Fitness trade-offs and the origins of endosymbiosis.

Endosymbiosis drives evolutionary innovation and underpins the function of diverse ecosystems. The mechanistic origins of symbioses, however, remain unclear, in part because early evolutionary events are obscured by subsequent evolution and genetic drift. This Essay highlights how experimental studies of facultative, host-switched, and synthetic symbioses are revealing the important role of fitness trade-offs between within-host and free-living niches during the early-stage evolution of new symbiotic associations. The mutational targets underpinning such trade-offs are commonly regulatory genes, such that single mutations have major phenotypic effects on multiple traits, thus enabling and reinforcing the transition to a symbiotic lifestyle.

Greater ecophysiological stress tolerance in the core environment than in extreme environments of wild chickpea (Cicer reticulatum).

Global climate change and land use change underlie a need to develop new crop breeding strategies, and crop wild relatives (CWR) have become an important potential source of new genetic material to improve breeding efforts. Many recent approaches assume adaptive trait variation increases towards the relative environmental extremes of a species range, potentially missing valuable trait variation in more moderate or typical climates. Here, we leveraged distinct genotypes of wild chickpea (Cicer reticulatum) that differ in their relative climates from moderate to more extreme and perform targeted assessments of drought and heat tolerance. We found significance variation in ecophysiological function and stress tolerance between genotypes but contrary to expectations and current paradigms, it was individuals from more moderate climates that exhibited greater capacity for stress tolerance than individuals from warmer and drier climates. These results indicate that wild germplasm collection efforts to identify adaptive variation should include the full range of environmental conditions and habitats instead of only environmental extremes, and that doing so may significantly enhance the success of breeding programs broadly.

Microstructure and crystallographic texture data in modern giant clam shells (Tridacna squamosa and Hippopus hippopus).

This article provides novel data on the microstructure and crystallographic texture of modern giant clam shells (Tridacna squamosa and Hippopus hippopus) from the Coral Triangle region of northeast Borneo. Giant clams have two aragonitic shell layers-the inner and outer shell layer. This dataset focuses on the inner shell layer as this is well preserved and not affected by diagenetic alteration. To prepare samples for analysis, shells were cut longitudinally at the axis of maximum growth and mounted onto thin sections. Data collection involved scanning electron microscopy (SEM) to determine microstructure and SEM based electron backscatter diffraction (EBSD) for quantitative measurement of crystallographic orientation and texture. Post-acquisition reanalysis of saved EBSD patterns to optimize data quality included changing the number of reflectors and band detection mode. We provide EBSD data as band contrast images and colour-coded orientation maps (inverse pole figure maps). Crystallographic co-orientation strength obtained with multiple of uniform density (MUD) values are derived from density distributed pole figures of indexed EBSD points. Raw EBSD data files are also given to ensure repeatability of the steps provided in this article and to allow extraction of further crystallographic properties for future researchers. Overall, this dataset provides 1. a better understanding of shell growth and biomineralization in giant clams and 2. important steps for optimizing data collection with EBSD analyses in biogenic carbonates.

Does F4TCNQ Adsorption on Cu(111) Form a 2D-MOF?

The results of a quantitative experimental structural investigation of the adsorption phases formed by 2,3,5,6-tetrafluoro-7,7',8,8'-tetracyanoquinodimethane (F4TCNQ) on Cu(111) are reported. A particular objective was to establish whether Cu adatoms are incorporated into the molecular overlayer. A combination of normal incidence X-ray standing waves, low-energy electron diffraction, scanning tunneling microscopy, and X-ray photoelectron spectroscopy measurements, complemented by dispersion-inclusive density functional theory calculations, demonstrates that F4TCNQ on Cu(111) does cause Cu adatoms to be incorporated into the overlayer to form a two-dimensional metal-organic framework (2D-MOF). This conclusion is shown to be consistent with the behavior of F4TCNQ adsorption on other coinage metal surfaces, despite an earlier report concluding that the adsorption structure on Cu(111) is consistent with the absence of any substrate reconstruction.

Ecophysiological adaptations shape distributions of closely related trees along a climatic moisture gradient.

