Antimicrobial resistance (AMR) is an ever-present threat to the treatment of infectious diseases. However, the potential relevance of this phenomenon in environmental reservoirs still raises many questions. Detection of antimicrobial-resistant bacteria in the environment is a critical aspect for understanding the prevalence of resistance outside of clinical settings, as detection in the environment indicates that resistance is likely already widespread. We isolated antimicrobial-resistant Escherichia coli from three urban waterbodies over a 15-month time series, determined their antimicrobial susceptibilities, investigated their population structure, and identified genetic determinants of resistance. We found that E. coli populations at each site were composed of different dominant phylotypes and showed distinct patterns of antimicrobial and multidrug resistance, despite close geographic proximity. Many strains that were genome-sequenced belonged to sequence types of international concern, particularly the ST131 clonal complex. We found widespread resistance to clinically important antimicrobials such as amoxicillin, cefotaxime, and ciprofloxacin, but found that all strains were susceptible to amikacin and the last-line antimicrobials meropenem and fosfomycin. Resistance was most often due to acquirable antimicrobial resistance genes, while chromosomal mutations in gyrA, parC, and parE conferred resistance to quinolones. Whole-genome analysis of a subset of strains further revealed the diversity of the population of E. coli present, with a wide array of AMR and virulence genes identified, many of which were present on the chromosome, including blaCTX-M. Finally, we determined that environmental persistence, transmission between sites, most likely mediated by wild birds, and transfer of mobile genetic elements likely contributed significantly to the patterns observed.IMPORTANCEA One Health perspective is crucial to understand the extent of antimicrobial resistance (AMR) globally, and investigation of AMR in the environment has been increasing in recent years. However, most studies have focused on waterways that are directly polluted by sewage, industrial manufacturing, or agricultural activities. Therefore, there remains a lack of knowledge about more natural, less overtly impacted environments. Through phenotypic and genotypic investigation of AMR in Escherichia coli, this study adds to our understanding of the extent and patterns of resistance in these types of environments, including over a time series, and showed that complex biotic and abiotic factors contribute to the patterns observed. Our study further emphasizes the importance of incorporating the surveillance of microbes in freshwater environments in order to better comprehend potential risks for both human and animal health and how the environment may serve as a sentinel for potential future clinical infections.

In methane (CH4) generating sediments, methane oxidation coupled with iron reduction was suggested to be catalyzed by archaea and bacterial methanotrophs of the order Methylococcales. However, the co-existence of these aerobic and anaerobic microbes, the link between the processes, and the oxygen requirement for the bacterial methanotrophs have remained unclear. Here, we show how stimulation of aerobic methane oxidation at an energetically low experimental environment influences net iron reduction, accompanied by distinct microbial community changes and lipid biomarker patterns. We performed incubation experiments (between 30 and 120 days long) with methane generating lake sediments amended with 13C-labeled methane, following the additions of hematite and different oxygen levels in nitrogen headspace, and monitored methane turnover by 13C-DIC measurements. Increasing oxygen exposure (up to 1%) promoted aerobic methanotrophy, considerable net iron reduction, and the increase of microbes, such as Methylomonas, Geobacter, and Desulfuromonas, with the latter two being likely candidates for iron recycling. Amendments of 13C-labeled methanol as a potential substrate for the methanotrophs under hypoxia instead of methane indicate that this substrate primarily fuels methylotrophic methanogenesis, identified by high methane concentrations, strongly positive δ13CDIC values, and archaeal lipid stable isotope data. In contrast, the inhibition of methanogenesis by 2-bromoethanesulfonate (BES) led to increased methanol turnover, as suggested by similar 13C enrichment in DIC and high amounts of newly produced bacterial fatty acids, probably derived from heterotrophic bacteria. Our experiments show a complex link between aerobic methanotrophy and iron reduction, which indicates iron recycling as a survival mechanism for microbes under hypoxia.

Lake Villarrica, one of Chile\'s main freshwater water bodies, was recently declared a nutrient-saturated lake due to increased phosphorus (P) and nitrogen (N) levels. Although a decontamination plan based on environmental parameters is being established, it does not consider microbial parameters. Here, we conducted high-throughput DNA sequencing and quantitative polymerase chain reaction (qPCR) analyses to reveal the structure and functional properties of bacterial communities in surface sediments collected from sites with contrasting anthropogenic pressures in Lake Villarrica. Alpha diversity revealed an elevated bacterial richness and diversity in the more anthropogenized sediments. The phylum Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria dominated the community. The principal coordinate analysis (PCoA) and redundancy analysis (RDA) showed significant differences in bacterial communities of sampling sites. Predicted functional analysis showed that N cycling functions (e.g., nitrification and denitrification) were significant. The microbial co-occurrence networks analysis suggested Chitinophagaceae, Caldilineaceae, Planctomycetaceae, and Phycisphaerae families as keystone taxa. Bacterial functional genes related to P (phoC, phoD, and phoX) and N (nifH and nosZ) cycling were detected in all samples by qPCR. In addition, an RDA related to N and P cycling revealed that physicochemical properties and functional genes were positively correlated with several nitrite-oxidizing, ammonia-oxidizing, and N-fixing bacterial genera. Finally, denitrifying gene (nosZ) was the most significant factor influencing the topological characteristics of co-occurrence networks and bacterial interactions. Our results represent one of a few approaches to elucidate the structure and role of bacterial communities in Chilean lake sediments, which might be helpful in conservation and decontamination plans.

