Feeding habits and multifunctional classification of soil-associated consumers from protists to vertebrates.

Soil organisms drive major ecosystem functions by mineralising carbon and releasing nutrients during decomposition processes, which supports plant growth, aboveground biodiversity and, ultimately, human nutrition. Soil ecologists often operate with functional groups to infer the effects of individual taxa on ecosystem functions and services. Simultaneous assessment of the functional roles of multiple taxa is possible using food-web reconstructions, but our knowledge of the feeding habits of many taxa is insufficient and often based on limited evidence. Over the last two decades, molecular, biochemical and isotopic tools have improved our understanding of the feeding habits of various soil organisms, yet this knowledge is still to be synthesised into a common functional framework. Here, we provide a comprehensive review of the feeding habits of consumers in soil, including protists, micro-, meso- and macrofauna (invertebrates), and soil-associated vertebrates. We have integrated existing functional group classifications with findings gained with novel methods and compiled an overarching classification across taxa focusing on key universal traits such as food resource preferences, body masses, microhabitat specialisation, protection and hunting mechanisms. Our summary highlights various strands of evidence that many functional groups commonly used in soil ecology and food-web models are feeding on multiple types of food resources. In many cases, omnivory is observed down to the species level of taxonomic resolution, challenging realism of traditional soil food-web models based on distinct resource-based energy channels. Novel methods, such as stable isotope, fatty acid and DNA gut content analyses, have revealed previously hidden facets of trophic relationships of soil consumers, such as food assimilation, multichannel feeding across trophic levels, hidden trophic niche differentiation and the importance of alternative food/prey, as well as energy transfers across ecosystem compartments. Wider adoption of such tools and the development of open interoperable platforms that assemble morphological, ecological and trophic data as traits of soil taxa will enable the refinement and expansion of the multifunctional classification of consumers in soil. The compiled multifunctional classification of soil-associated consumers will serve as a reference for ecologists working with biodiversity changes and biodiversity-ecosystem functioning relationships, making soil food-web research more accessible and reproducible.

Catalogue of the free-living and arthropod-associated Laelapidae Canestrini (Acari: Mesostigmata), with revised generic concepts and a key to genera.

The cosmopolitan mite family Laelapidae includes both free-living predatory species and species associated with arthropods, mammals or birds. This work presents a list of free-living and arthropod-associated species of laelapids, with corresponding taxonomic information and references. It includes 1088 species (in addition to three subspecies) assigned to 73 genera, 61 new combinations and two new synonymies at the generic level. Laelaps (Apolaelaps) Silvestri is raised to the generic level. Many of the species described before about 1950 are poorly characterised and cannot be classified with confidence at the family or generic level. Hence, ten genera, one subgenus, 121 species (ca. 70% of which were reported as Hypoaspis Canestrini or Laelaps (Hypoaspis) Canestrini) and one subspecies, are considered incertae sedis, because of their inadequate morphological characterisation in the literature. Some of these may not even belong to the Laelapidae or to the groups of interest for this publication. A total of 89 species, 30 genera, one subgenus, one tribe and one subfamily previously associated with genera treated in this catalogue are now placed in other families or, less commonly, in laelapid genera not considered here because they are considered essentially vertebrate parasites (taxa excluded). Twenty-six other species (one cited as a "variety") are cited as nomina nuda. An illustrated key to the 73 genera included in the catalogue along with revised generic diagnoses are provided.

Review of the mite genus Ololaelaps (Acari, Laelapidae) and redescription of O.formidabilis Berlese.

A species of laelapid mite, Ololaelapsformidabilis, is redescribed based on male and female adults from soil in Sumatra, Indonesia. This species is distinguished from other Ololaelaps species by its metapodal platelet narrowly fused with the parapodal plate and by its hologastric shield having two inverted-V-like ridges. The genus is redescribed based on a review of the literature and examination of specimens of some species. Valid species of Ololaelaps are listed and accompanied by notes on morphological characters to assist future revision of the genus.

Acarine biocontrol agents Neoseiulus californicus sensu Athias-Henriot (1977) and N. barkeri Hughes (Mesostigmata: Phytoseiidae) redescribed, their synonymies assessed, and the identity of N. californicus (McGregor) clarified based on examination of types.

