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AbstractRacism and colonialism within restoration science continue to perpetuate exclusionary and oppressive paradigms in ecosystem restoration and in wider societal contexts, from setting scientific agendas to translating findings into policy. These paradigms impair progress and cause harm by (1) tokenizing epistemic diversity, (2) perpetuating injustice in frontline communities by ignoring power dynamics and other local contexts, and (3) rejecting "unconventional" methods for connecting knowledge to action. To challenge exclusion, biological scientists must listen to path-making conversations in Native American and Indigenous studies on grounded normativity, an ethical framework informed by place-based practices that make respectful, nonexploitative coexistence between human and nonhuman communities possible. Rather than treat Western science as the objective arbiter of truth, Indigenous and feminist science approaches can draw on multiple sciences to design restoration interventions and unsettle power dynamics and historical legacies in the biological sciences. We put these approaches into practice and discuss the methodologies and outcomes of two restoration projects, one on the Duwamish River and one on the Klamath River. We use the lessons learned to discuss how scientists in all biological fields can prevent harmful inequities in restoration work while building capacity in and supporting crucial work by frontline communities.

Crop harvest followed by a fallow period can act as a disturbance on soil microbial communities. Cropping systems intended to improve alpha-diversity of communities may also confer increased compositional stability during succeeding growing seasons. Over a single growing season in a long-term (18 year) agricultural field experiment incorporating conventional (CON), conservation (CA), organic (ORG) and integrated (INT) cropping systems, temporal changes in prokaryote, fungal and arbuscular mycorrhizal fungi (AMF) communities were investigated overwinter, during crop growth and at harvest. While certain prokaryote phyla were influenced by cropping system (e.g. Acidobacteria), the community as a whole was primarily driven by temporal changes over the growing season as distinct overwinter and crop-associated communities, with the same trend observed regardless of cropping system. Species-rich prokaryote communities were most stable over the growing season. Cropping system exerted a greater effect on fungal communities, with alpha-diversity highest and temporal changes most stable under CA. CON was particularly detrimental for alpha-diversity in AMF communities, with AMF alpha-diversity and stability improved under all other cropping systems. Practices that promoted alpha-diversity tended to also increase the similarity and temporal stability of soil fungal (and AMF) communities during a growing season, while prokaryote communities were largely insensitive to management., (© The Author(s) 2021. Published by Oxford University Press on behalf of FEMS. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

The concentration of atmospheric methane (CH 4 ) continues to increase with microbial communities controlling soil-atmosphere fluxes. While there is substantial knowledge of the diversity and function of prokaryotes regulating CH 4 production and consumption, their active interactions with viruses in soil have not been identified. Metagenomic sequencing of soil microbial communities enables identification of linkages between viruses and hosts. However, this does not determine if these represent current or historical interactions nor whether a virus or host are active. In this study, we identified active interactions between individual host and virus populations in situ by following the transfer of assimilated carbon. Using DNA stable-isotope probing combined with metagenomic analyses, we characterized CH 4 -fueled microbial networks in acidic and neutral pH soils, specifically primary and secondary utilizers, together with the recent transfer of CH 4 -derived carbon to viruses. A total of 63% of viral contigs from replicated soil incubations contained homologs of genes present in known methylotrophic bacteria. Genomic sequences of 13 C-enriched viruses were represented in over one-third of spacers in CRISPR arrays of multiple closely related Methylocystis populations and revealed differences in their history of viral interaction. Viruses infecting nonmethanotrophic methylotrophs and heterotrophic predatory bacteria were also identified through the analysis of shared homologous genes, demonstrating that carbon is transferred to a diverse range of viruses associated with CH 4 -fueled microbial food networks., Competing Interests: The authors declare no competing interest.

Functional, physiological traits are the underlying drivers of niche differentiation. A common framework related to niches occupied by terrestrial prokaryotes is based on copiotrophy or oligotrophy, where resource investment is primarily in either rapid growth or stress tolerance, respectively. A quantitative trait-based approach sought relationships between taxa, traits and niche in terrestrial prokaryotes. With 175 taxa from 11 Phyla and 35 Families (n = 5 per Family), traits were considered as discrete counts of shared genome-encoded proteins. Trait composition strongly supported non-random functional distributions as preferential clustering of related taxa via unweighted pair-group method with arithmetic mean. Trait similarity between taxa increased as taxonomic rank decreased. A suite of Random Forest models identified traits significantly enriched or depleted in taxonomic groups. These traits conveyed functions related to rapid growth, nutrient acquisition and stress tolerance consistent with their presence in copiotroph-oligotroph niches. Hierarchical clustering of traits identified a clade of competitive, copiotrophic Families resilient to oxidative stress versus glycosyltransferase-enriched oligotrophic Families resistant to antimicrobials and environmental stress. However, the formation of five clades suggested a more nuanced view to describe niche differentiation in terrestrial systems is necessary. We suggest considering traits involved in both resource investment and acquisition when predicting niche., (© The Author(s) 2021. Published by Oxford University Press on behalf of FEMS.)

