First historical genome of a crop bacterial pathogen from herbarium specimen: Insights into citrus canker emergence

Over the past decade, ancient genomics has been used in the study of various pathogens. In this context, herbarium specimens provide a precious source of dated and preserved DNA material, enabling a better understanding of plant disease emergences and pathogen evolutionary history. We report here the first historical genome of a crop bacterial pathogen, Xanthomonas citri pv. citri (Xci), obtained from an infected herbarium specimen dating back to 1937. Comparing the 1937 genome within a large set of modern genomes, we reconstructed their phylogenetic relationships and estimated evolutionary parameters using Bayesian tip-calibration inferences. The arrival of Xci in the South West Indian Ocean islands was dated to the 19th century, probably linked to human migrations following slavery abolishment. We also assessed the metagenomic community of the herbarium specimen, showed its authenticity using DNA damage patterns, and investigated its genomic features including functional SNPs and gene content, with a focus on virulence factors.

Development and comparative validation of genomic-driven PCR-based assays to detect Xanthomonas citri pv. citri in citrus plants

Background

Asiatic Citrus Canker, caused by Xanthomonas citri pv. citri, severely impacts citrus production worldwide and hampers international trade. Considerable regulatory procedures have been implemented to prevent the introduction and establishment of X. citri pv. citri into areas where it is not present. The effectiveness of this surveillance largely relies on the availability of specific and sensitive detection protocols. Although several PCR- or real-time PCR-based methods are available, most of them showed analytical specificity issues. Therefore, we developed new conventional and real-time quantitative PCR assays, which target a region identified by comparative genomic analyses, and compared them to existing protocols.

Results

Our assays target the X. citri pv. citri XAC1051 gene that encodes for a putative transmembrane protein. The real-time PCR assay includes an internal plant control (5.8S rDNA) for validating the assay in the absence of target amplification. A receiver-operating characteristic approach was used in order to determine a reliable cycle cut-off for providing accurate qualitative results. Repeatability, reproducibility and transferability between real-time devices were demonstrated for this duplex qPCR assay (XAC1051-2qPCR). When challenged with an extensive collection of target and non-target strains, both assays displayed a high analytical sensitivity and specificity performance: LOD_95% = 754 CFU ml^− 1 (15 cells per reaction), 100% inclusivity, 97.2% exclusivity for XAC1051-2qPCR; LOD_95% = 5234 CFU ml^− 1 (105 cells per reaction), 100% exclusivity and inclusivity for the conventional PCR. Both assays can detect the target from naturally infected citrus fruit. Interestingly, XAC1051-2qPCR detected X. citri pv. citri from herbarium citrus samples. The new PCR-based assays displayed enhanced analytical sensitivity and specificity when compared with previously published PCR and real-time qPCR assays.

Conclusions

We developed new valuable detection assays useful for routine diagnostics and surveillance of X. citri pv. citri in citrus material. Their reliability was evidenced through numerous trials on a wide range of bacterial strains and plant samples. Successful detection of the pathogen was achieved from both artificially and naturally infected plants, as well as from citrus herbarium samples, suggesting that these assays will have positive impact both for future applied and academic research on this bacterium.

Estimating the global conservation status of more than 15,000 Amazonian tree species

Estimates of extinction risk for Amazonian plant and animal species are rare and not often incorporated into land-use policy and conservation planning. We overlay spatial distribution models with historical and projected deforestation to show that at least 36% and up to 57% of all Amazonian tree species are likely to qualify as globally threatened under International Union for Conservation of Nature (IUCN) Red List criteria. If confirmed, these results would increase the number of threatened plant species on Earth by 22%. We show that the trends observed in Amazonia apply to trees throughout the tropics, and we predict that most of the world's >40,000 tropical tree species now qualify as globally threatened. A gap analysis suggests that existing Amazonian protected areas and indigenous territories will protect viable populations of most threatened species if these areas suffer no further degradation, highlighting the key roles that protected areas, indigenous peoples, and improved governance can play in preventing large-scale extinctions in the tropics in this century.

