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California is increasingly investing in policies and programs that promote soil stewardship on natural and working lands as a way to help achieve multiple goals, including improved forage production and climate change mitigation. To inform the growing expectations for rangeland management activities to promote such services, we conducted an evidence synthesis assessing how four commonly suggested practices (silvopasture, prescribed grazing, compost application and riparian restoration) affect a suite of soil properties and plant-related metrics throughout the state. We extracted data on soil properties that are potentially responsive to management and relevant to soil health. We also extracted data on aboveground forage production, forage nitrogen content and herbaceous species richness. Our search resulted in 399 individual soil observations and 64 individual plant observations. We found that the presence of oaks had the largest effects on soil properties, with soil organic carbon, microbial biomass and other measures of soil fertility increasing beneath oak canopies. The presence of grazing increased compaction and total nitrogen, and decreased pH. Compost applications did not significantly affect any of the measured soil properties, but did boost forage production. Due to a lack of published data, we were unable to characterize the influence of rangeland riparian restoration on any of the soil or plant metrics in our review.

Small genes (40,000 small-gene families in ~2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially secreted or transmembrane proteins, more than 5,000 families encode predicted anti-CRISPR proteins, and more than 500 families encode predicted antimicrobial proteins. By combining homology and genomic-neighborhood analyses, we reveal substantial novelty and diversity within phage biology, including small phage genes found in multiple host phyla, small genes encoding proteins that play essential roles in host infection, and small genes that share genomic neighborhoods and whose encoded proteins may share related functions.

Many global changes take the form of resource enhancements that have potential to transform multiple aspects of ecosystems from slower to faster cycling, including a suite of both above- and belowground variables. We developed a novel analytic approach to measure integrated ecosystem responses to resource-enhancing global changes, and how such whole ecosystem slow-to-fast transitions are linked to diversity and exotic invasions in real-world ecosystems. We asked how 5-year experimental rainfall and nutrient enhancements in a natural grassland system affected 16 ecosystem functions, pools and stoichiometry variables considered to indicate slow versus fast cycling. We combined these metrics into a novel index we termed "slow-fast multifunctionality" and assessed its relationship to plant community diversity and exotic plant dominance. Nutrient and rainfall addition interacted to affect average slow-fast multifunctionality. Nutrient addition alone pushed the system towards faster cycling, but this effect weakened with the joint addition of rainfall and nutrients. Variables associated with soil nutrient pools and cycling most strongly contributed to this antagonistic interaction. Nutrient and water addition together, respectively, had additive or synergistic effects on plant trait composition and productivity, demonstrating divergence of above- and belowground ecosystem responses. Our novel metric of faster cycling was strongly associated with decreased plant species richness and increased exotic species dominance. These results demonstrate the breadth of interacting community and ecosystem changes that ensue when resource limitation is relaxed.

Interest in land application of organic amendments—such as biosolids, composts, and manures—is growing due to their potential to increase soil carbon and help mitigate climate change, as well as to support soil health and regenerative agriculture. While organic amendments are predominantly applied to croplands, their application is increasingly proposed on relatively arid rangelands that do not typically receive fertilizers or other inputs, creating unique concerns for outcomes such as native plant diversity and water quality. To maximize environmental benefits and minimize potential harms, we must understand how soil, water, and plant communities respond to particular amendments and site conditions. We conducted a global meta‐analysis of 92 studies in which organic amendments had been added to arid, semiarid, or Mediterranean rangelands. We found that organic amendments, on average, provide some environmental benefits (increased soil carbon, soil water holding capacity, aboveground net primary productivity, and plant tissue nitrogen; decreased runoff quantity), as well as some environmental harms (increased concentrations of soil lead, runoff nitrate, and runoff phosphorus; increased soil CO2 emissions). Published data were inadequate to fully assess impacts to native plant communities. In our models, adding higher amounts of amendment benefitted four outcomes and harmed two outcomes, whereas adding amendments with higher nitrogen concentrations benefitted two outcomes and harmed four outcomes. This suggests that trade‐offs among outcomes are inevitable; however, applying low‐N amendments was consistent with both maximizing benefits and minimizing harms. Short study time frames (median 1–2 years), limited geographic scope, and, for some outcomes, few published studies limit longer‐term inferences from these models. Nevertheless, they provide a starting point to develop site‐specific amendment application strategies aimed toward realizing the potential of this practice to contribute to climate change mitigation while minimizing negative impacts on other environmental goals., On rangelands, application of organic amendments such as compost and biosolids is increasingly proposed for climate change mitigation. Considering a range of ecosystem outcomes, this meta‐analysis found that organic amendments, on average, provide some environmental benefits (increased soil carbon, soil water holding capacity, aboveground net primary productivity, and plant tissue nitrogen; decreased runoff quantity), as well as some environmental harms (increased concentrations of soil lead, runoff nitrate, and runoff phosphorus; increased soil CO2 emissions). Our models can be used to design site‐specific amendment application strategies, helping to realize the potential benefits of this practice while minimizing environmental harms.