Intensively managed agriculture land is a significant contributor to nitrous oxide (N 2 O) emissions, which adds to global warming and the depletion of the ozone layer. Recent studies have suggested that fungal dominant N 2 O production may be promoted by pathogenic fungi under high nitrogen fertilization and continuous cropping. Here, we measured the contribution of fungal communities to N 2 O production under intensively managed strawberry fields of three continuous cropping years (1, 5, and 10 years) and compared this adjacent bare soil. Higher N 2 O emission was observed from the 10-year field, of which fungi and prokaryotes accounted for 79.7% and 21.3%, respectively. Fungal population density in the 10-year field soil (4.25 × 10 5 colony forming units per g (CFU/g) of air-dried soil) was greater than the other cropping years. Illumina MiSeq sequencing of the nirK gene showed that long-term continuous cropping decreased the diversity of the fungal denitrifier community, but increased the abundance of Fusarium oxysporum. Additionally, F. oxysporum produced large amounts of N 2 O in culture and in sterile 10-year field soil. A systemic infection displayed by bioassay strawberry plants after inoculation demonstrated that F. oxysporum was a pathogenic fungus. Together, results suggest that long-term intensively managed monocropping significantly influenced the denitrifying fungal community and increased their biomass, which increased fungal contribution to N 2 O emissions and specifically by pathogenic fungi. KEY POINTS: • Distinguishing the role of fungi in long-term continuous cropping field. • Identifying the abundant fungal species with denitrifying ability.

Contents Summary 1122 I. Introduction 1122 II. Are there consistent patterns in diversity of mycorrhizal fungal genotypes and species across space? 1125 III. What is the variation in functional traits and genes of mycorrhizal fungi at different taxonomic scales? 1125 IV. How will environmental change impact the relationships between genotypic and species diversity of mycorrhizal fungi and ecosystem function? 1126 V. Conclusions: considerations for future MEF research 1127 Acknowledgements 1127 References 1127 SUMMARY: Both genotypes and species of mycorrhizal fungi exhibit considerable variation in traits, and this variation can result in their diversity regulating ecosystem function. Yet, the nature of mycorrhizal fungal diversity-ecosystem function (MEF) relationships for both genotypes and species is currently poorly defined. New experiments should reflect the richness of genotypes and species in nature, but we still lack information about the extent to which fungal populations in particular are structured. Sampling designs should quantify the diversity of mycorrhizal fungal genotypes and species at three key broad spatial scales (root fragment, root system and interacting root systems) in order to inform manipulation experiments and to test how mycorrhizal fungal diversity both responds, and confers resilience to, environmental drivers., (© 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.)

Effects of biodiversity on productivity are more likely to be expressed when there is greater potential for niche complementarity. In soil, chemically complex pools of nutrient resources should provide more opportunities for niche complementarity than chemically simple pools. Ectomycorrhizal (ECM) fungal genotypes can exhibit substantial variation in nutrient acquisition traits and are key components of soil biodiversity. Here, we tested the hypothesis that increasing the chemical complexity and forms of soil nutrients would enhance the effects of intraspecific ECM diversity on host plant and fungal productivity. In pure culture, we found substantial variation in growth of strains of the ECM fungus Laccaria bicolor on a range of inorganic and organic forms of nutrients. Subsequent experiments examined the effects of intraspecific identity and richness using Scots pine ( Pinus sylvestris ) seedlings colonized with different strains of L. bicolor growing on substrates supplemented with either inorganic or organic forms of nitrogen and phosphorus. Intraspecific identity effects on plant productivity were only found under the inorganic nutrient amendment, whereas intraspecific identity affected fungal productivity to a similar extent under both nutrient treatments. Overall, there were no significant effects of intraspecific richness on plant and fungal productivity. Our findings suggest soil nutrient composition does not interact strongly with ECM intraspecific richness, at least under experimental conditions where mineral nutrients were not limiting. Under these conditions, intraspecific identity of ECM fungi becomes more important than richness in modulating plant and fungal performance.

