Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists

Rapid evolution of a coastal marsh ecosystem engineer in response to global change

There is increasing evidence that global change can alter ecosystems by eliciting rapid evolution of foundational plants capable of shaping vital attributes and processes. Here we describe results of a field-scale exposure experiment and multilocus assays illustrating that elevated CO2 (eCO2) and nitrogen (N) enrichment can result in rapid shifts in genetic and genotypic variation in Phragmites australis, an ecologically dominant plant that acts as an ecosystem engineer in coastal marshes worldwide. Compared to control treatments, genotypic diversity declined over three years of exposure, especially to N enrichment. The magnitude of loss also increased over time under conditions of N enrichment. Comparisons of genotype frequencies revealed that proportional abundances shifted with exposure to eCO2 and N in a manner consistent with expected responses to selection. Comparisons also revealed evidence of tradeoffs that constrained exposure responses, where any particular genotype responded favorably to one factor rather than to different factors or to combinations of factors. These findings challenge the prevailing view that plant-mediated ecosystem outcomes of global change are governed primarily by differences in species responses to shifting environmental pressures and highlight the value of accounting for organismal evolution in predictive models to improve forecasts of ecosystem responses to global change

Rising ecosystem water demand exacerbates the lengthening of tropical dry seasons

International audiencePrecipitation-based assessments show a lengthening of tropical dry seasons under climate change, without considering simultaneous changes in ecosystem water demand. Here, we compare changes in tropical dry season length and timing when dry season is defined as the period when precipitation is less than: its climatological average, potential evapotranspiration, or actual evapotranspiration. While all definitions show more widespread tropical drying than wetting for 1983-2016, we find the largest fraction (48.7%) of tropical land probably experiencing longer dry seasons when dry season is defined as the period when precipitation cannot meet the need of actual evapotranspiration. Southern Amazonia (due to delayed end) and central Africa (due to earlier onset and delayed end) are hotspots of dry season lengthening, with greater certainty when accounting for water demand changes. Therefore, it is necessary to account for changing water demand when characterizing changes in tropical dry periods and ecosystem water deficits

Standardized metrics are key for assessing drought severity

3 Pags.- 2 Figs.This article is a response to Zang... [et al.], Global Change Biology 26: 322–324 (2020)Peer reviewe

Grassland productivity responds unexpectedly to dynamic light and soil water environments induced by photovoltaic arrays

Abstract Agrivoltaic (AV) systems are designed to coproduce photovoltaic (PV) energy on lands simultaneously supporting agriculture (food/forage production). PV infrastructure in agroecosystems alters resources critical for plant growth, and water‐limited agroecosystems such as grasslands are likely to be particularly sensitive to the unique spatial and temporal patterns of incident sunlight and soil water inherent within AV systems. However, the impact of resource alteration on forage production, the primary ecosystem service from managed grasslands, is poorly resolved. Here, we evaluated seasonal patterns of soil moisture (SM) and diurnal variation in incident sunlight (photosynthetic photon flux density [PPFD]) in a single‐axis‐tracking AV system established in a formerly managed semiarid C3 grassland in Colorado. Our goals were to (1) quantify dynamic patterns of PPFD and SM within a 1.2 MW PV array in a perennial grassland, and (2) determine how aboveground net primary production (ANPP) and photosynthetic parameters responded to the resource patterns created by the PV array. We hypothesized that spatial variability in ANPP would be strongly related to SM patterns, typical of most grasslands. We measured significant reductions in ANPP directly beneath PV panels, where SM and PPFD were both low. However, in locations with significantly increased SM from the shedding and redistribution of precipitation by PV panels, ANPP was not increased. Instead, ANPP was greatest in locations where plants were shaded in the afternoon but received high levels of PPFD in the morning hours, when air temperatures and vapor pressure deficits were relatively low. Thus, contrary to expectations, we found relatively weak relationships between SM and ANPP despite significant spatial variability in both. Further, there was little evidence that light‐saturated photosynthesis (Asat) and quantum yield of CO2 assimilation (ϕCO2) differed for plants growing directly beneath (lowest PPFD) versus between (highest PPFD) PV panels. Overall, the AV system established in this semiarid managed grassland did not alter patterns of ANPP in ways predictable from past studies of controls of ANPP in open grasslands. However, our results suggest that the diurnal timing of low versus high periods of PPFD incident on plants is an important determinant of productivity patterns in grasslands

