Nonribosomal peptide synthetase gene clusters and characteristics of predicted NRPS-dependent siderophore synthetases in Armillaria and other species in the Physalacriaceae.

Fungal secondary metabolites are often pathogenicity or virulence factors synthesized by genes contained in secondary metabolite gene clusters (SMGCs). Nonribosomal polypeptide synthetase (NRPS) clusters are SMGCs which produce peptides such as siderophores, the high affinity ferric iron chelating compounds required for iron uptake under aerobic conditions. Armillaria spp. are mostly facultative necrotrophs of woody plants. NRPS-dependent siderophore synthetase (NDSS) clusters of Armillaria spp. and selected Physalacriaceae were investigated using a comparative genomics approach. Siderophore biosynthesis by strains of selected Armillaria spp. was evaluated using CAS and split-CAS assays. At least one NRPS cluster and other clusters were detected in the genomes studied. No correlation was observed between the number and types of SMGCs and reported pathogenicity of the species studied. The genomes contained one NDSS cluster each. All NDSSs were multi-modular with the domain architecture (ATC)3(TC)2. NDSS clusters of the Armillaria spp. showed a high degree of microsynteny. In the genomes of Desarmillaria spp. and Guyanagaster necrorhizus, NDSS clusters were more syntenic with NDSS clusters of Armillaria spp. than to those of the other Physalacriaceae species studied. Three A-domain orthologous groups were identified in the NDSSs, and atypical Stachelhaus codes were predicted for the A3 orthologous group. In vitro biosynthesis of mainly hydroxamate and some catecholate siderophores was observed. Hence, Armillaria spp. generally contain one highly conserved, NDSS cluster although some interspecific variations in the products of these clusters is expected. Results from this study lays the groundwork for future studies to elucidate the molecular biology of fungal phyto-pathogenicity.

Sapwood mycobiome varies across host, plant compartment and environments in Nothofagus forests from Northern Patagonia.

Global forests are increasingly being threatened by altered climatic conditions and increased attacks by pests and pathogens. The complex ecological interactions among pathogens, microbial communities, tree hosts and the environment are important drivers of forest dynamics. Little is known about the ecology of forest pathology and related microbial communities in temperate forests of the southern hemisphere. In this study, we used next-generation sequencing to characterize sapwood-inhabiting fungal communities in North Patagonian Nothofagus forests and assessed patterns of diversity of taxa and ecological guilds across climatic, site and host variables (health condition and compartment) as a contribution to Nothofagus autecology. The diversity patterns inferred through the metabarcoding analysis were similar to those obtained through culture-dependent approaches. However, we detected additional heterogeneity and greater richness with culture-free methods. Host species was the strongest driver of fungal community structure and composition, while host health status was the weakest. The relative impacts of site, season, plant compartment and health status were different for each tree species; these differences can be interpreted as a matter of water availability. For Nothofagus dombeyi, which is distributed across a wide range of climatic conditions, site was the strongest driver of community composition. The microbiome of N. pumilio varied more with season and temperature, a relevant factor for forest conservation in the present climate change scenario. Both species carry a number of potential fungal pathogens in their sapwood, whether they exhibit symptoms or not. Our results provide insight into the diversity of fungi associated with the complex pathobiome of the dominant Nothofagus species in southern South America.

Los bosques del mundo están cada vez más amenazados por las condiciones climáticas alteradas y el aumento de los ataques de plagas y patógenos. Las complejas interacciones ecológicas entre los patógenos, las comunidades microbianas, los árboles hospedantes y el medio ambiente son impulsores importantes de la dinámica forestal. Poco se sabe sobre la ecología de la patología forestal y las comunidades microbianas relacionadas en los bosques templados del hemisferio sur. En este estudio, utilizamos la secuenciación Illumina para caracterizar las comunidades de hongos que habitan en la albura en los bosques de Nothofagus de la Patagonia Norte y evaluamos los patrones de diversidad de taxones y gremios ecológicos a través de variables climáticas, de sitio y de hospedante (identidad, condición de salud y compartimento) como una contribución a la autoecología de los Nothofagus. Los patrones de diversidad inferidos a través del análisis metabarcoding fueron similares a los obtenidos a través de enfoques dependientes de cultivo. Sin embargo, detectamos mayor heterogeneidad y mayor riqueza con métodos independientes de cultivo. La especie hospedante fue el modelador más fuerte de la estructura y composición de la comunidad fúngica, mientras que el estado de salud del hospedante fue el más débil. El impacto relativo del sitio, la estación, el compartimento y el estado de salud fueron diferentes para cada especie de árbol; estas diferencias pueden interpretarse en clave de disponibilidad de agua. Para N. dombeyi, que se distribuye a lo largo de una amplia gama de condiciones climáticas, el sitio fue el principal modelador de la composición de la comunidad. El micobioma de Nothofagus pumilio varió más con la estación y la temperatura, un factor relevante para la conservación de los bosques en el escenario actual de cambio climático. Ambas especies portan una serie de patógenos fúngicos potenciales en su albura, ya sea que muestren síntomas o no. Nuestros resultados brindan una idea de la diversidad de hongos asociados con el complejo patobioma de las especies dominantes de Nothofagus en el sur de América del Sur.

