Effects of agri-environment management for cirl buntings on other biodiversity

Agri-environment scheme (AES) management has increased populations of cirl buntings (Emberiza cirlus) in South Devon, England, and might be expected to provide benefits for other declining biodiversity, due to less intensive farm management. Fields managed under AES for cirl buntings (low-input spring barley or permanent pasture without inputs) were contrasted with control fields under conventional management (spring barley without management restrictions and winter cereals, or grazed without management restrictions) to identify such benefits for vascular plants, butterflies, bumblebees, carabid beetles, foliar invertebrates and bats. Activity-density and species richness of carabid beetles were both higher in AES spring barley fields than in control spring barley and winter cereal fields. Forb cover and abundance of butterflies and bumblebees were higher in AES spring barley fields than in winter cereals, but did not differ between AES and control spring barley. No difference was observed in plant species richness between any of the arable field types. Plant species richness and butterfly abundance were higher in AES pasture fields than in controls. Abundance, activity-density and/or species richness of other taxa did not differ between AES and control pastures. Benefits observed in AES spring barley fields arise from management specific to AES agreements, and also, we suggest, from the maintenance of spring-sown barley in the landscape. Benefits in AES pasture fields are ascribed to the absence of fertiliser and pesticide inputs, and reductions in stocking arising from this; there is also likely to have been some pre-selection for older pastures to be entered into AES management agreements. Agri-environment measures for cirl buntings have benefits for a range of taxa beyond the target species, and therefore, largely through reduction of management intensity and maintenance of land-use diversity, improve the overall biodiversity of the farmed landscape where they are present.     

The HIV-2 Rev-response element: determining secondary structure and defining folding intermediates

Interaction between the viral protein Rev and the RNA motifs known as Rev response elements (RREs) is required for transport of unspliced and partially spliced human immunodeficiency virus (HIV)-1 and HIV-2 RNAs from the nucleus to the cytoplasm during the later stages of virus replication. A more detailed understanding of these nucleoprotein complexes and the host factors with which they interact should accelerate the development of new antiviral drugs targeting cis-acting RNA regulatory signals. In this communication, the secondary structures of the HIV-2 RRE and two RNA folding precursors have been identified using the SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) chemical probing methodology together with a novel mathematical approach for determining the secondary structures of RNA conformers present in a mixture. A complementary chemical probing technique was also used to support these secondary structure models, to confirm that the RRE2 RNA undergoes a folding transition and to obtain information about the relative positioning of RRE2 substructures in three dimensions. Our analysis collectively suggests that the HIV-2 RRE undergoes two conformational transitions before assuming the energetically most favorable conformer. The 3D models for the HIV-2 RRE and folding intermediates are also presented, wherein the Rev-binding stem–loops (IIB and I) are located coaxially in the former, which is in agreement with previous models for HIV-1 Rev-RRE binding.     

Two major groups of colicin factors: Their molecular weights

Summary Colicin factors are thought to fall into two taxonomic groups which differ in, amongst other properties, the molecular weight of the plasmid DNA and the host range of the colicin protein. This hypothesis is supported by the plasmids found in 26 colicinogenic strains. Two small Col factors may have arisen from larger factors, judging from similarities between their colicins.     

Deep subsurface microbial life in impact-altered Late Paleozoic granitoid rocks from the Chicxulub impact crater

In 2016, IODP-ICDP Expedition 364 recovered an 829-meter-long core within the peak ring of the Chicxulub impact crater (Yucatán, Mexico), allowing us to investigate the post-impact recovery of the heat-sterilized deep continental microbial biosphere at the impact site. We recently reported increased cell biomass in the impact suevite, which was deposited within the first few hours of the Cenozoic, and that the overall microbial communities differed significantly between the suevite and the other main core lithologies (i.e., the granitic basement and the overlying Early Eocene marine sediments; Cockell et al., 2021). However, only seven rock intervals were previously analyzed from the geologically heterogenic and impact-deformed 587-m-long granitic core section below the suevite interval. Here, we used 16S rRNA gene profiling to study the microbial community composition in 45 intervals including (a) 31 impact-shocked granites, (b) 7 non-granitic rocks (i.e., consisting of suevite and impact melt rocks intercalated into the granites during crater formation and strongly serpentinized pre-impact sub-volcanic, ultramafic basanite/dolerite), and (c) 7 cross-cut mineral veins of anhydride and silica. Most recovered microbial taxa resemble those found in hydrothermal systems. Spearman correlation analysis confirmed that the borehole temperature, which gradually increased from 47 to 69°C with core depth, significantly shaped a subset of the vertically stratified modern microbial community composition in the granitic basement rocks. However, bacterial communities differed significantly between the impoverished shattered granites and nutrient-enriched non-granite rocks, even though both lithologies were at similar depths and temperatures. Furthermore, Spearman analysis revealed a strong correlation between the microbial communities and bioavailable chemical compounds and suggests the presence of chemolithoautotrophs, which most likely still play an active role in metal and sulfur cycling. These results indicate that post-impact microbial niche separation has also occurred in the granitic basement lithologies, as previously shown for the newly formed lithologies. Moreover, our data suggest that the impact-induced geochemical boundaries continue to shape the modern-day deep biosphere in the granitic basement underlying the Chicxulub crater.     