Even though lake sediments are globally important organic carbon (OC) sinks, the controls on long-term OC storage in these sediments are unclear. Using a multiproxy approach, we investigate changes in diatom, green algae, and vascular plant biomolecules in sedimentary records from the past centuries across five temperate lakes with different trophic histories. Despite past increases in the input and burial of OC in sediments of eutrophic lakes, biomolecule quantities in sediments of all lakes are primarily controlled by postburial microbial degradation over the time scales studied. We, moreover, observe major differences in biomolecule degradation patterns across diatoms, green algae, and vascular plants. Degradation rates of labile diatom DNA exceed those of chemically more resistant diatom lipids, suggesting that chemical reactivity mainly controls diatom biomolecule degradation rates in the lakes studied. By contrast, degradation rates of green algal and vascular plant DNA are significantly lower than those of diatom DNA, and in a similar range as corresponding, much less reactive lipid biomarkers and structural macromolecules, including lignin. We propose that physical shielding by degradation-resistant cell wall components, such as algaenan in green algae and lignin in vascular plants, contributes to the long-term preservation of labile biomolecules in both groups and significantly influences the long-term burial of OC in lake sediments.

Orbital-scale global climatic changes during the late Quaternary are dominated by high-latitude influenced ~100,000-year global ice-age cycles and monsoon influenced ~23,000-year low-latitude hydroclimate variations. However, the shortage of highly-resolved land temperature records remains a limiting factor for achieving a comprehensive understanding of long-term low-latitude terrestrial climatic changes. Here, we report paired mean annual air temperature (MAAT) and monsoon intensity proxy records over the past 88,000 years from Lake Tengchongqinghai in southwestern China. While summer monsoon intensity follows the ~23,000-year precession beat found also in previous studies, we identify previously unrecognized warm periods at 88,000-71,000 and 45,000-22,000 years ago, with 2-3 °C amplitudes that are close to our recorded full glacial-interglacial range. Using advanced transient climate simulations and comparing with forcing factors, we find that these warm periods in our MAAT record probably depends on local annual mean insolation, which is controlled by Earth\'s ~41,000-year obliquity cycles and is anti-phased to annual mean insolation at high latitudes. The coincidence of our identified warm periods and intervals of high-frequent dated archaeological evidence highlights the importance of temperature on anatomically modern humans in Asia during the last glacial stage.

Exploring functional gene composition is essential for understanding the biogeochemical functions of lakes. However, little is known about the diversity and composition of biogeochemical cycling genes and their influencing factors in saline lakes. In this study, metagenomic analysis was employed to characterize the diversity and composition of microbial functions predicted from genes involved in carbohydrate metabolisms, nitrogen, and sulfur cycles in 17 surface sediments of Qinghai-Tibetan lakes with salinity ranging from 0.7 to 31.5 g L-1. The results showed that relative abundances of carbohydrate-active enzyme (CAZy), nitrogen, and sulfur cycling genes were 92.7-116.5, 15.1-18.7, 50.8-63.9 per 1,000 amino acid coding reads, respectively. The Shannon diversity indices of CAZy and sulfur cycling genes decreased with increasing salinity, whereas nitrogen cycling gene diversity showed an opposite trend. Relative abundances of many CAZy (i.e., carbohydrate-binding module and carbohydrate esterase), nitrogen (i.e., anammox and organic degradation and synthesis) and sulfur (i.e., dissimilatory sulfur reduction and oxidation, link between inorganic and organic sulfur transformation, sulfur disproportionation and reduction) cycling gene categories decreased with increasing salinity, whereas some CAZy (i.e., auxiliary activity), nitrogen (i.e., denitrification) and sulfur (i.e., assimilatory sulfate reduction and sulfur oxidation) gene categories showed an increasing trend. The compositions of CAZy, nitrogen, and sulfur cycling genes in the studied lake sediments were significantly (p < 0.05) affected by environmental factors such as salinity, total organic carbon, total nitrogen, and total phosphorus, with salinity having the greatest influence. Together, our results suggest that salinity may regulate the biogeochemical functions of carbohydrate metabolisms, nitrogen, and sulfur cycles in lakes through changing the diversity and composition of microbial functional genes. This finding has great implications for understanding the impact of environmental change on microbial functions in lacustrine ecosystems.

