Spatial variability in nitrification rates and ammonia-oxidizing microbial communities in the agriculturally impacted Elkhorn Slough estuary, California

Ammonia oxidation-the microbial oxidation of ammonia to nitrite and the first step in nitrification-plays a central role in nitrogen cycling in coastal and estuarine systems. Nevertheless, questions remain regarding the connection between this biogeochemical process and the diversity and abundance of the mediating microbial community. In this study, we measured nutrient fluxes and rates of sediment nitrification in conjunction with the diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing betaproteobacteria (β-AOB). Sediments were examined from four sites in Elkhorn Slough, a small agriculturally impacted coastal California estuary that opens into Monterey Bay. Using an intact sediment core flowthrough incubation system, we observed significant correlations among NO(3)(-), NO(2)(-), NH(4)(+), and PO(4)(3+) fluxes, indicating a tight coupling of sediment biogeochemical processes. (15)N-based measurements of nitrification rates revealed higher rates at the less impacted, lower-nutrient sites than at the more heavily impacted, nutrient-rich sites. Quantitative PCR analyses revealed that β-AOB amoA (encoding ammonia monooxygenase subunit A) gene copies outnumbered AOA amoA gene copies by factors ranging from 2- to 236-fold across the four sites. Sites with high nitrification rates primarily contained marine/estuarine Nitrosospira-like bacterial amoA sequences and phylogenetically diverse archaeal amoA sequences. Sites with low nitrification rates were dominated by estuarine Nitrosomonas-like amoA sequences and archaeal amoA sequences similar to those previously described in soils. This is the first report measuring AOA and β-AOB amoA abundance in conjunction with (15)N-based nitrification rates in estuary sediments.     

The depth of porphyrin in a membrane and the membrane's physical properties affect the photosensitizing efficiency

Photosensitized biological processes, as applied in photodynamic therapy, are based on light-triggered generation of molecular singlet oxygen by a membrane-residing sensitizer. Most of the sensitizers currently used are hydrophobic or amphiphilic porphyrins and their analogs. The possible activity of the short-lived singlet oxygen is limited to the time it is diffusing in the membrane, before it emerges into the aqueous environment. In this paper we demonstrate the enhancement of the photosensitization process that is obtained by newly synthesized protoporphyrin derivatives, which insert their tetrapyrrole chromophore deeper into the lipid bilayer of liposomes. The insertion was measured by fluorescence quenching by iodide and the photosensitization efficiency was measured with 9,10-dimethylanthracene, a fluorescent chemical target for singlet oxygen. We also show that when the bilayer undergoes a melting phase transition, or when it is fluidized by benzyl alcohol, the sensitization efficiency decreases because of the enhanced diffusion of singlet oxygen. The addition of cholesterol or of dimyristoyl phosphatydilcholine to the bilayer moves the porphyrin deeper into the bilayer; however, the ensuing effect on the sensitization efficiency is different in these two cases. These results could possibly define an additional criterion for the choice and design of hydrophobic, membrane-bound photosensitizers.     

Agency and intervention

Novel ways to intervene on brain function raise questions about agency and responsibility. Here, I discuss whether direct brain interventions, and in particular, deep brain stimulation, pose a threat to agency in individual cases, or to our general conceptualization of what it is to be a responsible agent. While I do not currently see evidence that these interventions constitute a global challenge to our concept of agency, they do have the potential to diminish agency in individuals. I consider whether the lack of evidence for a global challenge ratifies our folk conceptions, or is a necessary consequence of them. In closing, I propose that our theoretical understanding of agency and our therapeutic approaches could be improved with a more nuanced, multidimensional view of agency.     

Multiple phylogenetically-diverse,differentially-virulent Burkholderia pseudomallei isolated from a single soil sample collected in Thailand

Burkholderia pseudomallei is a soil-dwelling bacterium endemic to Southeast Asia and northern Australia that causes the disease, melioidosis. Although the global genomic diversity of clinical B. pseudomallei isolates has been investigated, there is limited understanding of its genomic diversity across small geographic scales, especially in soil. In this study, we obtained 288 B. pseudomallei isolates from a single soil sample (~100g; intensive site 2, INT2) collected at a depth of 30cm from a site in Ubon Ratchathani Province, Thailand. We sequenced the genomes of 169 of these isolates that represent 7 distinct sequence types (STs), including a new ST (ST1820), based on multi-locus sequence typing (MLST) analysis. A core genome SNP phylogeny demonstrated that all identified STs share a recent common ancestor that diverged an estimated 796–1260 years ago. A pan-genomics analysis demonstrated recombination between clades and intra-MLST phylogenetic and gene differences. To identify potential differential virulence between STs, groups of BALB/c mice (5 mice/isolate) were challenged via subcutaneous injection (500 CFUs) with 30 INT2 isolates representing 5 different STs; over the 21-day experiment, eight isolates killed all mice, 2 isolates killed an intermediate number of mice (1–2), and 20 isolates killed no mice. Although the virulence results were largely stratified by ST, one virulent isolate and six attenuated isolates were from the same ST (ST1005), suggesting that variably conserved genomic regions may contribute to virulence. Genomes from the animal-challenged isolates were subjected to a bacterial genome-wide association study to identify genomic regions associated with differential virulence. One associated region is a unique variant of Hcp1, a component of the type VI secretion system, which may result in attenuation. The results of this study have implications for comprehensive sampling strategies, environmental exposure risk assessment, and understanding recombination and differential virulence in B. pseudomallei.     