Objectives: Subharmonic imaging (SHI) is a technique that uses the nonlinear oscillations of microbubbles when exposed to ultrasound at high pressures transmitting at the fundamental frequency ie, f o and receiving at half the transmit frequency (ie, f o /2). Subharmonic aided pressure estimation (SHAPE) is based on the inverse relationship between the subharmonic amplitude of the microbubbles and the ambient pressure change., Methods: Eight waveforms with different envelopes were optimized with respect to acoustic power at which the SHAPE study is most sensitive. The study was run with four input transmit cycles, first in vitro and then in vivo in three canines to select the waveform that achieved the best sensitivity for detecting changes in portal pressures using SHAPE. A Logiq 9 scanner with a 4C curvi-linear array was used to acquire 2.5 MHz radio-frequency data. Scanning was performed in dual imaging mode with B-mode imaging at 4 MHz and a SHI contrast mode transmitting at 2.5 MHz and receiving at 1.25 MHz. Sonazoid, which is a lipid stabilized gas filled bubble of perfluorobutane, was used as the contrast agent in this study., Results: A linear decrease in subharmonic amplitude with increased pressure was observed for all waveforms (r from -0.77 to -0.93; P < .001) in vitro. There was a significantly higher correlation of the SHAPE gradient with changing pressures for the broadband pulses as compared to the narrowband pulses in both in vitro and in vivo results. The highest correlation was achieved with a Gaussian windowed binomial filtered square wave with an r-value of -0.95. One of the three canines was eliminated for technical reasons, while the other two produced very similar results to those obtained in vitro (r from -0.72 to -0.98; P <.01). The most consistent in vivo results were achieved with the Gaussian windowed binomial filtered square wave (r = -0.95 and -0.96)., Conclusions: Using this waveform is an improvement to the existing SHAPE technique (where a square wave was used) and should make SHAPE more sensitive for noninvasively determining portal hypertension., (© 2016 by the American Institute of Ultrasound in Medicine.)

A major gap in our understanding of biodiversity-ecosystem function relationships concerns the role of intra- and interspecific diversity of mycorrhizal fungi, which are critical for plant fitness, biogeochemical cycling and other processes. Here, we test the hypothesis that the identity and richness of ectomycorrhizal (ECM) fungi at the intra- and interspecific levels affect ecosystem multifunctionality by regulating plant and fungal productivity, soil CO 2 efflux and nutrient retention. Microcosms containing Scots pine (Pinus sylvestris) seedlings colonized by different ECM fungal isolates, in monocultures and mixtures, enabled us to test for both intra- and interspecific identity and richness effects, and transgressive overyielding. Intra- and interspecific identity had modest but significant effects on plant and fungal productivity and nutrient retention, but no effect on CO 2 efflux. Intraspecific richness increased plant root productivity and ECM root tips but decreased hyphal length, whereas interspecific richness had no effects. Interspecific mixtures outperformed the most productive monocultures in only 10% of the cases, compared with 42% for the intraspecific mixtures. Both intra- and interspecific identity and richness of ECM fungi regulate ecosystem multifunctionality, but their effects on the direction and magnitude of individual variables differ. Transgressive overyielding suggests that positive niche complementarity effects are driving some of the responses to intraspecific richness., (© 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.)

Objectives: The precise measurement of fat accumulation in the liver, or steatosis, is an important clinical goal. Our previous studies in phantoms and mouse livers support the hypothesis that, starting with a normal liver, increasing accumulations of microsteatosis and macrosteatosis will increase the lossy viscoelastic properties of shear waves in a medium. This increase results in an increased dispersion (or slope) of the shear wave speed in the steatotic livers., Methods: In this study, we moved to a larger animal model, lean versus obese rat livers ex vivo, and a higher-frequency imaging system to estimate the shear wave speed from crawling waves., Results: The results showed elevated dispersion in the obese rats and a separation of the lean versus obese liver parameters in a 2-dimensional parameter space of the dispersion (slope) and shear wave speed at a reference frequency of 150 Hz., Conclusions: We have confirmed in 3 separate studies the validity of our dispersion hypothesis in animal models., (© 2015 by the American Institute of Ultrasound in Medicine.)