Refining trophic dynamics through multi‐factor Bayesian mixing models: A case study of subterranean beetles

Food web dynamics are vital in shaping the functional ecology of ecosystems. However, trophic ecology is still in its infancy in groundwater ecosystems due to the cryptic nature of these environments. To unravel trophic interactions between subterranean biota, we applied an interdisciplinary Bayesian mixing model design (multi‐factor BMM) based on the integration of faunal C and N bulk tissue stable isotope data (δ¹³C and δ¹⁵N) with radiocarbon data (Δ¹⁴C), and prior information from metagenomic analyses. We further compared outcomes from multi‐factor BMM with a conventional isotope double proxy mixing model (SIA BMM), triple proxy (δ¹³C, δ¹⁵N, and Δ¹⁴C, multi‐proxy BMM), and double proxy combined with DNA prior information (SIA + DNA BMM) designs. Three species of subterranean beetles (Paroster macrosturtensis, Paroster mesosturtensis, and Paroster microsturtensis) and their main prey items Chiltoniidae amphipods (AM1: Scutachiltonia axfordi and AM2: Yilgarniella sturtensis), cyclopoids and harpacticoids from a calcrete in Western Australia were targeted. Diet estimations from stable isotope only models (SIA BMM) indicated homogeneous patterns with modest preferences for amphipods as prey items. Multi‐proxy BMM suggested increased—and species‐specific—predatory pressures on amphipods coupled with high rates of scavenging/predation on sister species. SIA + DNA BMM showed marked preferences for amphipods AM1 and AM2, and reduced interspecific scavenging/predation on Paroster species. Multi‐factorial BMM revealed the most precise estimations (lower overall SD and very marginal beetles' interspecific interactions), indicating consistent preferences for amphipods AM1 in all the beetles' diets. Incorporation of genetic priors allowed crucial refining of the feeding preferences, while integration of more expensive radiocarbon data as a third proxy (when combined with genetic data) produced more precise outcomes but close dietary reconstruction to that from SIA + DNA BMM. Further multidisciplinary modeling from other groundwater environments will help elucidate the potential behind these designs and bring light to the feeding ecology of one the most vital ecosystems worldwide.     

The role of fire in germinating Wild Rice (Oryza meridionalis), an annual grass of northern Australian wetlands threatened by exotic grass invasion

Para Grass (Urochloa mutica (Forssk.) Nguyen) has invaded large areas of north Australian wetlands, out‐competing native flora. Post‐fire observations indicated that the native grass, Wild Rice (Oryza meridionalis Ng), re‐established where gaps in Para grass mats had been created by burning. We tested whether it was fire itself or simply the removal of Para Grass that promoted Wild Rice, by subjecting comparable buried seed batches to one of three treatments: fire (at two intensities) and no fire. Subsequent germination tests confirmed current laboratory research that suggests post‐fire promotion of Wild Rice is not a function of fire per se (neither heat or smoke) but is likely to be due to the removal of the smothering grass layer, even though fire is a efficient way of removing Para Grass.     

Survival motor neuron protein regulates stem cell division, proliferation, and differentiation in Drosophila

Spinal muscular atrophy is a severe neurogenic disease that is caused by mutations in the human survival motor neuron 1 (SMN1) gene. SMN protein is required for the assembly of small nuclear ribonucleoproteins and a dramatic reduction of the protein leads to cell death. It is currently unknown how the reduction of this ubiquitously essential protein can lead to tissue-specific abnormalities. In addition, it is still not known whether the disease is caused by developmental or degenerative defects. Using the Drosophila system, we show that SMN is enriched in postembryonic neuroblasts and forms a concentration gradient in the differentiating progeny. In addition to the developing Drosophila larval CNS, Drosophila larval and adult testes have a striking SMN gradient. When SMN is reduced in postembryonic neuroblasts using MARCM clonal analysis, cell proliferation and clone formation defects occur. These SMN mutant neuroblasts fail to correctly localise Miranda and have reduced levels of snRNAs. When SMN is removed, germline stem cells are lost more frequently. We also show that changes in SMN levels can disrupt the correct timing of cell differentiation. We conclude that highly regulated SMN levels are essential to drive timely cell proliferation and cell differentiation.