Large Roads Reduce Bat Activity across Multiple Species

Although the negative impacts of roads on many terrestrial vertebrate and bird populations are well documented, there have been few studies of the road ecology of bats. To examine the effects of large roads on bat populations, we used acoustic recorders to survey bat activity along ten 300 m transects bordering three large highways in northern California, applying a newly developed statistical classifier to identify recorded calls to the species level. Nightly counts of bat passes were analyzed with generalized linear mixed models to determine the relationship between bat activity and distance from a road. Total bat activity recorded at points adjacent to roads was found to be approximately one-half the level observed at 300 m. Statistically significant road effects were also found for the Brazilian free-tailed bat (Tadarida brasiliensis), big brown bat (Eptesicus fuscus), hoary bat (Lasiurus cinereus), and silver-haired bat (Lasionycteris noctivagans). The road effect was found to be temperature dependent, with hot days both increasing total activity at night and reducing the difference between activity levels near and far from roads. These results suggest that the environmental impacts of road construction may include degradation of bat habitat and that mitigation activities for this habitat loss may be necessary to protect bat populations.     

The Disconnect Between Restoration Goals and Practices: A Case Study of Watershed Restoration in the Russian River Basin, California

Over the past two decades, watershed restoration has dramatically increased internationally. California has been at the forefront, allocating billions of dollars to restoration activities through legislation and voter-approved bonds. Yet, the implications of restoration remain ambiguous because there has been little examination of restoration accomplishments and almost no analysis of the political context of restoration. This article addresses these gaps, utilizing a case study of the Russian River basin in Northern California. We identify trends that shed light on both the ecological and the political implications of restoration at a basin scale by examining a database of 787 restoration projects implemented in the Russian River basin since the early 1980s. Although a total of over $47 million has been spent on restoration in the basin, dominant forms of restoration are limited in scope to small-scale projects that focus on technical solutions to site-specific problems. The majority of restoration efforts are devoted to road repair, riparian stabilization, and in-stream structures, accounting for 62% of all projects. These types of projects do not address the broader social drivers of watershed change such as land and water uses. We suggest that restoration can become more effective by addressing the entire watershed as a combination of social and ecological forces that interact to produce watershed conditions.     

Characteristics and outcomes of hospital admissions for COVID-19 and influenza in the Toronto area

BACKGROUND:Patient characteristics, clinical care, resource use and outcomes associated with admission to hospital for coronavirus disease 2019 (COVID-19) in Canada are not well described.METHODS:We described all adults with COVID-19 or influenza discharged from inpatient medical services and medical–surgical intensive care units (ICUs) between Nov. 1, 2019, and June 30, 2020, at 7 hospitals in Toronto and Mississauga, Ontario. We compared patient outcomes using multivariable regression models, controlling for patient sociodemographic factors and comorbidity level. We validated the accuracy of 7 externally developed risk scores to predict mortality among patients with COVID-19.RESULTS:There were 1027 hospital admissions with COVID-19 (median age 65 yr, 59.1% male) and 783 with influenza (median age 68 yr, 50.8% male). Patients younger than 50 years accounted for 21.2% of all admissions for COVID-19 and 24.0% of ICU admissions. Compared with influenza, patients with COVID-19 had significantly greater in-hospital mortality (unadjusted 19.9% v. 6.1%, adjusted relative risk [RR] 3.46, 95% confidence interval [CI] 2.56–4.68), ICU use (unadjusted 26.4% v. 18.0%, adjusted RR 1.50, 95% CI 1.25–1.80) and hospital length of stay (unadjusted median 8.7 d v. 4.8 d, adjusted rate ratio 1.45, 95% CI 1.25–1.69). Thirty-day readmission was not significantly different (unadjusted 9.3% v. 9.6%, adjusted RR 0.98, 95% CI 0.70–1.39). Three points-based risk scores for predicting in-hospital mortality showed good discrimination (area under the receiver operating characteristic curve [AUC] ranging from 0.72 to 0.81) and calibration.INTERPRETATION:During the first wave of the pandemic, admission to hospital for COVID-19 was associated with significantly greater mortality, ICU use and hospital length of stay than influenza. Simple risk scores can predict in-hospital mortality in patients with COVID-19 with good accuracy.

International studies report that patients admitted to hospital with coronavirus disease 2019 (COVID-19) have high rates of critical illness and mortality.^1–5 Two small Canadian case series have described care for critically ill patients with COVID-19 and found mortality rates of up to 25%.^6,7 However, outcomes of patients admitted to hospital for COVID-19 in Canada are not well described, particularly outside of intensive care units (ICUs). Case fatality rates for COVID-19 vary dramatically worldwide,⁸ and outcomes of patients admitted to hospital for COVID-19 in Canada may differ from other countries because of differences in populations, public health and health care systems.Seasonal influenza is a useful comparator for COVID-19^9–11 as it is another respiratory virus, familiar to the general public, with high rates of morbidity and mortality. The purpose of this study was to describe patient characteristics, resource use, clinical care and outcomes for patients admitted to hospital with COVID-19 in Ontario, Canada, using influenza as a comparator. We also validated the performance of various prognostic risk scores for in-hospital mortality among patients with COVID-19.