The study focuses on the comprehensive research of geochemical and environmental roles of humic acids isolated from sediments of the urbanized lakes of Kola Peninsula, the Arctic. The sediments were collected from 5 water bodies located in the different parts of Murmansk city. The elemental analysis (C, H, N, and O percentage) of the samples was conducted. The molecular structure of the acids was investigated using solid-state CP/MAS 13C-NMR and FTIR spectroscopy methods. The findings revealed the specific geochemical and environmental features of the sediment humic acids in the urbanized aquatic ecosystems of the Arctic region. The process of humification in the studied lakes is slowed down due to cold climatic conditions and the high level of the pollution of the water bodies. The molecules of the humic acids are immature and high-oxygen. Therefore, on the one hand, they can actively leach the toxic metals from the components of the sediments. On the other hand, despite the relatively low content of chelate-forming groups in the structure of the humic acids, the stable organometallic compounds form due to high percentage of dispersed organic matter in the sediments and structural flexibility of the molecules of the acids. Furthermore, the geochemical composition of the sediments and their enrichment by the trace elements and hydrocarbons significantly influence on the character of the interaction between metals and humic acids.

We present a dataset of subfossil chironomid assemblages in the MUT-10 sediment core obtained from the high alpine lake Mutterbergersee in the Austrian Alps in 2010. The data were presented in the research article by Ilyashuk et al. (2019) \"The Little Ice Age signature in a 700-year high-resolution chironomid record of summer temperatures in the Central Eastern Alps\". In addition to the results of the chironomid analysis of 100 sediment samples presented in this article, we also include chironomid assemblage data from an additional 48 sediment samples that complement this dataset. The data includes raw chironomid counts, percent abundance of chironomid taxa, as well as mean July air temperature estimates derived from the chironomid record based on a chironomid-temperature transfer function. We also provide information on age-dating of the sedimentary sequence. Given the high temporal resolution and the robust age-depth model of the record, the chironomid-based reconstruction of temperature since AD 1300 provides a detailed documentation of climate change in the Eastern Alps from the Little Ice Age onwards and can be used for comparison with other independent proxy-based climate reconstructions. In addition to the data, we detail the sample processing for subfossil chironomid analysis and provide a detailed description of the reconstruction technique used for producing chironomid-based quantitative temperature inferences.

This paleoenvironmental database features postglacial lake-sediment records from 31 study sites located across New England. The study sites span an environmental gradient from the cooler, northern and inland part of the region to the warmer, southern and coastal areas of New England. Sediment-core chronologies were determined using 14C dating, 210Pb analysis, and pollen evidence. Detailed analyses of sediment lithology, pollen, and charcoal were used to reconstruct changes in climate, vegetation, and fire at centennial temporal scales and subregional spatial scales for the last 14,000 years. Analyses of paleoenvironmental data provide insights into the rates, patterns, and drivers of ecosystem change, helping us anticipate future ecosystem dynamics and guiding present-day conservation strategies and land management.

The Aare river system in Switzerland, with two nuclear power plants on the banks of the river, and its intermediate lakes and reservoirs, provides a unique opportunity to analyze the contribution of different sources to the radioactive contamination. Sediment cores were collected from two lakes and a reservoir, all connected by the river Aare. In order to study the influence of the Chernobyl accident, one sediment core was collected from a lake in the southern part of Switzerland. The sediment cores were sliced and analyzed with gamma ray spectrometry. Plutonium, americium, and uranium were extracted radiochemically, and their concentrations were measured with a sector field ICP-MS. The uranium isotope ratios were further measured with a multi collector ICP-MS. The maximum 137Cs activity from the Chernobyl accident and the Pu and 137Cs activities associated to the 1963 global fallout maximum were well identified in sediments from all three lakes. High-resolution records of plutonium isotopes in the zone of the sediments corresponding to the period of maximum fallout from the atmospheric nuclear weapon testing showed distinct fingerprints, depending on the different test activities. Pu isotope ratios could be used to detect non-global fallout plutonium. The ratio 241Am/241Pu was used to determine the age of the plutonium. Despite of very low 241Pu and 241Am concentrations, the calculated plutonium production dates seemed to be reasonable for the sediment layers corresponding to the NWT tests. The calculated production date of the plutonium in the upper most 15 cm of the sediment core seemed to be younger. The reason for this could be additional non-global fallout plutonium. For the lake sediments, natural ratios for 235U/238U and enriched or depleted ratios for 234U/238U were measured, depending on the lake. A small increase of the 236U/238U ratio could be recognized for the NWT zone in all three lakes and, for Lake Lugano, a further distinct increase in the Chernobyl layer.