Cattle grazing in CRP grasslands during the nesting season: effects on avian abundance and diversity

The Conservation Reserve Program (CRP) is a primary tool for restoring grassland in the United States, in part as wildlife habitat, which has benefited declining grassland bird populations. Among potential mid-contract management practices used to maintain early-successional CRP grasslands, cattle grazing had been prohibited and is currently disincentivized during the primary nesting season for birds (much of the growing season), despite the important role that large herbivores historically played in structuring grassland ecosystems. Conservative grazing of CRP grasslands could increase spatial heterogeneity in vegetation structure and plant diversity, potentially supporting higher densities of some grassland bird species and higher bird diversity. Our objective was to determine the effect of experimental cattle grazing on species-specific relative abundance and occupancy, species diversity, and community dissimilarity of grassland birds on CRP grasslands across the longitudinal extent of Kansas, USA (a 63.5-cm precipitation gradient) during the 2017–2019 avian breeding seasons. Fifty-three of 108 fields were grazed by cattle during the growing seasons of 2017 and 2018 and all fields were rested from grazing in 2019. For all analyses, we examined separate model sets for semiarid western versus more mesic eastern Kansas. Using data from line transect surveys, we modeled relative abundances of 5 songbird species: grasshopper sparrow (Ammodramus savannarum), dickcissel (Spiza americana), eastern meadowlark (Sturnella magna), western meadowlark (Sturnella neglecta), and brown-headed cowbird (Molothrus ater). Grazing had delayed yet positive effects on abundances of grasshopper sparrow in western Kansas, and eastern meadowlark in eastern Kansas, but negative effects on dickcissel abundance in western Kansas and especially on burned fields in eastern Kansas. Somewhat counterintuitively, brown-headed cowbirds in western Kansas were more abundant on ungrazed versus grazed fields in the years after grazing began. In addition, we modeled multi-season occupancy of 3 gamebird species (ring-necked pheasant [Phasianus colcicus], northern bobwhite [Colinus virginianus], mourning dove [Zenaida macroura]) and Henslow's sparrow (Centronyx henslowii); grazing did not affect occupancy of these species. In eastern Kansas, species diversity was highest in grazed, unburned fields. In western Kansas, bird communities in grazed and ungrazed fields were dissimilar, as determined from multivariate analysis. Though regionally variable, conservative stocking of cattle on CRP grasslands during the nesting season as a mid-contract management tool might increase bird species diversity by restructuring habitat that accommodates a greater variety of species and decreasing abundances of species associated with taller, denser stands of vegetation.     

Correction to: Who is the ocean? Preface to the future seas 2030 special issue

Reviews in Fish Biology and Fisheries - A correction to this paper has been published: https://doi.org/10.1007/s11160-021-09657-9     

Safeguarding marine life: conservation of biodiversity and ecosystems

Reviews in Fish Biology and Fisheries - Marine ecosystems and their associated biodiversity sustain life on Earth and hold intrinsic value. Critical marine ecosystem services include maintenance of...     

Nuclear domain ‘knock-in’ screen for the evaluation and identification of small molecule enhancers of CRISPR-based genome editing

CRISPR is a genome-editing platform that makes use of the bacterially-derived endonuclease Cas9 to introduce DNA double-strand breaks at precise locations in the genome using complementary guide RNAs. We developed a nuclear domain knock-in screen, whereby the insertion of a gene encoding the green fluorescent protein variant Clover is inserted by Cas9-mediated homology directed repair (HDR) within the first exon of genes that are required for the structural integrity of subnuclear domains such as the nuclear lamina and promyelocytic leukemia nuclear bodies (PML NBs). Using this approach, we compared strategies for enhancing CRISPR-mediated HDR, focusing on known genes and small molecules that impact non-homologous end joining (NHEJ) and homologous recombination (HR). Ultimately, we identified the small molecule RS-1 as a potent enhancer of CRISPR-based genome editing, enhancing HDR 3- to 6-fold depending on the locus and transfection method. We also characterized U2OS human osteosarcoma cells expressing Clover-tagged PML and demonstrate that this strategy generates cell lines with PML NBs that are structurally and functionally similar to bodies in the parental cell line. Thus, the nuclear domain knock-in screen that we describe provides a simple means of rapidly evaluating methods and small molecules that have the potential to enhance Cas9-mediated HDR.     