Trait selection and community weighting are key to understanding ecosystem responses to changing precipitation regimes

Plant traits can be used to predict ecosystem responses to environmental change using a response\u2013effect trait framework. To do this, appropriate traits must be identified that explain a species' influence on ecosystem function (\u201ceffect traits\u201d) and the response of those species to environmental change (\u201cresponse traits\u201d). Response traits are often identified and measured along gradients in plant resources, such as water availability; however, precipitation explains very little variation in most plant traits globally. Given the strong relationship between plant traits and ecosystem functions, such as net primary productivity (NPP), and between NPP and precipitation, the lack of correlation between precipitation and plant traits is surprising. We address this issue through a systematic review of >500 published studies that describe plant trait responses to altered water availability. The overarching goal of this review was to identify potential causes for the weak relationship between commonly measured plant traits and water availability so that we may identify more appropriate \u201cresponse traits.\u201d We attribute weak trait\u2013precipitation relationships to an improper selection of traits (e.g., nonhydraulic traits) and a lack of trait-based approaches that adjust for trait variation within communities (only 4% of studies measure community-weighted traits). We then highlight the mechanistic value of hydraulic traits as more appropriate \u201cresponse traits\u201d with regard to precipitation, which should be included in future community-scale trait surveys. Trait-based ecology has the potential to improve predictions of ecosystem responses to predicted changes in precipitation; however, this predictive power depends heavily on the identification of reliable response and effect traits. To this end, trait surveys could be improved by a selection of traits that reflect physiological functions directly related to water availability with traits weighted by species relative abundance. A plain language summary is available for this article

Pushing precipitation to the extremes in distributed experiments: recommendations for simulating wet and dry years.

Intensification of the global hydrological cycle, ranging from larger individual precipitation events to more extreme multiyear droughts, has the potential to cause widespread alterations in ecosystem structure and function. With evidence that the incidence of extreme precipitation years (defined statistically from historical precipitation records) is increasing, there is a clear need to identify ecosystems that are most vulnerable to these changes and understand why some ecosystems are more sensitive to extremes than others. To date, opportunistic studies of naturally occurring extreme precipitation years, combined with results from a relatively small number of experiments, have provided limited mechanistic understanding of differences in ecosystem sensitivity, suggesting that new approaches are needed. Coordinated distributed experiments (CDEs) arrayed across multiple ecosystem types and focused on water can enhance our understanding of differential ecosystem sensitivity to precipitation extremes, but there are many design challenges to overcome (e.g., cost, comparability, standardization). Here, we evaluate contemporary experimental approaches for manipulating precipitation under field conditions to inform the design of 'Drought-Net', a relatively low-cost CDE that simulates extreme precipitation years. A common method for imposing both dry and wet years is to alter each ambient precipitation event. We endorse this approach for imposing extreme precipitation years because it simultaneously alters other precipitation characteristics (i.e., event size) consistent with natural precipitation patterns. However, we do not advocate applying identical treatment levels at all sites - a common approach to standardization in CDEs. This is because precipitation variability varies >fivefold globally resulting in a wide range of ecosystem-specific thresholds for defining extreme precipitation years. For CDEs focused on precipitation extremes, treatments should be based on each site's past climatic characteristics. This approach, though not often used by ecologists, allows ecological responses to be directly compared across disparate ecosystems and climates, facilitating process-level understanding of ecosystem sensitivity to precipitation extremes

Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists