundance of antibiotic resistance genes and facultative pathogenic bacteria in downstream river sediments.

Wastewater treatment plants (WWTPs) are point sources for both, the release of antibiotic resistance genes (ARGs) and the discharge of antibiotics (ABs) into the environment. While it is well established that ARGs emission by WWTPs leads to an ARGs increase in receiving rivers, also the role of sub-inhibitory AB concentrations in this context is being discussed. However, the results obtained in this study suggest that, at environmental concentrations, ABs do not have an effect on resistance selection. Instead, we emphasize the significance of ARG transport and, in that respect, highlight the relevance of wastewater particles and associated microorganisms. We can show that ARGs (ermB, blaTEM,tetM, qnrS) as well as facultative pathogenic bacteria (FPB) (enterococci, Pseudomonas aeruginosa, Acinetobacter baumannii) inside the particulate fraction of WWTP effluent are very likely to remain in the riverbed of the receiving water due to sedimentation. Moreover, ARG and FPB abundances measured in the particulate fraction strongly correlated with the delta ARG and FPB abundances measured in the receiving river sediment (downstream compared to upstream) (R2 = 0.93, p < 0.05). Apparently, the sheer amount of settleable ARGs and FPB from WWTP effluent is sufficient, to increase abundances in the receiving riverbed by 0.5 to 2 log units.

Reverse Flow: The Role of Built Environments in Shaping Disaster.

In contrast to approaches that examine the impacts of human-built efforts to ameliorate calamitous natural events, this essay argues that a wide array of large structures shape the outcomes of these events. Further, significant human artifacts can succeed in their function vis-à-vis one set of natural events, but can have unanticipated, even reverse effects when natural forces exceed planned expectations. Risk assessments do not normally consider such side effects, suffering from an agnotological narrowing of focus. The historian's emphasis on temporal contextualization and contingency has important implications for policy and assessment of risk.

Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation.

Archaea of the phylum Thaumarchaeota are among the most abundant prokaryotes on Earth and are widely distributed in marine, terrestrial, and geothermal environments. All studied Thaumarchaeota couple the oxidation of ammonia at extremely low concentrations with carbon fixation. As the predominant nitrifiers in the ocean and in various soils, ammonia-oxidizing archaea contribute significantly to the global nitrogen and carbon cycles. Here we provide biochemical evidence that thaumarchaeal ammonia oxidizers assimilate inorganic carbon via a modified version of the autotrophic hydroxypropionate/hydroxybutyrate cycle of Crenarchaeota that is far more energy efficient than any other aerobic autotrophic pathway. The identified genes of this cycle were found in the genomes of all sequenced representatives of the phylum Thaumarchaeota, indicating the environmental significance of this efficient CO2-fixation pathway. Comparative phylogenetic analysis of proteins of this pathway suggests that the hydroxypropionate/hydroxybutyrate cycle emerged independently in Crenarchaeota and Thaumarchaeota, thus supporting the hypothesis of an early evolutionary separation of both archaeal phyla. We conclude that high efficiency of anabolism exemplified by this autotrophic cycle perfectly suits the lifestyle of ammonia-oxidizing archaea, which thrive at a constantly low energy supply, thus offering a biochemical explanation for their ecological success in nutrient-limited environments.