In 1954, McGregor described two species of phytoseiids from lemon, in California, USA: Typhlodromus californicus McGregor and T. mungeri McGregor, the former represented by one male, and the latter by two females. Since its description, T. mungeri was synonymised under T. californicus, and the name T. (now Neoseiulus) californicus has been used extensively to represent a species that is now commonly used as a biocontrol agent of crop pests worldwide. However, the true identity of the biocontrol agent is uncertain because the original descriptions of T. californicus and T. mungeri were not adequate enough to allow an irrefutable identification, with each description being based on specimens of a single sex. An examination of the types of N. californicus and N. mungeri revealed that they are morphologically identical to the male and female of N. barkeri Hughes, 1948, respectively, and that they are in fact junior synonyms of N. barkeri-and are therefore distinct from the biocontrol agent globally called N. californicus (sensu Athias-Henriot, 1977; see Griffiths, 2015). This is further supported by a comparison with male and female syntypes of N. barkeri, as well as other specimens of N. barkeri including some collected from the type host in the vicinity of the type location (i.e. lemon in southern California, 1952-1958). We redescribe the male and female of both N. barkeri and N. californicus sensu Athias-Henriot (1977), based on representative specimens from at least 14 and 19 populations, respectively. Based on examination of types, we confirm the synonymy of N. mckenziei (Schuster Pritchard, 1963), N. picketti (Specht, 1968), and N. oahuensis (Prasad, 1968) with N. barkeri, and that the names N. chilenensis (Dosse, 1958b) and N. wearnei (Schicha, 1987) represent the same species as N. californicus sensu Athias-Henriot (1977). We also provide a hypothesis as to why Chant (1959) had erroneously synonymised T. californicus and T. mungeri under T. marinus (Willmann). Finally, we suggest maintaining the prevailing usage of the name N. californicus (McGregor) for the species concept of Athias-Henriot (1977) as followed by subsequent authors, through submission of a separate application to the International Commission of Zoological Nomenclature (ICZN). In the meantime, the current meaning of N. californicus should be maintained until a ruling by the ICZN is made on the application.

An EPID-based method to determine mechanical deformations in a linear accelerator.

PURPOSE: Medical linear accelerators (linac) are delivering increasingly complex treatments using modern techniques in radiation therapy. Complete and precise mechanical QA of the linac is therefore necessary to ensure that there is no unexpected deviation from the gantry's planned course. However, state-of-the-art EPID-based mechanical QA procedures often neglect some degrees of freedom (DOF) like the in-plane rotations of the gantry and imager or the source movements inside the gantry head. Therefore, the purpose of this work is to characterize a 14 DOF method for the mechanical QA of linacs. This method seeks to measure every mechanical deformation in a linac, including source movements, in addition to relevant clinical parameters like mechanical and radiation isocenters. METHODS: A widely available commercial phantom and a custom-made accessory inserted in the linac's interface mount are imaged using the electronic portal imaging device (EPID) at multiple gantry angles. Then, simulated images are generated using the nominal geometry of the linac and digitized models of the phantoms. The nominal geometry used to generate these images can be modified using 14 DOF (3 rigid rotations and 3 translations for the imager and the gantry, and 2 in-plane translations of the source) and any change will modify the simulated image. The set of mechanical deformations that minimizes the differences between the simulated and measured image is found using a genetic algorithm coupled with a gradient-descent optimizer. Phantom mispositioning and gantry angular offset were subsequently calculated and extracted from the results. Simulations of the performances of the method for different levels of noise in the phantom models were performed to calculate the absolute uncertainty of the measured mechanical deformations. The measured source positions and the center of collimation were used to define the beam central axis and calculate the radiation isocenter position and radius. RESULTS: After the simultaneous optimization of the 14 DOF, the average distance between the center of the measured and simulated ball bearings on the imager was 0.086 mm. Over the course of a full counter-clockwise gantry rotation, all mechanical deformations were measured, showing sub-millimeter translations and rotations smaller than 1° along every axis. The average absolute uncertainty of the 14 DOF (1 SD) was 0.15 mm or degree. Phantom positioning errors were determined with more than 0.1 mm precision. Errors introduced in the experimental setup like phantom positioning errors, source movements or gantry angular offsets were all successfully detected by our QA method. The mechanical deformations measured are shown to be reproducible over the course of a few weeks and are not sensitive to the experimental setup. CONCLUSION: This work presents of new method for an accurate mechanical QA of the linacs. It features a 14 DOF model of the mechanical deformations that is both more complete and precise than other available methods. It has demonstrated sub-millimeter accuracy through simulation and experimentation. Introduced errors were successfully detected with high precision.