Culture-independent molecular studies have provided new insights into the diversity of fungi associating with ericaceous plant roots. However, there is little understanding of the distribution of these fungi across landscapes, or the effects of environmental heterogeneity on ericoid mycorrhizal (ERM) fungal diversity and distribution. Terminal-restriction fragment length polymorphism and selective sequence analyses of the internal transcribed spacer regions of rDNA were used to infer fungal diversity of bait Vaccinium macrocarpon grown in soils from nine peatland sites in Ireland, representing three different land uses (bog, rough grazing and forest plantation) and the fungal communities of field-collected Calluna vulgaris for five of these nine sites. A diverse range of potential ERM fungi were found, and the sampling approach significantly affected the diversity of the fungal community. Despite significant site groupings of the fungal communities associated with V. macrocarpon and C. vulgaris, fungal communities were significantly dissimilar between sites with different land uses. Soil nitrogen content significantly explained 52% of the variation in the V. macrocarpon fungal communities. Evidence suggests that environmental heterogeneity has a role in shaping ERM fungal community composition at the landscape scale.

Arbuscular fungi have a major role in directing the functioning of terrestrial ecosystems yet little is known about their biogeographical distribution. The Baas-Becking hypothesis ('everything is everywhere, but, the environment selects') was tested by investigating the distribution of arbuscular mycorrhizal fungi (AMF) at the landscape scale and the influence of environmental factors and geographical distance in determining community composition. AMF communities in Trifolium repens and Lolium perenne roots were assessed in 40 geographically dispersed sites in Ireland representing different land uses and soil types. Field sampling and laboratory bioassays were used, with AMF communities characterised using 18S rRNA terminal-restriction fragment length polymorphism. Landscape-scale distribution of AMF was driven by the local environment. AMF community composition was influenced by abiotic variables (pH, rainfall and soil type), but not land use or geographical distance. Trifolium repens and L. perenne supported contrasting communities of AMF, and the communities colonising each plant species were consistent across pasture habitats and over distance. Furthermore, L. perenne AMF communities grouped by soil type within pasture habitats. This is the largest and most comprehensive study that has investigated the landscape-scale distribution of AMF. Our findings support the Baas-Becking hypothesis at the landscape scale and demonstrate the strong influence the local environment has on determining AMF community composition.

Like other myco-heterotrophic plants, Pterospora andromedea (pinedrops) is dependent upon its specific fungal symbionts for survival. The rarity of pinedrops fungal symbiont was investigated in the eastern United States where pinedrops are rare. Wild populations of eastern pinedrops were sampled, and the plant haplotypes and fungal symbionts were characterized with molecular techniques; these data were compared to those from the West with phylogenetic analyses. The frequency of the fungal symbiont in eastern white pine forests was assessed using a laboratory soil bioassay and in situ pinedrops seed baiting. Only one plant haplotype and fungal symbiont was detected. The plant haplotype was not unique to the East. The fungal symbiont appears to be a new species within the genus Rhizopogon, closely related to the western symbionts. This fungal species was not frequent in soils with or without pinedrops, but was less frequent in the latter and in comparison to the fungal symbionts in western forests. Seed baiting resulted in few germinants, suggesting that mycelial networks produced by the eastern fungal symbiont were rare. Results suggest that eastern pinedrops rarity is influenced by the distribution and rarity of its fungal symbiont.

This paper introduces methods to generate crawling wave interference patterns from the displacement fields generated from radiation force pushes on a GE Logiq 9 scanner. The same transducer and system provides both the pushing pulses to generate the shear waves and the tracking pulses to measure the displacements. Acoustic power and system limitations result in largely impulsive displacement fields. Measured displacements from pushes on either side of a region-of-interest (ROI) are used to calculate continuously varying interference patterns. This technique is explained along with a brief discussion of the conventional mechanical source-driven crawling waves for comparison. We demonstrate the method on three example cases: a gelatin-based phantom with a cylindrical inclusion, an oil-gelatin phantom and mouse livers. The oil-gelatin phantom and the mouse livers demonstrate not only shear speed estimation, but the frequency dependence of the shear wave speeds., (Copyright © 2012 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.)

An ultrasound system (GE Logiq 9) was modified to produce a synthetic crawling wave using shear wave displacements generated by the radiation force of focused beams formed at the left and the right edge of the region of interest (ROI). Two types of focusing, normal and axicon, were implemented. Baseband (IQ) data was collected to determine the left and right displacements, which were then used to calculate an interference pattern. By imposing a variable delay between the two pushes, the interference pattern moves across the ROI to produce crawling waves. Also temperature and pressure measurements were made to assess the safety issues. The temperature profiles measured in a veal liver along the focal line showed the maximum temperature rise less than 0.8°C, and the pressure measurements obtained in degassed water and derated by 0.3 dB/cm/MHz demonstrate that the system can operate within FDA safety guidelines., (Copyright © 2012 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.)