Tradeoffs between the energetic benefits and costs of traits can shape species and trait distributions along environmental gradients. Here we test predictions based on such tradeoffs using survival, growth, and 50 photosynthetic, hydraulic, and allocational traits of ten Eucalyptus species grown in four common gardens along an 8-fold gradient in precipitation/pan evaporation (P/Ep) in Victoria, Australia. Phylogenetically structured tests show that most trait-environment relationships accord qualitatively with theory. Most traits appear adaptive across species within gardens (indicating fixed genetic differences) and within species across gardens (indicating plasticity). However, species from moister climates have lower stomatal conductance than others grown under the same conditions. Responses in stomatal conductance and five related traits appear to reflect greater mesophyll photosynthetic sensitivity of mesic species to lower leaf water potential. Our data support adaptive cross-over, with realized height growth of most species exceeding that of others in climates they dominate. Our findings show that pervasive physiological, hydraulic, and allocational adaptations shape the distributions of dominant Eucalyptus species along a subcontinental climatic moisture gradient, driven by rapid divergence in species P/Ep and associated adaptations.

Space controlled environment agriculture offers pathways to improve the sustainability of controlled environmental agriculture on Earth.

Terrestrial controlled environment agriculture (CEA) will have an increasingly important role in food production. However, present CEA systems are energy- and resource-hungry and rarely profitable, requiring a step change in design and optimization. Here we argue that the unique nature of space controlled environment agriculture (SpaCEA), which needs to be both highly resource efficient and circular in design, presents an opportunity to develop intrinsically circular CEA systems. Life-cycle analysis tools should be used to optimize the provision and use of natural or electrical light, power, nutrients and infrastructure in CEA and/or SpaCEA systems, and to guide research and development into subsystems that bring strong environmental advantages. We suggest that SpaCEA public outreach can also be used to improve the perception of terrestrial CEA on Earth by using space as a gateway for exhibiting CEA food growing technologies. A substantial focus on SpaCEA development should be viewed as an efficient contribution to addressing major current CEA challenges.

Linking stem rehydration kinetics to hydraulic traits using a novel method and mechanistic model.

BACKGROUND: Despite the recognized importance of hydraulic capacitance as a mechanism used by plants to maintain hydraulic functioning during high transpiration, characterizing the dynamics of capacitance remains a challenge. METHODS: We used a novel 'two-balance method' to investigate relationships between stem rehydration kinetics and other hydraulic traits in multiple tree species, and we developed a model to explore stem rehydration kinetics further. KEY RESULTS: We found that: (1) rehydration time constants and the amount of water uptake occurring during rehydration differed significantly across species; (2) time constants did not change with declining water potential (Ψ), while water uptake increased at lower Ψ in some species; (3) longer time constants were associated with lower wood density, higher capacitance and less negative stem pressures causing 50 % loss of hydraulic conductivity (P50); (4) greater water uptake occurred in stems with lower wood density and less negative P50 values; and (5) the model could estimate the total hydraulic resistance of the rehydration path, which cannot be measured directly. CONCLUSIONS: Overall, the two-balance method can be used to examine rehydration dynamics quickly and thoroughly in detached woody stems. This method has the potential to improve our understanding of how capacitance functions across tree species, which is an often-overlooked component of whole-plant hydraulics.

Methodological and Reporting Quality of Noninferiority Randomized Controlled Trials Comparing Antiretroviral Therapies: A Systematic Review.

BACKGROUND: It is unclear whether the reporting quality of antiretroviral (ARV) noninferiority (NI) randomized controlled trials (RCTs) has improved since the CONSORT guideline release in 2006. The primary objective of this systematic review was assessing the methodological and reporting quality of ARV NI-RCTs. We also assessed reporting quality by funding source and publication year. METHODS: We searched Medline, Embase, and Cochrane Central from inception to 14 November 2022. We included NI-RCTs comparing ≥2 ARV regimens used for human immunodeficiency virus treatment or prophylaxis. We used the Cochrane Risk of Bias 2.0 tool to assess risk of bias. Screening and data extraction were performed blinded and in duplicate. Descriptive statistics were used to summarize data; statistical tests were 2 sided, with significance defined as P < .05. The systematic review was prospectively registered (PROSPERO CRD42022328586), and not funded. RESULTS: We included 160 articles reporting 171 trials. Of these articles, 101 (63.1%) did not justify the NI margin used, and 28 (17.5%) did not provide sufficient information for sample size calculation. Eighty-nine of 160 (55.6%) reported both intention-to-treat and per-protocol analyses, while 118 (73.8%) described missing data handling. Ten of 171 trials (5.9%) reported potentially misleading results. Pharmaceutical industry-funded trials were more likely to be double-blinded (28.1% vs 10.3%; P = .03) and to describe missing data handling (78.5% vs 59.0%; P = .02). The overall risk of bias was low in 96 of 160 studies (60.0%). CONCLUSIONS: ARV NI-RCTs should improve NI margin justification, reporting of intention-to-treat and per-protocol analyses, and missing data handling to increase CONSORT adherence.