A new genus and species of Laelapidae (Acari: Mesostigmata) from Iran.

A new monotypic mite genus of the family Laelapidae, Persicolaelaps gen. nov., is described to accommodate a new species, P. hallidayi sp. nov., on the basis of adult female specimens collected from decaying wood, soil and litter in northern Iran, Golestan and Mazandaran provinces, respectively. The new genus can be distinguished from other members of the family by a combination of morphological attributes, some of which are unique or rarely observed in laelapids, such as (1) a series of small subrectangular sclerites flanking dorsally coxae I and gnathosomal base and adjoining podal plates anterolaterally, which are extending from and fused with sternal shield between coxae I and II; (2) an epigynal shield, so broad as to reach or even overlap acetabula III-IV, posteriorly axe-shaped; (3) metasternal setae absent; (4) a typical anal shield, though capturing pair of opisthogastric setae JV3; (5) gnathotectum triangular and acuminate; (6) the presence of six setae on trochanter IV; (7) genu IV with two ventral setae (occasional in Laelapidae); (8) internal malae with a series of thick, elongate filaments.

Two new mite species of the genus Zygoseius Berlese from Mexico (Acari, Mesostigmata).

Two new species of mites of the genus Zygoseius Berlese, Zygoseius papaversp. n. and Zygoseius lindquistisp. n., collected from moss and flood debris, respectively, in a creek in Chiapas State, Mexico, are described herein.

Two new species of Gaeolaelaps (Acari: Mesostigmata: Laelapidae) from Iran, with a revised generic concept and notes on significant morphological characters in the genus.

Two new species of laelapid mites of the genus Gaeolaelaps Evans & Till are described based on adult females collected from soil and litter in Kerman Province, southeastern Iran, and Mazandaran Province, northern Iran. Gaeolaelaps jondishapouri Nemati & Kavianpour is redescribed based on the holotype and additional specimens collected in southeastern Iran. The concept of the genus is revised to incorporate some atypical characters of recently described species. Finally, some morphological attributes with potential to define natural species groupings as well as hypoaspidine genera are discussed, particularly idiosomal gland pores and poroids.

Redescription of an early-derivative mite, Pentasetacus araucariae (Eriophyoidea, Phytoptidae), and new hypotheses on the eriophyoid reproductive anatomy.

A unique set of plesiomorphic characters, and its association with an ancient gymnosperm, Araucaria araucana, have made Pentasetacus araucariae a putative relict of a lineage of gymnosperm-associated mites, itself possibly basal to all extant eriophyoids. However, the suboptimal description of this species is impeding morphological comparisons with other species, which are fundamental to eriophyoid systematics. Herein, we designate a female lectotype from syntype specimens and use additional non-type material to redescribe P. araucariae based on external and internal anatomy using different microscopic and 3D reconstruction techniques. Contrarily to statements in the literature, P. araucariae has undivided empodia in all instars, short spermathecal tubes, and large, globose spermathecae in females, as well as rudimentary genital fovea in immatures. In addition, males of P. araucariae were shown to have genitalic attributes similar to a species of Trisetacus studied in parallel, including two reservoir-like structures, which may represent parts of the genital chamber and of the ductus ejaculatorius, respectively, as well as paired testes and ducti deferentes. This is contrary to previous, limited knowledge on eriophyoids indicating that they possess a single testis. Although their short spermathecal tubes weaken the cladistic relationship between P. araucariae (Pentasetacinae) and conifer-associated Nalepellinae (e.g. Trisetacus) having long tubes, the structural similarities in male genitalia may reinforce it.

Species boundaries and host range of tortoise mites (Uropodoidea) phoretic on bark beetles (Scolytinae), using morphometric and molecular markers.

