Search Results (3)

Currently, pJP4 is one of the best-known plasmids for the biodegradation of xenobiotics that mediate the degradation of 2,4-dichlorophenoxyacetic acid (2,4-D), which is associated with serious health and environmental risks. Although the sequencing and proposed theory of pJP4 formation occurred almost 20 years ago (2004), pJP4 is still the model object of many studies focused on the biodegradation of 2,4-D. The uniqueness of this plasmid is due to the presence of two evolutionarily distinct gene clusters, tfd_I and tfd_II, controlling the degradation of 2,4-D. Recent advances in plasmid biology, especially those concerning the characterization of new IncP-1 plasmids and the systematization of tfd gene cluster findings, serve as a basis for proposing new insights into the formation of the clusters’ architecture of the canonical plasmid, pJP4, and their distribution among other plasmids. In the present work, a comparative genomic and phylogenetic in silico study of plasmids with tfd_I and tfd_II clusters was carried out. The possible initial distribution patterns of tfd_I clusters among plasmids of different incompatibility groups (non-IncP-1) and tfd_II clusters among IncP-1 plasmids using the IS1071-based composite transposon were revealed. A new theory on the formation of the architecture of the tfd_I and tfd_II clusters of pJP4 through sequential internal rearrangements, recombination, and ISJP4 insertion, is proposed. In addition, small gene clusters resulting from internal rearrangements of pJP4 (tfd_IISA and ORF31/32) served as fingerprints for exploring the distribution of tfd_I and tfd_II clusters. The revealed patterns and formulated theory extend the frontiers of plasmid biology and will be beneficial for understanding the role of plasmids in bacterial adaptation to xenobiotic-contaminated environments. Full article

Solar-induced chlorophyll fluorescence (SIF) serves as a proxy indicator for vegetation photosynthesis and can directly reflect the growth status of vegetation. Using SIF for drought monitoring offers greater potential compared to traditional vegetation indices. This study aims to develop and validate a novel approach, the improved Temperature Fluorescence Dryness Index (iTFDI), for more accurate drought monitoring in Henan Province, China. However, the low spatial resolution, data dispersion, and short temporal sequence of SIF data hinder its direct application in drought studies. To overcome these challenges, this study constructs a random forest SIF downscaling model based on the TROPOspheric Monitoring Instrument SIF (TROPOSIF) and the Moderate-resolution Imaging Spectroradiometer (MODIS) data. Assuming an unchanging spatial scale relationship, an improved SIF (iSIF) product with a temporal resolution of 500 m over the period March to September, 2010–2022 was obtained for Henan Province. Subsequently, using the retrieved iSIF and the surface temperature difference data, the iTFDI was proposed, based on the assumption that under the same vegetation cover conditions, lower soil moisture and a greater diurnal temperature range of the surface indicate more severe drought. Results showed that: (1) The accuracy of the TROPOSIF downscaling model achieved coefficient of determination (R²), mean absolute error (MAE), and root mean square error (RMSE) values of 0.847, 0.073 mW m⁻² nm⁻¹ sr⁻¹, and 0.096 mW m⁻² nm⁻¹ sr⁻¹, respectively. (2) The 2022 iTFDI drought monitoring results indicated favorable soil moisture in Henan Province during March, April, July, and August, while extensive droughts occurred in May, June, and September, accounting for 70.27%, 71.49%, and 43.61%, respectively. The monitored results were consistent with the regional water conditions measured at ground stations. (3) The correlation between the Standardized Precipitation Evapotranspiration Index (SPEI) and iTFDI at five stations was significantly stronger than the correlation with the Temperature Vegetation Dryness Index (TVDI), with the values −0.631, −0.565, −0.612, −0.653, and −0.453, respectively. (4) The annual Sen’s slope and Mann–Kendall significance test revealed a significant decreasing trend in drought severity in the southern and western regions of Henan Province (6.74% of the total area), while the eastern region showed a significant increasing trend (4.69% of the total area). These results demonstrate that the iTFDI offers a significant advantage over traditional indices, providing a more accurate reflection of regional drought conditions. This enhances the ability to identify drought trends and supports the development of targeted drought management strategies. In conclusion, the iTFDI constructed using the downscaled iSIF data and surface temperature differential data shows great potential for drought monitoring. Full article

The tfd (tfd_I and tfd_II) are gene clusters originally discovered in plasmid pJP4 which are involved in the bacterial degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) via the ortho-cleavage pathway of chlorinated catechols. They share this activity, with respect to substituted catechols, with clusters tcb and clc. Although great effort has been devoted over nearly forty years to exploring the structural diversity of these clusters, their evolution has been poorly resolved to date, and their classification is clearly obsolete. Employing comparative genomic and phylogenetic approaches has revealed that all tfd clusters can be classified as one of four different types. The following four-type classification and new nomenclature are proposed: tfd_I, tfd_II, tfd_III and tfd_IV(A,B,C). Horizontal gene transfer between Burkholderiales and Sphingomonadales provides phenomenal linkage between tfd_I, tfd_II, tfd_III and tfd_IV type clusters and their mosaic nature. It is hypothesized that the evolution of tfd gene clusters proceeded within first (tcb, clc and tfd_I), second (tfd_II and tfd_III) and third (tfd_IV(A,B,C)) evolutionary lineages, in each of which, the genes were clustered in specific combinations. Their clustering is discussed through the prism of hot spots and driving forces of various models, theories, and hypotheses of cluster and operon formation. Two hypotheses about series of gene deletions and displacements are also proposed to explain the structural variations across members of clusters tfd_II and tfd_III, respectively. Taking everything into account, these findings reconstruct the phylogeny of tfd clusters, have delineated their evolutionary trajectories, and allow the contribution of various evolutionary processes to be assessed. Full article