Spatial heterogeneity in composition and function enables ecosystems to supply diverse services. For soil microbes and the ecosystem functions they catalyze, whether such heterogeneity can be maintained in the face of altered resource inputs is uncertain. In a 50-ha northern California grassland with a mosaic of plant communities generated by different soil types, we tested how spatial variability in microbial composition and function changed in response to nutrient and water addition. Fungal composition lost some of its spatial variability in response to nutrient addition, driven by decreases in mutualistic fungi and increases in antagonistic fungi that were strongest on the least fertile soils, where mutualists were initially most frequent and antagonists initially least frequent. Bacterial and archaeal community composition showed little change in their spatial variability with resource addition. Microbial functions related to nitrogen cycling showed increased spatial variability under nutrient, and sometimes water, additions, driven in part by accelerated nitrification on the initially more-fertile soils. Under anthropogenic changes such as eutrophication and altered rainfall, these findings illustrate the potential for significant changes in ecosystem-level spatial heterogeneity of microbial functions and communities.

Compost application to soil can have numerous agricultural benefits, but our understanding of the persistence and roles of compost microbes in soil following amendment is limited. Studies of microbial invasion ecology could improve this understanding, yet most studies to date have focused on single invaders in constant environments. In contrast, many real-world microbial invasions – such compost microbes invading agricultural soils – are “coalescence events” involving the mixing of entire communities as well as their environmental media. In a microcosm experiment, we mixed live composted poultry manure into row crop soils from three long-term agricultural management systems: no input wheat/fallow, conventional maize/tomato, and organic maize/tomato. We tracked bacterial and archaeal communities by 16S rRNA sequencing prior to mixing and then at 4 days and 32 days post-mixing. We investigated whether phylogenetic relatedness of the invaders (compost microbes) to the resident (soil) community predicted invader success, as well as whether the management systems differed in their invasibility. At both time points, invader persistence was associated with a closer phylogenetic relationship to a member of the resident community, with OTUs most closely related to a member of the resident community 1.65 times more likely to persist than OTUs most distantly related to a member of the resident community on average. Conversely, invaders that achieved greater relative abundances were less related to the resident community, with OTUs most closely related to the resident community as a whole achieving 1.96 times lower relative abundance than OTUs most distantly related to the resident community as a whole on average. Increases in relative abundance of the same bacterial groups (e.g., Actinobacteria, Gammaproteobacteria, Alphaproteobacteria) among residents and invaders post-mixing suggest that similar resident and invader responses to the post-mixing environment may have driven the relative abundance relatedness result. Invaders that were more abundant in the compost also had higher probability of persistence and greater relative abundance post-mixing, with OTUs most abundant in the compost being 16.2 times more likely to persist and having 4.4 times greater relative abundance in the post-mixing community than OTUs least abundant in the compost on average. The organic management system – which had a history of compost addition – was less susceptible to invasion than the other two management systems, with OTUs 1.39 times less likely to persist in the organic system than in the other two systems on average. Our results suggest that both environmental filtering and the potential success of residents and invaders in the novel mixed environment should be considered when predicting outcomes of microbial coalescence events. Agricultural soil management history may also mediate invasion outcomes.