Evolutionary Expansion of the Amidohydrolase Superfamily in Bacteria in Response to the Synthetic Compounds Molinate and Diuron

The amidohydrolase superfamily has remarkable functional diversity, with considerable structural and functional annotation of known sequences. In microbes, the recent evolution of several members of this family to catalyze the breakdown of environmental xenobiotics is not well understood. An evolutionary transition from binuclear to mononuclear metal ion coordination at the active sites of these enzymes could produce large functional changes such as those observed in nature, but there are few clear examples available to support this hypothesis. To investigate the role of binuclear-mononuclear active-site transitions in the evolution of new function in this superfamily, we have characterized two recently evolved enzymes that catalyze the hydrolysis of the synthetic herbicides molinate (MolA) and phenylurea (PuhB). In this work, the crystal structures, mutagenesis, metal ion analysis, and enzyme kinetics of both MolA and PuhB establish that these enzymes utilize a mononuclear active site. However, bioinformatics and structural comparisons reveal that the closest putative ancestor of these enzymes had a binuclear active site, indicating that a binuclear-mononuclear transition has occurred. These proteins may represent examples of evolution modifying the characteristics of existing catalysts to satisfy new requirements, specifically, metal ion rearrangement leading to large leaps in activity that would not otherwise be possible.     

The Putative Mevalonate Diphosphate Decarboxylase from Picrophilus torridus Is in Reality a Mevalonate-3-Kinase with High Potential for Bioproduction of Isobutene

Mevalonate diphosphate decarboxylase (MVD) is an ATP-dependent enzyme that catalyzes the phosphorylation/decarboxylation of (R)-mevalonate-5-diphosphate to isopentenyl pyrophosphate in the mevalonate (MVA) pathway. MVD is a key enzyme in engineered metabolic pathways for bioproduction of isobutene, since it catalyzes the conversion of 3-hydroxyisovalerate (3-HIV) to isobutene, an important platform chemical. The putative homologue from Picrophilus torridus has been identified as a highly efficient variant in a number of patents, but its detailed characterization has not been reported. In this study, we have successfully purified and characterized the putative MVD from P. torridus. We discovered that it is not a decarboxylase per se but an ATP-dependent enzyme, mevalonate-3-kinase (M3K), which catalyzes the phosphorylation of MVA to mevalonate-3-phosphate. The enzyme''s potential in isobutene formation is due to the conversion of 3-HIV to an unstable 3-phosphate intermediate that undergoes consequent spontaneous decarboxylation to form isobutene. Isobutene production rates were as high as 507 pmol min⁻¹ g cells⁻¹ using Escherichia coli cells expressing the enzyme and 2,880 pmol min⁻¹ mg protein⁻¹ with the purified histidine-tagged enzyme, significantly higher than reported previously. M3K is a key enzyme of the novel MVA pathway discovered very recently in Thermoplasma acidophilum. We suggest that P. torridus metabolizes MVA by the same pathway.     

Regulation of the Rev1–pol ζ complex during bypass of a DNA interstrand cross‐link

DNA interstrand cross‐links (ICLs) are repaired in S phase by a complex, multistep mechanism involving translesion DNA polymerases. After replication forks collide with an ICL, the leading strand approaches to within one nucleotide of the ICL (“approach”), a nucleotide is inserted across from the unhooked lesion (“insertion”), and the leading strand is extended beyond the lesion (“extension”). How DNA polymerases bypass the ICL is incompletely understood. Here, we use repair of a site‐specific ICL in Xenopus egg extracts to study the mechanism of lesion bypass. Deep sequencing of ICL repair products showed that the approach and extension steps are largely error‐free. However, a short mutagenic tract is introduced in the vicinity of the lesion, with a maximum mutation frequency of ~1%. Our data further suggest that approach is performed by a replicative polymerase, while extension involves a complex of Rev1 and DNA polymerase ζ. Rev1–pol ζ recruitment requires the Fanconi anemia core complex but not FancI–FancD2. Our results begin to illuminate how lesion bypass is integrated with chromosomal DNA replication to limit ICL repair‐associated mutagenesis.     

Every inch a finch: a commentary on Grant (1993) ‘Hybridization of Darwin's finches on Isla Daphne Major,Galapagos’

One of the most familiar features of the natural world is that most animals and plants fall into distinct categories known as species. The attempt to understand the nature of species and the origin of new species was the enterprise that drove the early development of evolutionary biology and has continued to be a major focus of research. Individuals belonging to the same species usually share a distinctive appearance and way of life, and they can mate together successfully and produce viable offspring. New species may evolve, therefore, either through ecological divergence or through sexual isolation. The balance between these processes will depend on the extent of hybridization, especially in the early stages of divergence. Detecting and measuring hybridization in natural populations, however, requires intensive, long-term field programmes that are seldom undertaken, leaving a gap in our understanding of species formation. The finch community of a small, isolated island in the Galapagos provided an opportunity to discover how frequently hybridization takes place between closely related species in a pristine location, and Peter Grant''s paper, published in Philosophical Transactions B in 1993, reports the observations that he and his collaborators made during the first 20 years of what is now one of the classical studies of evolution in action. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society.