Bradyrhizobium altum sp. nov., Bradyrhizobium oropedii sp. nov. and Bradyrhizobium acaciae sp. nov. from South Africa show locally restricted and pantropical nodA phylogeographic patterns.

Africa is known for its rich legume diversity with a significant number of endemic species originating in South Africa. Many of these legumes associate with rhizobial symbionts of the genus Bradyrhizobium, of which most represent new species. Yet, none of the Bradyrhizobium species from South Africa have been described. In this study, phylogenetic analysis of 16S rRNA gene sequences of fourteen strains isolated in southern Africa from root nodules of diverse legumes (i.e., from the tribes Crotalarieae, Acacieae, Genisteae, Phaseoleae and Cassieae) revealed that they belong to the Bradyrhizobium elkanii supergroup. The taxonomic position and possible novelty of these strains were further interrogated using genealogical concordance of five housekeeping genes (atpD, dnaK, glnII, gyrB and rpoB). These phylogenies consistently recovered four monophyletic groups and one singleton within Bradyrhizobium. Of these groups, two were conspecific with Bradyrhizobium brasilense UFLA 03-321T and Bradyrhizobium ivorense CI-1BT, while the remaining three represented novel taxa. Their existence was further supported with genome data, as well as metabolic and physiological traits. Analysis of nodA gene sequences further showed that the evolution of these bacteria likely involved adapting to local legume hosts and environmental conditions through the acquisition, via horizontal gene transfer, of optimal symbiotic loci. We accordingly propose the following names Bradyrhizobium acaciae sp. nov. 10BBT (SARCC 730T = LMG 31409T), Bradyrhizobium oropedii sp. nov. Pear76T (SARCC 731T = LMG 31408T), and Bradyrhizobium altum sp. nov. Pear77T (SARCC 754T = LMG 31407T) to accommodate three novel species, all of which are symbionts of legumes in South Africa.

Acoustic scattering and the exact Green function.

Acoustic waves are scattered by a bounded three-dimensional sound-soft obstacle. The scattered field can be given explicitly in terms of the exact Green function, defined as the solution of the scattering problem when the incident waves are generated by a point source. Methods for constructing the exact Green function are described, with emphasis on a recent paper by Rother and Hawkins [J. Acoust. Soc. Am. 149, 2179-2188 (2021)]. These methods include boundary integral equations and null-field equations.

Acoustic scattering by a small obstacle in the time domain.

Acoustic scattering by small obstacles in the frequency domain has an extensive literature, going back to Lord Rayleigh in the 19th century. However, analogous results in the time domain are rare. A typical problem concerns the interaction of a sound pulse with a small obstacle. The beginning of a theory for such problems is outlined, using time domain boundary integral equations. A key question is "What does it mean for an obstacle to be 'small'?"

The benefits of the Papanicolaou Society of Cytopathology System for reporting pancreatobiliary cytology: A 2-year review from a single academic institution.