Understanding the ecology and evolutionary history of symbionts and their hosts requires accurate taxonomic knowledge, including clear species boundaries and phylogenies. Tortoise mites (Mesostigmata: Uropodoidea) are among the most diverse arthropod associates of bark beetles (Curculionidae: Scolytinae), but their taxonomy and host associations are largely unstudied. We tested the hypotheses that (1) morphologically defined species are supported by molecular data, and that (2) bark beetle uropodoids with a broad host range comprise cryptic species. To do so, we assessed the species boundaries of uropodoid mites collected from 51 host species, across 11 countries and 103 sites, using morphometric data as well as partial cytochrome oxidase I (COI) and nuclear large subunit ribosomal DNA (28S). Overall, morphologically defined species were confirmed by molecular datasets, with a few exceptions. Twenty-nine of the 36 uropodoid species (Trichouropoda, Nenteria and Uroobovella) collected in this study had narrow host ranges, while seven species had putative broad host ranges. In all but one species, U. orri, our data supported the existence of these host generalists, which contrasts with the typical finding that widespread generalists are actually complexes of cryptic specialists.

Cryptic species of mites (Uropodoidea: Uroobovella spp.) associated with burying beetles (Silphidae: Nicrophorus): the collapse of a host generalist revealed by molecular and morphological analyses.

Uroobovella (Mesostigmata: Uropodoidea: Urodinychidae) species are among the most common mites associated with carrion-feeding Nicrophorus (Silphidae) beetles. Previous taxonomic understanding suggests that a single host generalist, U. nova, disperses and lives with Nicrophorus species worldwide (reported from at least seven host species). Using morphometrics and morphological characteristics, as well as partial cytochrome oxidase I (COI) and the entire internal transcribed spacer 2 (ITS2) markers, we tested whether this apparent generalist is truly a generalist or rather a complex of cryptic species with narrower host ranges. Based on deutonymph mites collected from 14 host species across six countries and 17 provinces or states, we show that U. nova represents at least five morphologically similar species with relatively restricted host ranges. Except for one species which yielded no molecular data (but did exhibit morphological differences), both molecular and morphological datasets were congruent in delimiting species boundaries. Moreover, comparing the mite phylogeny with the known ecology and phylogenetic relationships of their host species suggests that these mites are coevolving with their silphid hosts rather than tracking ecologically similar species.

Functional avoidance of lung in plan optimization with an aperture-based inverse planning system.

PURPOSE: To implement SPECT-based optimization in an anatomy-based aperture inverse planning system for the functional avoidance of lung in thoracic irradiation. MATERIAL AND METHODS: SPECT information has been introduced as a voxel-by-voxel modulation of lung importance factors proportionally to the local perfusion count. Fifteen cases of lung cancer have been retrospectively analyzed by generating angle-optimized non-coplanar plans, comparing a purely anatomical approach and our functional approach. Planning target volume coverage and lung sparing have been compared. Statistical significance was assessed by a Wilcoxon matched pairs test. RESULTS: For similar target coverage, perfusion-weighted volume receiving 10 Gy was reduced by a median of 2.2% (p=0.022) and mean perfusion-weighted lung dose, by a median of 0.9 Gy (p=0.001). A separate analysis of patients with localized or non-uniform hypoperfusion could not show which would benefit more from SPECT-based treatment planning. Redirection of dose sometimes created overdosage regions in the target volume. Plans consisted of a similar number of segments and monitor units. CONCLUSIONS: Angle optimization and SPECT-based modulation of importance factors allowed for functional avoidance of the lung while preserving target coverage. The technique could be also applied to implement PET-based modulation inside the target volume, leading to a safer dose escalation.

Optimization of photon beam energy in aperture-based inverse planning.

Optimal choice of beam energy in radiation therapy is easy in many well-documented cases, but less obvious in some others. Low-energy beams may provide better conformity around the target than their high-energy counterparts due to reduced lateral scatter, but they also contribute to overdosage of peripheral normal tissue. Beam energy was added as an optimization parameter in an automatic aperture-based inverse planning system. We have investigated two sites (prostate and lung), representative of deep-seated and moderately deep-seated tumors. For each case and different numbers of beam incidences, four plans were optimized: 6 MV, 23 MV, and mixed energy plans with one or two energies per incidence. Each plan was scored with a dose-volume cost function. Cost function values, number of segments, monitor units, dose-volume parameters and isodose distributions were compared. For the prostate and lung cases, energy mixing improved plans in terms of cost function values, with a more important reduction for a small number of beam incidences. Use of high energy allows better peripheral tissue sparing, while keeping similar target coverage and sensitive structures avoidance. Low energy contribution to monitor units usually increased with the number of beam incidences. Thus, for deep-seated and moderately deep-seated tumors, energy optimization can produce interesting plans with less peripheral dose and monitor units than for low energy alone.