© 2018 Schmidt et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Reducing tillage and growing cover crops, widely recommended practices for boosting soil health, have major impacts on soil communities. Surprisingly little is known about their impacts on soil microbial functional diversity, and especially so in irrigated Mediterranean ecosystems. In long-term experimental plots at the West Side Research and Extension Center in California’s Central Valley, we characterized soil microbial communities in the presence or absence of physical disturbance due to tillage, in the presence or absence of cover crops, and at three depths: 0–5, 5–15 and 15–30 cm. This characterization included qPCR for bacterial and archaeal abundances, DNA sequencing of the 16S rRNA gene, and phylogenetic estimation of two ecologically important microbial traits (rRNA gene copy number and genome size). Total (bacterial + archaeal) diversity was higher in no-till than standard till; diversity increased with depth in no-till but decreased with depth in standard till. Total bacterial numbers were higher in cover cropped plots at all depths, while no-till treatments showed higher numbers in 0–5 cm but lower numbers at lower depths compared to standard tillage. Trait estimates suggested that different farming practices and depths favored distinctly different microbial life strategies. Tillage in the absence of cover crops shifted microbial communities towards fast growing competitors, while no-till shifted them toward slow growing stress tolerators. Across all treatment combinations, increasing depth resulted in a shift towards stress tolerators. Cover crops shifted the communities towards ruderals–organisms with wider metabolic capacities and moderate rates of growth. Overall, our results are consistent with decreasing nutrient availability with soil depth and under no-till treatments, bursts of nutrient availability and niche homogenization under standard tillage, and increases in C supply and variety provided by cover crops. Understanding how agricultural practices shift microbial abundance, diversity and life strategies, such as presented here, can assist with designing farming systems that can support high yields, while enhancing C sequestration and increasing resilience to climate change.

Augmentation of small rare species populations is sometimes suggested on genetic grounds. However, outbreeding depression via dilution of local adaptation or break-up of genomic coadaptation may occur. These effects depend on the causes of population divergence. Here, we compare genetic measures of population divergence in Liatris scariosa var. novae-angliae, a rare New England perennial. We measured GST, neutral marker subdivision, and QST, quantitative subdivision of propagule and juvenile plant traits. GST was relatively high. QST for leaf shape exceeded GST, indicating local adaptation, while QST for other traits fell within or below the GST range. Local adaptation appears low for juvenile traits, although the high GST cautions against translocation because of potential coadaptation. If translocation is still required, however, donor populations should contain high quantitative genetic diversity. We assess population size and allozyme diversity as predictors of quantitative genetic variation, but find these poor proxies for direct measurement.

On exposure to ultraviolet radiation (UV), many plant species both reduce stem elongation and increase production of phenolic compounds that absorb in the UV region of the spectrum. To demonstrate that such developmental plasticity to UV is adaptive, it is necessary to show that the induced phenotype is both beneficial in inductive environments and maladaptive in non-inductive environments. We measured selection on stem elongation and phenolic content of seedlings of Impatiens capensis transplanted into ambient-UV and UV-removal treatments. We extended the range of phenotypes expressed, and thus the opportunity for selection in each UV treatment, by pretreating seedlings with either a low ratio of red:far-red wavelengths (R:FR), which induced stem elongation and reduced phenolic concentrations, or high R:FR, which had the opposite effect on these two phenotypic traits. Reduced stem length relative to biomass was advantageous for elongated plants under ambient UV, whereas increased elongation was favored in the UV-removal treatment. Selection favored an increase in the level of phenolics induced by UV in the ambient-UV treatment, but a decrease in phenolics in the absence of UV. These results are consistent with the hypotheses that reduced elongation and increased phenolic concentrations serve a UV-protective function and provide the first explicit demonstration in a wild species that plasticity of these traits to UV is adaptive. The observed cost to phenolics in the absence of UV may explain why many species plastically upregulate phenolic production when exposed to UV, rather than evolve constitutively high levels of these compounds. Finally, pretreatment with low R:FR simulating foliar shade did not exacerbate the fitness impact of UV exposure when plants had several weeks to acclimate to UV. This observation suggests that the evolution of adaptive shade avoidance responses to low R:FR in crowded stands will not be constrained by increased sensitivity to UV in elongated plants when they overtop their neighbors.