OBJECTIVE: Endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) is an essential tool in the diagnosis of pancreatic lesions. The aim of this study was to evaluate the diagnostic accuracy of cytology from EUS-FNA, to correlate the results with the corresponding histopathological diagnoses and to analyse the impact of retrospective assignment of the Papanicolaou Society of Cytopathology (PSC) reporting system categories. METHODS: All pancreatic FNA specimens reported at the Royal Free Hospital during a 2-year period were retrospectively collected and assigned to the PSC system categories. Any available corresponding histological samples were assessed for concordance. RESULTS: In total, 236 cytology specimens from 223 patients were identified, of which 108 (45.8%) had corresponding histology samples. The main reason for cyto-histological discrepancy was sampling error. Interpretive error was identified in one case. Overall, sensitivity was 92.5%, specificity was 100%, diagnostic accuracy of cytology was 95%, false-positive rate was 0% and false-negative rate was 7.5%. The implementation of the new reporting system reduced the number of cases in the atypical category. All cases previously categorised as suspicious or malignant remained in the same category. CONCLUSIONS: EUS-FNA is an accurate method for evaluating pancreatobiliary lesions. The implementation of the Papanicolaou Society of Cytopathology diagnostic system enhances standardisation of the reporting terminology and reduces the number of samples in the non-standardised and equivocal atypical category.

Scattering by a sphere in a tube, and related problems.

Time-harmonic waves propagate along a cylindrical waveguide in which there is an obstacle. The problem is to calculate the reflection and transmission coefficients. Simple explicit approximations are found assuming that the waves are long compared to the diameter of the cross-section d. Simpler but useful approximations are found when the lateral dimensions of the obstacle are small compared to d. Results for spheres, discs, and spheroids are given.

An in situ FTIR study of the plasma- and thermally-driven reaction of isopropyl alcohol at CeO2: evidence for a loose transition state involving Ce3+?

This paper reports on the thermally-driven and non-thermal plasma-driven reaction of IsoPropyl Alcohol (IPA) on ceria (CeO2) with the aim to investigate the differences between plasma catalytic interactions and the analogous thermal reactions. Both were studied by in situ infrared spectroscopy: using diffuse reflectance for the thermal reaction and reflectance infrared for the plasma. For the thermal reaction, the activity towards the formation of acetone and acetaldehyde and, at higher temperatures, CO2 was dependent upon the coverage of surface carbonates and bicarbonates, suggesting at least some of these species blocked the relevant active sites. However, for the first time, methane and cold CO was observed and this was interpreted in terms of a roaming mechanism taking place at the surface via a loose transition state. By contrast, the plasma-driven process was not inhibited by adsorbed carbonaceous species producing acetone followed by isophorone and a polymethylacetylene-like polymer. Comparisons are made between the equivalent thermal and plasma reactions of isopropyl alcohol on Macor and tin oxide surfaces. On Macor the plasma produced similar products whereas on tin oxide there was no reaction. This suggests that the selection of catalysts for plasma processing cannot necessarily be determined from the equivalent thermal process.

Acoustic scattering by one bubble before 1950: Spitzer, Willis, and Division 6.

The solution of the problem of acoustic scattering by a single bubble is an ingredient in many theories used to predict the behavior of bubbly liquids. Significant work on this problem was done in the 1940s, but much of that work was described in unpublished wartime reports. However, it is now possible to access most of those reports, enabling a more coherent summary to be given. That is the purpose of this paper.

Application of Chloroplast Phylogenomics to Resolve Species Relationships Within the Plant Genus Amaranthus.

Amaranthus species are an emerging and promising nutritious traditional vegetable food source. Morphological plasticity and poorly resolved dendrograms have led to the need for well resolved species phylogenies. We hypothesized that whole chloroplast phylogenomics would result in more reliable differentiation between closely related amaranth species. The aims of the study were therefore: to construct a fully assembled, annotated chloroplast genome sequence of Amaranthus tricolor; to characterize Amaranthus accessions phylogenetically by comparing barcoding genes (matK, rbcL, ITS) with whole chloroplast sequencing; and to use whole chloroplast phylogenomics to resolve deeper phylogenetic relationships. We generated a complete A. tricolor chloroplast sequence of 150,027 bp. The three barcoding genes revealed poor inter- and intra-species resolution with low bootstrap support. Whole chloroplast phylogenomics of 59 Amaranthus accessions increased the number of parsimoniously informative sites from 92 to 481 compared to the barcoding genes, allowing improved separation of amaranth species. Our results support previous findings that two geographically independent domestication events of Amaranthus hybridus likely gave rise to several species within the Hybridus complex, namely Amaranthus dubius, Amaranthus quitensis, Amaranthus caudatus, Amaranthus cruentus and Amaranthus hypochondriacus. Poor resolution of species within the Hybridus complex supports the recent and ongoing domestication within the complex, and highlights the limitation of chloroplast data for resolving recent evolution. The weedy Amaranthus retroflexus and Amaranthus powellii was found to share a common ancestor with the Hybridus complex. Leafy amaranth, Amaranthus tricolor, Amaranthus blitum, Amaranthus viridis and Amaranthus graecizans formed a stable sister lineage to the aforementioned species across the phylogenetic trees. This study demonstrates the power of next-generation sequencing data and reference-based assemblies to resolve phylogenies, and also facilitated the identification of unknown Amaranthus accessions from a local genebank. The informative phylogeny of the Amaranthus genus will aid in selecting accessions for breeding advanced genotypes to satisfy global food demand.