A novel elasticity imaging system founded on the use of acoustic radiation forces from a dual beam arrangement to generate shear wave interference patterns is described. Acquired pulse-echo data and correlation-based techniques were used to estimate the resultant deformation and to visualize tissue viscoelastic response. The use of normal versus axicon focal configurations was investigated for effects on shear wave generation. Theoretical models were introduced and shown in simulation to accurately predict shear wave propagation and interference pattern properties. In a tissue-mimicking phantom, experimental results are in congruence with theoretical predictions. Using dynamic acoustic radiation force excitation, results confirm that shear wave interference patterns can be produced remotely in a particular tissue region of interest (ROI). Overall, preliminary results are encouraging and the system described may prove feasible for interrogating the viscoelastic properties of normal and diseased tissue types.

This paper describes a liver elasticity and viscosity measurement system based on existing medical ultrasound platforms. This system relies on acoustic radiation force to invoke transient response on soft tissue, and employs displacement estimation algorithms to detect the propagation of shear wave. The research proves that the velocity of the shear wave may serve as a reliable estimation of the Young's modulus and viscosity coefficient of the liver tissue, and existing commercial products may be easily adapted to support this technique without extra hardware cost.

Crawling waves are generated by an interference of two oscillating waves traveling in opposite directions, with a progressive movement resulting from a frequency difference or a phase difference between the sources. While the idea has been applied to numerous applications, all the previous reports used mechanical sources to vibrate the medium. It is shown, through experiments and simulation, that crawling waves can be generated from focused beams that produce radiation force excitation within the tissue. Some examples are also shown.

A real-time 3-D imaging system requires the development of a beamformer that can generate many beams simultaneously. In this paper, we discuss and evaluate a suitable synthetic aperture beamformer. The proposed beamformer is based on a pipelined network of high speed digital signal processors (DSP). By using simple interpolation-based beamforming, only a few calculations per pixel are required for each channel, and an entire 2-D synthetic aperture image can be formed in the time of one transmit event. The performance of this beamformer was explored using a computer simulation of the radiation pattern. The simulations were done for a full 64-element array and a sparse array with the same receive aperture but only five transmit elements. We assessed the effects of changing the sampling rate and amplitude quantization by comparing the relative levels of secondary lobes in the radiation patterns. The results show that the proposed beamformer produces a radiation pattern equivalent to a conventional beamformer using baseband demodulation, provided that the sampling rate is approximately 10 times the center frequency of the transducer (34% bandwidth pulse). The simulations also show that the sparse array is not significantly more sensitive to delay or amplitude quantization than the full array.

Classification of causes of death by a nosologist is standardized and relatively inexpensive, although the quality of the data recorded on death certificates has been subjected to criticism and the level of detail may not allow examination of specific circumstances of the death. A costly alternative is classification by a panel of physicians reviewing additional clinical information. The costs associated with both methods of classification as utilized by the Lipid Research Clinics Program Mortality Follow-up Study are presented along with their advantages and disadvantages. For deaths among the elderly (65 years or older), determination of the underlying cause of death may be difficult, especially as regards cardiovascular disease causes of death using only the death certificate, and impossible for classifying sudden death. Both classification methods are compared for 268 deaths among the elderly and 155 deaths among the nonelderly males and females participating in the study. The kappa statistics for observer agreement indicate moderate agreement (k = 0.58) and were not significantly different between the two age-groups (p greater than 0.10). Thus, the agreement between the methods was not affected significantly by the age of the deaths being classified. However, examination of the agreement chart showed a preference by the nosological classification for cardiovascular classification in the elderly population. The effect of the different classifications upon the analysis of the predictive value of high-density lipoprotein cholesterol on coronary heart disease mortality showed little difference between both methods of classification.

The authors report a case of retrograde invagination of the duodenum 8 years after vagotomy and gastroenterostomy: gastric aspiration then reoperation permitted verification of the disinvagination. Cure by gastro-enterostomy and excision of the remaining duodenal ulcer.

Association, in one patient, of the following malformations: brachydactylia of all segments but terminal phalanges; proximal symphalangism of many fingers and toes; abnormalities of carpal and tarsal bones; partial duplication of both big toes; mild hypertelorism. Genetic transmission seems to be recessive autosomal.