Untangling the Complexities of Processing and Analysis for Untargeted LC-MS Data Using Open-Source Tools.

Untargeted metabolomics is a powerful tool for measuring and understanding complex biological chemistries. However, employment, bioinformatics and downstream analysis of mass spectrometry (MS) data can be daunting for inexperienced users. Numerous open-source and free-to-use data processing and analysis tools exist for various untargeted MS approaches, including liquid chromatography (LC), but choosing the 'correct' pipeline isn't straight-forward. This tutorial, in conjunction with a user-friendly online guide presents a workflow for connecting these tools to process, analyse and annotate various untargeted MS datasets. The workflow is intended to guide exploratory analysis in order to inform decision-making regarding costly and time-consuming downstream targeted MS approaches. We provide practical advice concerning experimental design, organisation of data and downstream analysis, and offer details on sharing and storing valuable MS data for posterity. The workflow is editable and modular, allowing flexibility for updated/changing methodologies and increased clarity and detail as user participation becomes more common. Hence, the authors welcome contributions and improvements to the workflow via the online repository. We believe that this workflow will streamline and condense complex mass-spectrometry approaches into easier, more manageable, analyses thereby generating opportunities for researchers previously discouraged by inaccessible and overly complicated software.

Seasonal Phenology and Climate Associated Feeding Activity of Introduced Marchalina hellenica in Southeast Australia.

Invasive insects pose an increasing risk to global agriculture, environmental stability, and public health. Giant pine scale (GPS), Marchalina hellenica Gennadius (Hemiptera: Marchalinidae), is a phloem feeding scale insect endemic to the Eastern Mediterranean Basin, where it primarily feeds on Pinus halepensis and other Pinaceae. In 2014, GPS was detected in the southeast of Melbourne, Victoria, Australia, infesting the novel host Pinus radiata. An eradication program was unsuccessful, and with this insect now established within the state, containment and management efforts are underway to stop its spread; however, there remains a need to understand the insect's phenology and behaviour in Australia to better inform control efforts. We documented the annual life cycle and seasonal fluctuations in activity of GPS in Australia over a 32 month period at two contrasting field sites. Onset and duration of life stages were comparable to seasons in Mediterranean conspecifics, although the results imply the timing of GPS life stage progression is broadening or accelerating. GPS density was higher in Australia compared to Mediterranean reports, possibly due to the absence of key natural predators, such as the silver fly, Neoleucopis kartliana Tanasijtshuk (Diptera, Chamaemyiidae). Insect density and honeydew production in the Australian GPS population studied varied among locations and between generations. Although insect activity was well explained by climate, conditions recorded inside infested bark fissures often provided the weakest explanation of GPS activity. Our findings suggest that GPS activity is strongly influenced by climate, and this may in part be related to changes in host quality. An improved understanding of how our changing climate is influencing the phenology of phloem feeding insects such as GPS will help with predictions as to where these insects are likely to flourish and assist with management programs for pest species.

Donor-Acceptor Co-Adsorption Ratio Controls the Structure and Electronic Properties of Two-Dimensional Alkali-Organic Networks on Ag(100).

The results are presented of a detailed combined experimental and theoretical investigation of the influence of coadsorbed electron-donating alkali atoms and the prototypical electron acceptor molecule 7,7,8,8-tetracyanoquinodimethane (TCNQ) on the Ag(100) surface. Several coadsorption phases were characterized by scanning tunneling microscopy, low-energy electron diffraction, and soft X-ray photoelectron spectroscopy. Quantitative structural data were obtained using normal-incidence X-ray standing wave (NIXSW) measurements and compared with the results of density functional theory (DFT) calculations using several different methods of dispersion correction. Generally, good agreement between theory and experiment was achieved for the quantitative structures, albeit with the prediction of the alkali atom heights being challenging for some methods. The adsorption structures depend sensitively on the interplay of molecule-metal charge transfer and long-range dispersion forces, which are controlled by the composition ratio between alkali atoms and TCNQ. The large difference in atomic size between K and Cs has negligible effects on stability, whereas increasing the ratio of K/TCNQ from 1:4 to 1:1 leads to a weakening of molecule-metal interaction strength in favor of stronger ionic bonds within the two-dimensional alkali-organic network. A strong dependence of the work function on the alkali donor-TCNQ acceptor coadsorption ratio is predicted.