Mixta gen. nov., a new genus in the Erwiniaceae.

The Erwiniaceae contain many species of agricultural and clinical importance. Although relationships among most of the genera in this family are relatively well resolved, the phylogenetic placement of several taxa remains ambiguous. In this study, we aimed to address these uncertainties by using a combination of phylogenetic and genomic approaches. Our multilocus sequence analysis and genome-based maximum-likelihood phylogenies revealed that the arsenate-reducing strain IMH and plant-associated strain ATCC 700886, both previously presumptively identified as members of Pantoea, represent novel species of Erwinia. Our data also showed that the taxonomy of Erwinia teleogrylli requires revision as it is clearly excluded from Erwinia and the other genera of the family. Most strikingly, however, five species of Pantoea formed a distinct clade within the Erwiniaceae, where it had a sister group relationship with the Pantoea + Tatumella clade. By making use of gene content comparisons, this new clade is further predicted to encode a range of characters that it shares with or distinguishes it from related genera. We thus propose recognition of this clade as a distinct genus and suggest the name Mixta in reference to the diverse habitats from which its species were obtained, including plants, humans and food products. Accordingly, a description for Mixta gen. nov. is provided to accommodate the four species Mixta calida comb. nov., M. gaviniae comb. nov., M. intestinalis comb. nov. and M. theicola comb. nov., with M. calida as the type species for the genus.

First detection of Edwardsiella ictaluri (Proteobacteria: Enterobacteriaceae) in wild Australian catfish.

The bacterium Edwardsiella ictaluri is considered to be one of the most significant pathogens of farmed catfish in the United States of America and has also caused mortalities in farmed and wild fishes in many other parts of the world. E. ictaluri is not believed to be present in wild fish populations in Australia, although it has previously been detected in imported ornamental fishes held in quarantine facilities. In an attempt to confirm freedom from the bacterium in Australian native fishes, we undertook a risk-based survey of wild catfishes from 15 sites across northern Australia. E. ictaluri was detected by selective culturing, followed by DNA testing, in Wet Tropics tandan (Tandanus tropicanus) from the Tully River, at a prevalence of 0.40 (95% CI 0.21-0.61). The bacterium was not found in fishes sampled from any of the other 14 sites. This is the first report of E. ictaluri in wild fishes in Australia.

Multiple scattering and scattering cross sections.

The scattering cross section for a cluster of scatterers can be calculated using various methods, either exactly or by invoking various approximations. Of special interest are methods in which the scattering properties of individual members of the cluster are used. The underlying question is: Can the contribution to the cluster's cross section from any one member of the cluster be identified? Except for situations in which all effects of multiple scattering are ignored, no such method of identification has been found.

Metals and Organohalogen Contaminants in Bald Eagles (Haliaeetus leucocephalus) from Ontario, 1991-2008.

