Whole genome sequence analysis reveals the broad distribution of the RtxA type 1 secretion system and four novel putative type 1 secretion systems throughout the Legionella genus.

Type 1 secretion systems (T1SSs) are broadly distributed among bacteria and translocate effectors with diverse function across the bacterial cell membrane. Legionella pneumophila, the species most commonly associated with Legionellosis, encodes a T1SS at the lssXYZABD locus which is responsible for the secretion of the virulence factor RtxA. Many investigations have failed to detect lssD, the gene encoding the membrane fusion protein of the RtxA T1SS, in non-pneumophila Legionella, which has led to the assumption that this system is a virulence factor exclusively possessed by L. pneumophila. Here we discovered RtxA and its associated T1SS in a novel Legionella taurinensis strain, leading us to question whether this system may be more widespread than previously thought. Through a bioinformatic analysis of publicly available data, we classified and determined the distribution of four T1SSs including the RtxA T1SS and four novel T1SSs among diverse Legionella spp. The ABC transporter of the novel Legionella T1SS Legionella repeat protein secretion system shares structural similarity to those of diverse T1SS families, including the alkaline protease T1SS in Pseudomonas aeruginosa. The Legionella bacteriocin (1-3) secretion systems T1SSs are novel putative bacteriocin transporting T1SSs as their ABC transporters include C-39 peptidase domains in their N-terminal regions, with LB2SS and LB3SS likely constituting a nitrile hydratase leader peptide transport T1SSs. The LB1SS is more closely related to the colicin V T1SS in Escherichia coli. Of 45 Legionella spp. whole genomes examined, 19 (42%) were determined to possess lssB and lssD homologs. Of these 19, only 7 (37%) are known pathogens. There was no difference in the proportions of disease associated and non-disease associated species that possessed the RtxA T1SS (p = 0.4), contrary to the current consensus regarding the RtxA T1SS. These results draw into question the nature of RtxA and its T1SS as a singular virulence factor. Future studies should investigate mechanistic explanations for the association of RtxA with virulence

Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution

This is the final version of the article. Available from the publisher via the DOI in this record.Around all human activity, there are zones of pollution with pesticides, heavy metals, pharmaceuticals, personal care products and the microorganisms associated with human waste streams and agriculture. This diversity of pollutants, whose concentration varies spatially and temporally, is a major challenge for monitoring. Here, we suggest that the relative abundance of the clinical class 1 integron-integrase gene, intI1, is a good proxy for pollution because: (1) intI1 is linked to genes conferring resistance to antibiotics, disinfectants and heavy metals; (2) it is found in a wide variety of pathogenic and nonpathogenic bacteria; (3) its abundance can change rapidly because its host cells can have rapid generation times and it can move between bacteria by horizontal gene transfer; and (4) a single DNA sequence variant of intI1 is now found on a wide diversity of xenogenetic elements, these being complex mosaic DNA elements fixed through the agency of human selection. Here we review the literature examining the relationship between anthropogenic impacts and the abundance of intI1, and outline an approach by which intI1 could serve as a proxy for anthropogenic pollution.MRG is supported by the Australian Research Council, AP is supported by the Alfred P Sloan Foundation Microbiology of the Built Environment program and the National Science Foundation RAPID award no. 1402651, KS is supported by the Deutsche Forschungsgemeinschaft (DFG) funding the Research Unit FOR 566 ‘Veterinary Medicines in Soil: Basic Research for Risk Analysis’ (Grant No. SM59/5-3) and by the Umweltbundesamt (3713 63 402), JMT is supported by the US National Science Foundation and Y-GZ is supported by the National Science Foundation of China