At least it is a dry cold: the global distribution of freeze-thaw and drought stress and the traits that may impart poly-tolerance in conifers.

Conifers inhabit some of the most challenging landscapes where multiple abiotic stressors (e.g., aridity, freezing temperatures) often co-occur. Physiological tolerance to multiple stressors ('poly-tolerance') is thought to be rare because exposure to one stress generally limits responses to another through functional trade-offs. However, the capacity to exhibit poly-tolerance may be greater when combined abiotic stressors have similar physiological impacts, such as the disruption of hydraulic function imposed by drought or freezing. Here, we reviewed empirical data in light of theoretical expectations for conifer adaptations to drought and freeze-thaw cycles with particular attention to hydraulic traits of the stem and leaf. Additionally, we examined the commonality and spatial distribution of poly-stress along indices of these combined stressors. We found that locations with the highest values of our poly-stress index (PSi) are characterized by moderate drought and moderate freeze-thaw, and most of the global conifer distribution occupies areas of moderate poly-stress. Among traits examined, we found diverse responses to the stressors. Turgor loss point did not correlate with freeze-thaw or drought stress individually, but did with the PSi, albeit inverse to what was hypothesized. Leaf mass per area was more strongly linked with drought stress than the poly-stress and not at all with freeze-thaw stress. In stems, the water potential causing 50% loss of hydraulic conductivity became more negative with increasing drought stress and poly-stress but did not correlate with freeze-thaw stress. For these traits, we identified a striking lack of coverage for substantial portions of species ranges, particularly at the upper boundaries of their respective PSis, demonstrating a critical gap in our understanding of trait prevalence and plasticity along these stress gradients. Future research should investigate traits that confer tolerance to both freeze-thaw and drought stress in a wide range of species across broad geographic scales.

FoamPi: An open-source raspberry Pi based apparatus for monitoring polyurethane foam reactions.

Adiabatic temperature rise is an important method for determining isocyanate conversion in polyurethane foam reactions as well as many other exothermic chemical reactions. Adiabatic temperature rise can be used in conjunction with change in height and mass measurements to gain understanding into the blowing and gelling reactions that occur during polyurethane foaming as well as give important information on cell morphology. FoamPi is an open-source Raspberry Pi device for monitoring polyurethane foaming reactions. The device effectively monitors temperature rise, change in foam height as well as changes in the mass during the reaction. Three Python scripts are also presented. The first logs raw data during the reaction. The second corrects temperature data such that it can be used in adiabatic temperature rise reactions for calculating isocyanate conversion; additionally this script reduces noise in all the data and removes erroneous readings. The final script extracts important information from the corrected data such as maximum temperature change and maximum height change as well as the time to reach these points. Commercial examples of such equipment exist however the price (>£10000) of these equipment make these systems inaccessible for many research laboratories. The FoamPi build presented is inexpensive (£350) and test examples are shown here to indicate the reproducibility of results as well as precision of the FoamPi.

Experimental evaluation of biological regeneration of arable soil: The effects of grass-clover leys and arbuscular mycorrhizal inoculants on wheat growth, yield, and shoot pathology.