We examined the degree of exposure of lead (Pb), mercury (Hg), and several organohalogen contaminants and its potential impact on survival of bald eagles in Ontario from 1991 to 2008. Overall, results for 43 dead or dying bald eagles collected in the province indicate that 23% (10/43) of birds died of Pb poisoning and 9% (4/43) died of suspected Hg poisoning. Pb poisoning was diagnosed based on exceedances of toxicity thresholds in liver and kidney and supported by clinical observations, necropsy results, and histology findings when available. Evidence for Hg poisoning in eagles was limited; however, Hg concentrations exceeded the toxicity threshold in kidney. Pb concentrations ranged widely in liver and kidney. Total Hg concentrations were relatively higher in kidney compared with liver and were significantly correlated with selenium (Se) concentrations in both tissues. Concentrations of p,p'-DDE and sum PCBs in livers of 12 bald eagles collected from 2001 to 2004 were likely below concentrations associated with adverse effects. Hepatic concentrations of total polybrominated diphenyl ethers were generally higher in birds collected from southern Ontario compared with northern Ontario. Potential impacts of exposure to these flame retardants and others are not known. Elevated metal exposure appears to influence survivorship and may affect the recovery of bald eagles in the province, particularly in southern Ontario and along the Great Lakes where a disproportionate number of poisoned eagles were collected. Increased efforts are needed to identify sources of exposure and develop measures to reduce metal exposure in this top predator.

Phylogenomic resolution of the bacterial genus Pantoea and its relationship with Erwinia and Tatumella.

Investigation of the evolutionary relationships between related bacterial species and genera with a variety of lifestyles have gained popularity in recent years. For analysing the evolution of specific traits, however, a robust phylogeny is essential. In this study we examined the evolutionary relationships among the closely related genera Erwinia, Tatumella and Pantoea, and also attempted to resolve the species relationships within Pantoea. To accomplish this, we used the whole genome sequence data for 35 different strains belonging to these three genera, as well as nine outgroup taxa. Multigene datasets consisting of the 1039 genes shared by these 44 strains were then generated and subjected to maximum likelihood phylogenetic analyses, after which the results were compared to those using conventional multi-locus sequence analysis (MLSA) and ribosomal MLSA (rMLSA) approaches. The robustness of the respective phylogenies was then explored by considering the factors typically responsible for destabilizing phylogenetic trees. We found that the nucleotide datasets employed in the MLSA, rMLSA and 1039-gene datasets contained significant levels of homoplasy, substitution saturation and differential codon usage, all of which likely gave rise to the observed lineage specific rate heterogeneity. The effects of these factors were much less pronounced in the amino acid dataset for the 1039 genes, which allowed reconstruction of a fully supported and resolved phylogeny. The robustness of this amino acid tree was also supported by different subsets of the 1039 genes. In contrast to the smaller datasets (MLSA and rMLSA), the 1039 amino acid tree was also not as sensitive to long-branch attraction. The robust and well-supported evolutionary hypothesis for the three genera, which confidently resolved their various inter- and intrageneric relationships, represents a valuable resource for future studies. It will form the basis for studies aiming to understand the forces driving the divergence and maintenance of lineages, species and biological traits in this important group of bacteria.

On the far-field computation of acoustic radiation forces.

It is known that the steady acoustic radiation force on a scatterer due to incident time-harmonic waves can be calculated by evaluating certain integrals of velocity potentials over a sphere surrounding the scatterer. The goal is to evaluate these integrals using far-field approximations and appropriate limits. Previous derivations are corrected, clarified, and generalized. Similar corrections are made to textbook derivations of optical theorems.

Are WWTPs effluents responsible for acute toxicity? Seasonal variations of sediment quality at the Bay of Cádiz (SW, Spain).

Adverse effects of wastewater treatment plants (WWTPs) on sediment quality at the Bay of Cádiz (SW, Spain) were evaluated by a battery of acute bioassays and chemical contamination. Five sites directly affected by WWTPs effluents and one control site were chosen. Results evidenced clear deterioration of ecological sediment quality parameters and possible effects on aquatic communities towards WWTPs areas. Acute toxicity and chemical contamination varied significantly across the studied sites and differed between winter and summer seasons. The Bay of Cádiz is contaminated by PAHs, metals, detergents (SAS) and pharmaceutical products. Principal Component Analyses indicated metals, SAS and pharmaceutical products as the major environmental stresses. Sea-urchin embryo-larval and microalgae growth rate were the most sensitive bioassays to evaluate resuspension of contaminants (elutriate) from bulk sediment. Amphipods mortality and Microtox(®) solid phase test bioassays were recommended to evaluate bulk sediment quality. Therefore, the use of multiple-bioassays, sensitive to sediment pollution, may provide complementary information to diagnose environmental factors that can impair aquatic communities. The battery of bioassays is recommended to assess and monitor marine sediments directly affected by a mixture of contaminants released from WWTPs.