The State of Digital Media Data Research, 2024

The purpose of this report is to reflect on the state of digital media data research in 2024. This is the second in a series of reports on the state of digital media research, which we originally published in 2023. We reflect on changes to digital media research since our report in 2023. Specifically, we highlight the following trends: 1. From 2023 to 2024, access to digital media data changed drastically. Researchers were largely priced out of the Twitter API, and Pushshift–a commonly used archive for Reddit data–went private to comply with Reddit’s API policies. Meta also announced the imminent sunsetting of CrowdTangle, a transparency tool popular amongst researchers and journalists alike. At the same time, however, many platforms announced academic programs for data access, including the YouTube researcher program, TikTok’s Research API, and the Meta Content Library. 2. Federated social media platforms became more popular. Following Elon Musk’s purchase of Twitter, Twitter users flocked to Mastodon, Threads, BlueSky, and other federated (or soon to be federated) platforms. This presents unique challenges for researchers studying digital media data. As new platforms are created, researchers must build new tools to analyze them or wait for third parties or the platforms themselves to make data available. 3. Generative AI’s explosion may change how we study digital media. First, researchers using computational methods to measure social media content have turned to OpenAI’s ChatGPT and other Large Language Models (LLMs) to classify content. Second, researchers and civil society groups are increasingly concerned about the possibility for Generative AI to flood the information environment with fake content. 4. In February 2024, the EU Digital Services Act (DSA) went into effect, mandating that large platforms give researchers near real-time access to public data. We don’t yet know how these policies will impact data access in the United States, and it remains unclear what this data access will look like in practice. In the United States, legislative efforts to mandate researcher access stalled. While the last year brought many welcome and unwelcome changes to digital media data research, the findings in this report renew our encouragement that digital media data research should be guided by collaboration, transparency, preparation, and consistency.Journalism and Medi

Shotgun Metagenomics Reveals Taxonomic and Functional Shifts in Hot Water Microbiome Due to Temperature Setting and Stagnation

Hot water premise plumbing has emerged as a critical nexus of energy, water, and public health. The composition of hot water microbiomes is of special interest given daily human exposure to resident flora, especially opportunistic pathogens (OPs), which rely on complex microbial ecological interactions for their proliferation. Here, we applied shotgun metagenomic sequencing to characterize taxonomic and functional shifts in microbiomes as a function of water heater temperature setting, stagnation in distal pipes, and associated shifts in water chemistry. A cross-section of samples from controlled, replicated, pilot-scale hot water plumbing rigs representing different temperature settings (39, 42, and 51°C), stagnation periods (8 h vs. 7 days), and time-points, were analyzed. Temperature setting exhibited an overarching impact on taxonomic and functional gene composition. Further, distinct taxa were selectively enriched by specific temperature settings (e.g., Legionella at 39°C vs. Deinococcus at 51°C), while relative abundances of genes encoding corresponding cellular functions were highly consistent with expectations based on the taxa driving these shifts. Stagnation in distal taps diminished taxonomic and functional differences induced by heating the cold influent water to hot water in recirculating line. In distal taps relative to recirculating hot water, reads annotated as being involved in metabolism and growth decreased, while annotations corresponding to stress response (e.g., virulence disease and defense, and specifically antibiotic resistance) increased. Reads corresponding to OPs were readily identified by metagenomic analysis, with L. pneumophila reads in particular correlating remarkably well with gene copy numbers measured by quantitative polymerase chain reaction. Positive correlations between L. pneumophila reads and those of known protozoan hosts were also identified. Elevated proportions of genes encoding metal resistance and hydrogen metabolism were noted, which was consistent with elevated corrosion-induced metal concentrations and hydrogen generation. This study provided new insights into real-world factors influencing taxonomic and functional compositions of hot water microbiomes. Here metagenomics is demonstrated as an effective tool for screening for potential presence, and even quantities, of pathogens, while also providing diagnostic capabilities for assessing functional responses of microbiomes to various operational conditions. These findings can aid in informing future monitoring and intentional control of hot water microbiomes

The nitrogen cycle in the Broadbalk Wheat Experiment : recovery and losses of 15N-labelled fertilizer applied in spring and inputs of nitrogen from the atmosphere

