The acidithiobacilli are sulfur-oxidizing acidophilic bacteria that thrive in both natural and anthropogenic low pH environments. They contribute to processes that lead to the generation of acid rock drainage in several different geoclimatic contexts, and their properties have long been harnessed for the biotechnological processing of minerals. Presently, the genus is composed of seven validated species, described between 1922 and 2015: Acidithiobacillus thiooxidans, A. ferrooxidans, A. albertensis, A. caldus, A. ferrivorans, A. ferridurans, and A. ferriphilus. However, a large number of Acidithiobacillus strains and sequence clones have been obtained from a variety of ecological niches over the years, and many isolates are thought to vary in phenotypic properties and cognate genetic traits. Moreover, many isolates remain unclassified and several conflicting specific assignments muddle the picture from an evolutionary standpoint. Here we revise the phylogenetic relationships within this species complex and determine the phylogenetic species boundaries using three different typing approaches with varying degrees of resolution: 16S rRNA gene-based ribotyping, oligotyping, and multi-locus sequencing analysis (MLSA). To this end, the 580 16S rRNA gene sequences affiliated to the Acidithiobacillus spp. were collected from public and private databases and subjected to a comprehensive phylogenetic analysis. Oligotyping was used to profile high-entropy nucleotide positions and resolve meaningful differences between closely related strains at the 16S rRNA gene level. Due to its greater discriminatory power, MLSA was used as a proxy for genome-wide divergence in a smaller but representative set of strains. Results obtained indicate that there is still considerable unexplored diversity within this genus. At least six new lineages or phylotypes, supported by the different methods used herein, are evident within the Acidithiobacillus species complex. Although the diagnostic characteristics of these subgroups of strains are as yet unresolved, correlations to specific metadata hint to the mechanisms behind econiche-driven divergence of some of the species/phylotypes identified. The emerging phylogenetic structure for the genus outlined in this study can be used to guide isolate selection for future population genomics and evolutionary studies in this important acidophile model.

The promotion of native vegetation as a habitat for natural enemies, which could increase their abundance and fitness, is especially useful in highly simplified settings such as Mediterranean greenhouse landscapes. Spiders as generalist predators may also be involved in intra-guild predation. However, the niche complementarity provided by spiders as a group means that increased spider diversity may facilitate complementary control actions. In this study, the interactions between spiders, the two major horticultural pests, Bemisia tabaci and Frankliniella occidentalis, and their naturally occurring predators and parasitoids were evaluated in a mix of 21 newly planted shrubs selected for habitat management in a highly disturbed horticultural system. The effects of all factors were evaluated using redundancy analysis (RDA) and the generalized additive model (GAM) to assess the statistical significance of abundance of spiders and pests. The GAM showed that the abundance of both pests had a significant effect on hunter spider’s abundance, whereas the abundance of B. tabaci, but not F. occidentalis, affected web-weavers’ abundance. Ordination analysis showed that spider abundance closely correlated with that of B. tabaci but not with that of F. occidentalis, suggesting that complementarity occurs, and thereby probability of biocontrol, with respect to the targeted pest B. tabaci, although the temporal patterns of the spiders differed from those of F. occidentalis. Conservation strategies involving the establishment of these native plants around greenhouses could be an effective way to reduce pest populations outdoors.

Large‐bodied frugivorous birds play an important role in dispersing large‐sized seeds in Neotropical rain forests, thereby maintaining tree species richness and diversity. Conversion of contiguous forest land to forest fragments is thought to be driving population declines in large‐bodied frugivores, but the mechanistic drivers of this decline remain poorly understood. To assess the importance of fragment‐level versus local landscape attributes in influencing the species richness of large‐bodied (>100 g) frugivorous birds, we surveyed 15 focal species in 22 forest fragments (2.7 to 33.6 ha, avg. = 16.0 ha) in northwest Ecuador in 2014. Fragment habitat variables included density of large trees, canopy openness and height, and fragment size; landscape variables included elevation and the proportion of tree cover within a 1 km radius of each fragment. At both the individual species level, and across the community of 12 species of avian frugivore we detected, there was higher richness and probability of presence in fragments with more tree cover on surrounding land. This tendency was particularly pronounced among some endangered species. These findings corroborate the idea that partially forested land surrounding fragments may effectively increase the suitable habitat for forest‐dwelling frugivorous birds in fragmented landscapes. These results can help guide conservation priorities within fragmented landscapes, with particular reference to retaining trees and reforesting to attain high levels of tree cover in areas between forest patches.

Natural control by predators and parasitoids provides an important and often unnoticed ecosystem service to agricultural landscapes by reducing pest populations in crops. The current model of horticultural intensification in south-eastern Spain produces high yields but has also resulted in a landscape almost completely covered by plastic. Promoting natural areas among greenhouses could enhance biodiversity, by being beneficial insects, and reduce pest pressure outdoors. The first step is to ascertain how pests and their natural enemies (NEs) use Mediterranean vegetation for selecting the best plants for pest suppression outdoors. The abundance of the two major horticultural pests, the tobacco whitefly, Bemisia tabaci, and the western flower thrips, Frankliniella occidentalis, together with their NEs, were assayed in 22 flowering perennial plants, which were newly planted in an experimental field surrounded by greenhouses. Eight plant species were identified as the most critical species for sustaining pest populations outdoors. A set of five plant species supported a medium level of pests, and another set of ten plant species supported the lowest level of both pests. Tobacco whitefly occurred in a few plants species, whereas western flower thrips occurred on almost all the plant species studied, and was favoured by the presence of flowers in perennial plants. The results suggest that plant diversity may provide relatively few acceptable host plants for tobacco whitefly than for western flower thrips. NEs were generally collected in plants that also supported abundance of pests, indicating that host/prey availability, more than food resources from flowers, was a stronger predictor of NE abundance in perennial plants. Field trials using the plants with the lowest host acceptance by pests are needed in order to ascertain whether pest abundance outdoors is reduced.

Sustainability transitions in agriculture are explored through an analysis of niche initiatives within a common production system, relying on sustainable transitions, multi-level perspectives, and agroecological frameworks, and involving multi-actor, agricultural knowledge, and innovation systems (AKIS). The article focuses on how experimental niches and sustainable activities affect farmers’ relationships with nature, and the reconceptualisation of the production system in which they operate, particularly where this system is embedded in less sustainable conventional or dominant regimes and landscapes. The need for fundamental changes, in the way that humans interact with nature, is widely argued for in order to achieve sustainable development, and farmers occupy a central role through participation in complex networks of agri-food systems. They have also found themselves disconnected from nature through conventional agri-industrial production practices. Four niches (biological control, ecological restoration, soil health, and ecological pond management) within the greenhouse sector of Almeria (SE Spain) are explored in a case study. Our results indicate that a farmer’s interaction with nature is functional, but through agroecological practices, a deeper understanding of the ecosystems in which greenhouse landscapes are embedded may be gained. As they become more connected to nature and benefit from ecosystem services, they can transition to more sustainable agricultural systems.