Wheat yields have plateaued in the UK over the last 25 years, during which time most arable land has been annually cropped continuously with short rotations dominated by cereals. Arable intensification has depleted soil organic matter and biology, including mycorrhizas, which are affected by tillage, herbicides, and crop genotype. Here, we test whether winter wheat yields, mycorrhization, and shoot health can be improved simply by adopting less intensive tillage and adding commercial mycorrhizal inoculum to long-term arable fields, or if 3-year grass-clover leys followed direct drilling is more effective for biological regeneration of soil with reduced N fertiliser. We report a trial of mycorrhization, ear pathology, and yield performance of the parents and four double haploid lines from the Avalon x Cadenza winter wheat population in a long-term arable field that is divided into replicated treatment plots. These plots comprised wheat lines grown using ploughing or disc cultivation for 3 years, half of which received annual additions of commercial arbuscular mycorrhizal (AM) inoculum, compared to 3-year mown grass-clover ley plots treated with glyphosate and direct-drilled. All plots annually received 35 kg of N ha-1 fertiliser without fungicides. The wheat lines did not differ in mycorrhization, which averaged only 34% and 40% of root length colonised (RLC) in the ploughed and disc-cultivated plots, respectively, and decreased with inoculation. In the ley, RLC increased to 52%. Two wheat lines were very susceptible to a sooty ear mould, which was lowest in the ley, and highest with disc cultivation. AM inoculation reduced ear infections by >50% in the susceptible lines. In the ley, yields ranged from 7.2 to 8.3 t ha-1, achieving 92 to 106% of UK average wheat yield in 2018 (7.8 t ha-1) but using only 25% of average N fertiliser. Yields with ploughing and disc cultivation averaged only 3.9 and 3.4 t ha-1, respectively, with AM inoculum reducing yields from 4.3 to 3.5 t ha-1 in ploughed plots, with no effect of disc cultivation. The findings reveal multiple benefits of reintegrating legume-rich leys into arable rotations as part of a strategy to regenerate soil quality and wheat crop health, reduce dependence on nitrogen fertilisers, enhance mycorrhization, and achieve good yields.

Hydroscapes, hydroscape plasticity and relationships to functional traits and mesophyll photosynthetic sensitivity to leaf water potential in Eucalyptus species.

The isohydric-anisohydric continuum describes the relative stringency of stomatal control of leaf water potential (ψleaf ) during drought. Hydroscape area (HA)-the water potential landscape over which stomata regulate ψleaf -has emerged as a useful metric of the iso/anisohydric continuum because it is strongly linked to several hydraulic, photosynthetic and structural traits. Previous research on HA focused on broad ecological patterns involving several plant clades. Here we investigate the relationships between HA and climatic conditions and functional traits across ecologically diverse but closely related species while accounting for phylogeny. Across a macroclimatic moisture gradient, defined by the ratio of mean annual precipitation to mean annual pan evaporation (P/Ep ), HA decreased with increased P/Ep across 10 Eucalyptus species. Greater anisohydry reflects lower turgor loss points and greater hydraulic safety, mirroring global patterns. Larger HA coincides with mesophyll photosynthetic capacity that is more sensitive to ψleaf . Hydroscapes exhibit little plasticity in response to variation in water supply, and the extent of plasticity does not vary with P/Ep of native habitats. These findings strengthen the case that HA is a useful metric for characterizing drought tolerance and water-status regulation.

Earth observation and geospatial data can predict the relative distribution of village level poverty in the Sundarban Biosphere Reserve, India.

There is increasing interest in leveraging Earth Observation (EO) and geospatial data to predict and map aspects of socioeconomic conditions to support survey and census activities. This is particularly relevant for the frequent monitoring required to assess progress towards the UNs' Sustainable Development Goals (SDGs). The Sundarban Biosphere Reserve (SBR) is a region of international ecological importance, containing the Indian portion of the world's largest mangrove forest. The region is densely populated and home to over 4.4 million people, many living in chronic poverty with a strong dependence on nature-based rural livelihoods. Such livelihoods are vulnerable to frequent natural hazards including cyclone landfall and storm surges. In this study we examine associations between environmental variables derived from EO and geospatial data with a village level multidimensional poverty metric using random forest machine learning, to provide evidence in support of policy formulation in the field of poverty reduction. We find that environmental variables can predict up to 78% of the relative distribution of the poorest villages within the SBR. Exposure to cyclone hazard was the most important variable for prediction of poverty. The poorest villages were associated with relatively small areas of rural settlement (<∼30%), large areas of agricultural land (>∼50%) and moderate to high cyclone hazard. The poorest villages were also associated with less productive agricultural land than the wealthiest. Analysis suggests villages with access to more diverse livelihood options, and a smaller dependence on agriculture may be more resilient to cyclone hazard. This study contributes to the understanding of poverty-environment dynamics within Low-and middle-income countries and the associations found can inform policy linked to socio-environmental scenarios within the SBR and potentially support monitoring of work towards SDG1 (No Poverty) across the region.