15N-labelled nitrogen fertilizer (containing equal quantities of ammonium-N and nitrate-N) was applied in 4 consecutive years (1980–3) to different microplots located within the Broadbalk Wheat Experiment at Rothamsted, an experiment which has carried winter wheat continuously since 1843. Plots receiving 48, 96, 144 and 192 kg N/ha every year were given labelled fertilizer in mid-April at (nominally) these rates.Grain yields ranged from 1–2 t/ha on plots given no N fertilizer since 1843 to a maximum of 7·3 t/ha with 196 kg N/ha. On plots given adequate P and K fertilizer, between 51 and 68% of the labelled N was recovered in the above-ground crop; only about 40% was recovered where P deficiency limited crop growth. In 1981 fertilizerderived N retained in soil (0–70 cm) at harvest increased from 16 kg/ha, where 48 kg/ha was applied, to 38 kg/ha, where 192 kg/ha was applied. More than 80% of this retained N was in the plough layer (0–23 cm).Overall recovery of fertilizer N in crop plus soil ranged from 70 % to more than 90 % over the 4 years of the experiments. Losses of N were larger in years when spring rainfall was above average and when soil moisture deficits shortly after application were small.Crop uptake of unlabelled N derived from soil increased from 28 kg N/ha on the plot given no fertilizer N to 67 kg N/ha on the plot given 144 kg N/ha. The extra uptake of unlabelled N was mainly, if not entirely, due to greater mineralization of soil N in the plots that had been given N fertilizer for many years. Presumably fertilizer N increased the annual return of crop residues, which in turn led to an accumulation of mineralizable organic N, although there was only a small increase in total soil N content.Wheat given NH4-N grew less well and took up less N than wheat given N08-N in the relatively dry spring of 1980; there was little difference between the two forms of N in the wetter spring of 1981. In both years more fertilizer N was retained in the soil at harvest when fertilizer was applied as NH4-N than as N03-N.The N content of the soil in several plots of the experiment has been constant for many years, so that the annual removal of N is balanced by the annual input. A nitrogen balance for the plot given 144 kg fertilizer N/ha showed an average annual input of non-fertilizer N of at least 48 kg/ha, of which N in rain and seed accounts for about 14 kg/ha. The remainder may come from biological fixation of atmospheric N2 by blue-green algae, or from dry deposition of oxides of nitrogen and/or NH3 onto crop and soil. The overall annual loss of N from the crop–soil system on this particular plot was 54 kg N/ha per year, 28% of the total annual input from fertilizer and nonfertilizer N

Labels direct infants’ attention to commonalities during novel category learning

Recent studies have provided evidence that labeling can influence the outcome of infants’ visual categorization. However, what exactly happens during learning remains unclear. Using eye-tracking, we examined infants’ attention to object parts during learning. Our analysis of looking behaviors during learning provide insights going beyond merely observing the learning outcome. Both labeling and non-labeling phrases facilitated category formation in 12-month-olds but not 8-month-olds (Experiment 1). Non-linguistic sounds did not produce this effect (Experiment 2). Detailed analyses of infants’ looking patterns during learning revealed that only infants who heard labels exhibited a rapid focus on the object part successive exemplars had in common. Although other linguistic stimuli may also be beneficial for learning, it is therefore concluded that labels have a unique impact on categorization

Tertiary-Treated Municipal Wastewater is a Significant Point Source of Antibiotic Resistance Genes Into Duluth-Superior Harbor

In this study, the impact of tertiary-treated municipal wastewater on the quantity of several antibiotic resistance determinants in Duluth-Superior Harbor was investigated by collecting surface water and sediment samples from 13 locations in Duluth-Superior Harbor, the St. Louis River, and Lake Superior. Quantitative PCR (qPCR) was used to target three different genes encoding resistance to tetracycline (tet(A), tet(X), and tet(W)), the gene encoding the integrase of class 1 integrons (intI1), and total bacterial abundance (16S rRNA genes) as well as total and human fecal contamination levels (16S rRNA genes specific to the genus Bacteroides). The quantities of tet(A), tet(X), tet(W), intI1, total Bacteroides, and human-specific Bacteroides were typically 20-fold higher in the tertiary-treated wastewater than in nearby surface water samples. In contrast, the quantities of these genes in the St. Louis River and Lake Superior were typically below detection. Analysis of sequences of tet(W) gene fragments from four different samples collected throughout the study site supported the conclusion that tertiary-treated municipal wastewater is a point source of resistance genes into Duluth-Superior Harbor. This study demonstrates that the discharge of exceptionally treated municipal wastewater can have a statistically significant effect on the quantities of antibiotic resistance genes in otherwise pristine surface waters