Dose escalation in the radiotherapy of non-small-cell lung cancer with aperture-based intensity modulation and photon beam energy optimization for non-preselected patients.

PURPOSE: To verify the potential of aperture-based intensity-modulated radiotherapy (AB-IMRT) to realize dose escalation plans for non-preselected non-small-cell lung cancer (NSCLC) patients, using photon beam energy optimization. METHODS AND MATERIALS: Seven cases of NSCLC were retrospectively studied. Clinical reference plans were made at 60 Gy by an experienced dosimetrist. Dose escalation was applied to PTV2, a subvolume within the main PTV1. Escalation plans were optimized by considering beam angles (table and gantry), energy (6 and 23 MV) and weights, for an increasing dose to the PTV2, starting from 66 Gy and keeping 30 fractions. RESULTS: In five cases, doses over 78 Gy could be achieved before exceeding organs at risk (OARs) standard tolerance. Peripheral overdosages, as well as lung and spinal cord tolerance doses, limited escalation. Means+/-SD V(95%) parameters were (97.3+/-0.9)% for PTV1s and (96.7+/-2.2)% for PTV2s. Doses to OARs were also maintained at acceptable levels. Optimized plans made use of both low- and high-energy beams and had a similar number of monitor units compared to the 60 Gy clinical plans. CONCLUSIONS: The AB-IMRT system can successfully realize dose escalation for a sizeable number of cases. Plans produced contained few large segments, and are applicable to a wide range of tumor volumes and locations.

Clinical outcome of adjuvant treatment of endometrial cancer using aperture-based intensity-modulated radiotherapy.

PURPOSE: To assess disease control and acute and chronic toxicity with aperture-based intensity-modulated radiotherapy (AB-IMRT) for postoperative pelvic irradiation of endometrial cancer. METHODS AND MATERIALS: Between January and July 2005, after hysterectomy for endometrial cancer, 15 patients received 45 Gy to the pelvis using AB-IMRT. The AB-IMRT plans were generated by an in-house treatment planning system (Ballista). The AB-IMRT plans were used for treatment and were dosimetrically compared with three other approaches: conventional four-field, enlarged four-field, and beamlet-based IMRT (BB-IMRT). Disease control and toxicity were prospectively recorded and compared with retrospective data from 30 patients treated with a conventional four-field technique. RESULTS: At a median follow-up of 27 months (range, 23-30), no relapse was noted among the AB-IMRT group compared with five relapses in the control group (p = 0.1). The characteristics of each group were similar, except for the mean body mass index, timing of brachytherapy, and applicator type used. Patients treated with AB-IMRT experienced more frequent Grade 2 or greater gastrointestinal acute toxicity (87% vs. 53%, p = 0.02). No statistically significant difference was noted between the two groups regarding the incidence or severity of chronic toxicities. AB-IMRT plans significantly improved target coverage (93% vs. 76% of planning target volume receiving 45 Gy for AB-IMRT vs. conventional four-field technique, respectively). The sparing of organs at risk was similar to that of BB-IMRT. CONCLUSION: The results of our study have shown that AB-IMRT provides excellent disease control with equivalent late toxicity compared with the conventional four-field technique. AB-IMRT provided treatment delivery and quality assurance advantages compared with BB-IMRT and could reduce the risk of second malignancy compared with BB-IMRT.

Postoperative irradiation of gynecologic malignancies: improving treatment delivery using aperture-based intensity-modulated radiotherapy.