Propagule dispersal biology is a crucial avenue of research for rare plant species, especially those adapted to disturbance, such as northern blazing star (Liatris scariosa var. novae-angliae), a rare, early-successional New England grassland perennial. We examined the dispersal ability of northern blazing star propagules collected from 14 populations covering the entire latitudinal range of the taxon. Multiple regression demonstrated that dispersal ability, as measured by drop time in still air and flight distance in a low-speed wind tunnel, decreased significantly with propagule size and achene length, and increased with achene width and (for flight distance) pappus length. We used this multiple regression model to test for differences in predicted dispersal capability among maternal families, populations, and inland, coastal, and island habitats. Dispersal capability differed significantly among families and populations but not regions, and allometric relationships between morphological measurements were consistent across populations. Overall, dispersal capability was negatively correlated with germination success in a common greenhouse environment. However, germination success for a given dispersal ability, as well as achene shape, differed among populations. These results suggest specific populations to be targeted for management efforts promoting dispersal and establishment.

It has proven difficult, when focused only on biological determinants, to explain why some plant species become naturalized in or invade new locations, whereas others fail. We analyzed the invasion of Trifolium (true clover) species into New Zealand, assessing a range of human, biogeographic, and biological influences at three key invasion stages: introduction, naturalization, and spread. We used sparse principal component analysis (SPCA) to define suites of related attributes and aggregated boosted trees to model relationships with invasion outcomes. Human and biogeographic attributes were strongly associated with success at all stages. Whereas biogeographic attributes, notably large native range, were consistently associated with success, different human factors appeared to favor success at different stages, such as presence in early trade/immigration hotspots (introduction), intentional large-scale planting (naturalization), and frequent presence as a seed contaminant (relative spread rate). Biological traits were less strongly associated with success for introduction and spread and little if at all for naturalization; we found that tall perennials with long flowering periods were more frequently selected for introduction, whereas species with extended flowering in New Zealand spread more rapidly. In addition to causal relationships, the importance of human factors may reflect indirect associations, including ecological traits associated with both human use and invasion. Nevertheless, our results highlight key roles that humans can play in facilitating plant invasion via two pathways: ( i ) commercial introduction leading to widespread planting and concomitant naturalization and spread and ( ii ) unintentional introduction and spread of species associated with human activities, such as seed contaminants.

Crystallographic studies of the catalytic core domain of avian sarcoma virus integrase (ASV IN) have provided the most detailed picture so far of the active site of this enzyme, which belongs to an important class of targets for designing drugs against AIDS. Recently, crystals of an inactive D64N mutant were obtained under conditions identical to those used for the native enzyme. Data were collected at different pH values and in the presence of divalent cations. Data were also collected at low pH for the crystals of the native ASV IN core domain. In the structures of native ASV IN at pH 6.0 and below, as well as in all structures of the D64N mutants, the side chain of the active site residue Asx-64 (Asx denotes Asn or Asp) is rotated by approximately 150 degrees around the Calpha---Cbeta bond, compared with the structures at higher pH. In the new structures, this residue makes hydrogen bonds with the amide group of Asn-160, and thus, the usual metal-binding site, consisting of Asp-64, Asp-121, and Glu-157, is disrupted. Surprisingly, however, a single Zn2+ can still bind to Asp-121 in the mutant, without restoration of the activity of the enzyme. These structures have elucidated an unexpected mechanism of inactivation of the enzyme by lowering the pH or by mutation, in which a protonated side chain of Asx-64 changes its orientation and interaction partner.

The retroviral integrase protein catalyzes the insertion of linear viral DNA ends into the host cell DNA. Although integration in vivo is not site-specific, the detection of local and regional preferences within cellular DNA suggests that the integration reaction can be influenced by specific features of host DNA or chromatin. Here we describe highly preferred in vitro integration sites for avian sarcoma virus and human immunodeficiency virus-1 integrases within the stems of plasmid DNA cruciform structures. The preferred sites are adjacent to the loops in the cruciform and are strand-specific. We suggest that the observed preference is due to the end-like character of the stem loop structure that allows DNA unpairing. From these results we propose that such unpairing may enhance both the processing and the joining steps in the integration reaction, and perhaps other cellular recombination reactions as well.