A candidate short-term toxicity test using Ampelisca brevicornis to assess sublethal responses to pharmaceuticals bound to marine sediments.

Lethal and sublethal responses related to different phases of metabolism (phases I and II enzymatic activities), neurotoxicity (acetylcholinesterase activity), oxidative stress (lipid peroxidation and antioxidant enzyme activities), and genetic damage (DNA strand breaks) were analysed to assess the possible adverse effects of pharmaceuticals bound to marine sediments. The crustacean amphipod Ampelisca brevicornis was chosen as the bioindicator species. Organisms were exposed for 10 days to sediment spiked with pharmaceutical compounds frequently used and previously detected in the environment: carbamazepine (CBZ), ibuprofen (IBP), fluoxetine (FX), 17α-ethynylestradiol (EE2), propranolol (PRO), and caffeine (CAF). Short-term bioassay to evaluate amphipod mortality was recommended to assess pollution by CBZ, FX, and PRO. IBP and PRO were metabolized by phases I and II detoxification enzymatic activities. Oxidative stress was caused by PRO and CAF. Contrary to expected results, DNA damage (strand breaks) decreased after the exposure of amphipods to sediment spiked with IBP, FX, EE2, PRO, and CAF (including environmental concentrations). FX was neurotoxic to amphipods. The battery of biomarkers tested allowed the assessment of bioavailability, oxidative stress, genotoxicity, and neurotoxicity of the pharmaceuticals analysed. The results of this study suggested that pharmaceutical products at concentrations currently found in the environment might cause a wide variety of adverse effects (based on laboratory studies). The results obtained here are useful for environmental risk assessment of marine sediments contaminated by pharmaceuticals. Nevertheless, more research is needed using field-based marine sediments.

Bioavailability, oxidative stress, neurotoxicity and genotoxicity of pharmaceuticals bound to marine sediments. The use of the polychaete Hediste diversicolor as bioindicator species.

A set of "early warning responses", measured as biomarkers of exposure and effect, was applied in the marine bioindicator Hediste diversicolor, in a way to assess the environmental quality of sediment affected by pharmaceutical contamination. Sublethal responses were determined in the sea-worms after 14-days of exposure to sediment spiked with some of the most representative pharmaceutical products found in the environment: carbamazepine (CBZ), ibuprofen (IBP), fluoxetine (FX), 17α-ethynylestradiol (EE2) and propranolol (PRO), including the environmental concentrations. Phases I (ethoxyresorufin O-deethylase - EROD and dibenzylfluorescein dealkylase - DBF) and II (glutathione S-transferase - GST) of the metabolism, antioxidant system (glutathione peroxidase - GPX and glutathione reductase - GR), neurotoxicity (acetylcholinesterase - AChE) and oxidative effects (lipid peroxidation - LPO and DNA damage strand breaks) were selected to evaluate the sublethal responses in the sea-worms. FX, EE2 and PRO were detoxified by the phase I of the metabolism (EROD activity). On the other hand, phase II (GST-activity) did not respond in sea-worms exposed to pharmaceutical products, except for the environmental concentrations of CBZ (activation) and PRO (deactivation). Neurotoxicity was induced in sea-worms exposed to EE2 (only the environmental concentrations), FX, IBP and CBZ. Oxidative effect determined as LPO increased in sea-worms exposed to environmental concentrations of IBP, EE2 and PRO. Genetic damage increased in sea-worms exposed to IBP and diminished for FX, EE2 and PRO. Our results indicated the toxicity of pharmaceutical products and recommended the battery of biomarkers and the bioindicator specie H. diversicolor for the environmental quality assessment of sediment affected by pharmaceutical contamination.

A scaled mapping parabolic equation for sloping range-dependent environments.

Parabolic equation solutions use various techniques for approximating range-dependent interfaces. One is a mapping approach [M. D. Collins et al., J. Acoust. Soc. Am. 107, 1937-1942 (2000)] where at each range the domain is vertically translated so that sloping bathymetry becomes horizontal, and range dependence is transferred to the upper surface. In this paper, a scaled mapping is suggested where the domain is vertically distorted so that both the bathymetry and upper surface are horizontal. Accuracy is demonstrated for problems involving fluid sediments. Generalizations of the approach should be useful for environments with layer thicknesses that vary with range.