PURPOSE: To evaluate dosimetric and treatment delivery advantages of aperture-based intensity-modulated radiotherapy (AB-IMRT) for the treatment of patients receiving whole pelvic radiotherapy for gynecologic malignancies. METHODS AND MATERIALS: Nineteen patients undergoing pelvic radiotherapy after resection of endometrial cancers were selected. A 45-Gy dose was prescribed to the target volume delineated on a planning CT scan. An in-house inverse planning system, Ballista, was used to develop a treatment plan using aperture-based multileaf collimator segments. This approach was compared with conventional four-field, enlarged four-field, and static beamlet-based IMRT (BB-IMRT) techniques in terms of target coverage, dose-volume histogram statistics for surrounding normal tissues, and numbers of segments and monitor units (MU). RESULTS: Three quarters (76.4%) of the planning target volume received the prescription dose with conventional four-field plans. With adequate target coverage, the Ballista plans significantly reduced the volume of bowel and bladder irradiated at the prescribed dose (p < 0.001), whereas the two approaches provided equivalent results for the rectum (p = 0.5). On the other hand, AB-IMRT and BB-IMRT plans showed only small differences in dose-volume histogram statistics of unknown clinical impact, whereas Ballista plan delivery required on average 73% and 59% fewer segments and MU, respectively. CONCLUSION: With respect to conventional techniques, AB-IMRT for the treatment of gynecologic malignancies provides dosimetric advantages similar to those with BB-IMRT but with clear treatment delivery improvements.

Mesostigmatid mites (Acari: Mesostigmata) on rainforest tree trunks: arboreal specialists, but substrate generalists?

Predatory mites (Acari: Mesostigmata) on tree trunks without significant epiphytic growth in a subtropical rainforest in Eastern Australia were assessed for habitat specificity (i.e. whether they are tree trunk specialists or occupying other habitats) and the influence of host tree and bark structure on their abundance, species richness and species composition. The trunks of nine tree species from eight plant families representing smooth, intermediate and rough bark textures were sampled using a knockdown insecticide spray. In total, 12 species or morphospecies of Mesostigmata (excluding Uropodina sensu stricto) were collected, most of which are undescribed. Comparison with collections from other habitats indicates that epicorticolous Mesostigmata are mainly represented by suspended soil dwellers (six species), secondarily by generalists (four species) and a bark specialist (one species). A typical ground-dwelling species was also found but was represented only by a single individual. In terms of abundance, 50.5% of individuals were suspended soil dwellers, 40.7% bark specialists, and 8.3% generalists. Host species and bark roughness had no significant effect on abundance or species richness. Furthermore, there was no clear effect on species composition. The distribution of the most frequently encountered species suggests that most mesostigmatid mites living on bark use many or most rainforest tree species, independent of bark roughness. These findings support the hypothesis that some epicorticolous Mesostigmata use tree trunks as 'highways' for dispersing between habitat patches, while others use it as a permanent habitat.

Multiobjective optimization with a modified simulated annealing algorithm for external beam radiotherapy treatment planning.

Inverse planning in external beam radiotherapy often requires a scalar objective function that incorporates importance factors to mimic the planner's preferences between conflicting objectives. Defining those importance factors is not straightforward, and frequently leads to an iterative process in which the importance factors become variables of the optimization problem. In order to avoid this drawback of inverse planning, optimization using algorithms more suited to multiobjective optimization, such as evolutionary algorithms, has been suggested. However, much inverse planning software, including one based on simulated annealing developed at our institution, does not include multiobjective-oriented algorithms. This work investigates the performance of a modified simulated annealing algorithm used to drive aperture-based intensity-modulated radiotherapy inverse planning software in a multiobjective optimization framework. For a few test cases involving gastric cancer patients, the use of this new algorithm leads to an increase in optimization speed of a little more than a factor of 2 over a conventional simulated annealing algorithm, while giving a close approximation of the solutions produced by a standard simulated annealing. A simple graphical user interface designed to facilitate the decision-making process that follows an optimization is also presented.

Automatic generation of anatomy-based MLC fields in aperture-based IMRT.

We have developed an algorithm to automatically generate anatomy-based MLC fields. For each beam, a first field is adjusted to the projection of the target in a beam's eye view, allowing subsequent fields to be derived from this conformal field by removing the overlapping surface of each organ at risk, respectively. The projections are based on a surface sampling of the anatomical structures. On top of the MLC mechanical constraints, verification constraints are imposed on the MLC segments, in order to get reliable dosimetry using a commercial dose calculation engine. Thus, in each direction, the aperture's cross-section must be greater than a specified threshold, in our case 2 cm. Furthermore, junctions are not tolerated in order to avoid underdosage, for instance from the tongue-and-groove effect. The use of such MLC fields simplifies the verification process. The performance of the algorithm is illustrated for head and neck, thorax and prostate cases. Only a fraction of a second of CPU time is required to perform the segmentation for each beam.