A New Classification of Ficus Subsection Urostigma (Moraceae) Based on Four Nuclear DNA Markers (ITS, ETS, G3pdh, and ncpGS), Morphology and Leaf Anatomy

Ficus subsection Urostigma as currently circumscribed contains 27 species, distributed in Africa, Asia, Australia and the Pacific, and is of key importance to understand the origin and evolution of Ficus and the fig-wasp mutualism. The species of subsection Urostigma are very variable in morphological characters and exhibit a wide range of often partly overlapping distributions, which makes identification often difficult. The systematic classification within and between this subsection and others is problematic, e.g., it is still unclear where to classify F. amplissima and F. rumphii. To clarify the circumscription of subsection Urostigma, a phylogenetic reconstruction based on four nuclear DNA markers (ITS, ETS, G3pdh, and ncpGS) combined with morphology and leaf anatomy is conducted. The phylogenetic tree based on the combined datasets shows that F. madagascariensis, a Madagascan species, is sister to the remainder of subsect. Urostigma. Ficus amplissima and F. rumphii, formerly constituting sect. Leucogyne, appear to be imbedded in subsect. Conosycea. The result of the phylogenetic analysis necessitates nomenclatural adjustments. A new classification of Ficus subsection Urostigma is presented along with the morphological and leaf anatomical apomorphies typical for the clades. Two new species are described ─ one in subsect. Urostigma, the other in Conosycea. One variety is raised to species level.

Hyperdominance in the Amazonian tree flora

The vast extent of the Amazon Basin has historically restricted the study of its tree communities to the local and regional scales. Here, we provide empirical data on the commonness, rarity, and richness of lowland tree species across the entire Amazon Basin and Guiana Shield (Amazonia), collected in 1170 tree plots in all major forest types. Extrapolations suggest that Amazonia harbors roughly 16,000 tree species, of which just 227 (1.4%) account for half of all trees. Most of these are habitat specialists and only dominant in one or two regions of the basin. We discuss some implications of the finding that a small group of species--less diverse than the North American tree flora--accounts for half of the world's most diverse tree community.

Demographic Threats to the Sustainability of Brazil Nut Exploitation

A comparative analysis of 23 populations of the Brazil nut tree (Bertholletia excelsa) across the Brazilian, Peruvian, and Bolivian Amazon shows that the history and intensity of Brazil nut exploitation are major determinants of population size structure. Populations subjected to persistent levels of harvest lack juvenile trees less than 60 centimeters in diameter at breast height; only populations with a history of either light or recent exploitation contain large numbers of juvenile trees. A harvesting model confirms that intensive exploitation levels over the past century are such that juvenile recruitment is insufficient to maintain populations over the long term. Without management, intensively harvested populations will succumb to a process of senescence and demographic collapse, threatening this cornerstone of the Amazonian extractive economy.

The soil seed bank during Atlantic Forest regeneration in Southeast Brazil

A survey was conducted to determine the density and species composition of viable seeds buried in four stands of a tropical montane forest at Parque Estadual Intervales, Brazil. The objective was to understand: (1) how numbers and composition of the soil seed bank change as the forest regrows, and (2) how such changes affect the species available for regeneration if forests of different ages are cut down. In each forest stand (5, 18, 27-yr-old and a mature forest), 57 soil samples were collected (0-2.5 and 2.5-5 cm deep). Viable seed density of herbaceous species ranged between 11,003 seeds. m-2 (5-yr-old vegetation) and 482 (mature forest), and between 25 (5-yr-old vegetation) and 389 seeds. m-2 (mature forest) for woody plant species in the 0-5 cm soil layer, suggesting a decrease in seed stocks in the course of forest regeneration. Seeds buried in the 0-2.5 cm soil layer represented between 56.9% and 67.4% of all viable seeds. Most of the viable seeds belonged to weeds of Asteraceae, Poaceae, Malvaceae and Solanaceae. The results provide evidence that, in forests of different ages, the soil does not store seeds of the same key ecological groups involved in the regeneration of Atlantic forest. Allochthonous seeds from remaining patches of forest, as well as their vertebrate dispersers, are needed for forest regeneration since the soil seed bank does not store large seeds of shade-tolerant species.