Xylella fastidiosa is a notorious plant pathogenic bacterium that represents a threat to crops worldwide. Its subspecies, Xylella fastidiosa subsp. fastidiosa is the causative agent of Pierce's disease of grapevines. Pierce's disease has presented a serious challenge for the grapevine industry in the United States and turned into an epidemic in Southern California due to the invasion of the insect vector Homalodisca vitripennis. In an attempt to minimize the effects of Xylella fastidiosa subsp. fastidiosa in vineyards, various studies have been developing and testing strategies to prevent the occurrence of Pierce's disease, i.e. prophylactic strategies. Research has also been undertaken to investigate therapeutic strategies to cure vines infected by Xylella fastidiosa subsp. fastidiosa. This report explicitly reviews all the strategies published to date and specifies their current status. Furthermore, an epidemiological model of Xylella fastidiosa subsp. fastidiosa is proposed and key parameters for the spread of Pierce's disease deciphered in a sensitivity analysis of all model parameters. Based on these results, it is concluded that future studies should prioritize therapeutic strategies, while investments should only be made in prophylactic strategies that have demonstrated promising results in vineyards.
Abstract As one of the only described degraders of the recalcitrant metabolite 2,6-dichlorobenzamide (BAM) of the pesticide dichlobenil, Aminobacter sp. MSH1 has been intensively studied for its characteristics with regards to physiology and its use in bioremediation. Two plasmid sequences from strain MSH1 have previously been published, while the remaining genome sequence has been left uninvestigated. We here present the complete genome sequence of this important strain, which consists of a chromosome, two megaplasmids and five smaller plasmids. Intriguingly, the plasmid copy numbers are mostly below one per bacterial chromosome, indicating that plasmids in strain MSH1 are under very unstable conservation. The results of this report improve our understanding of the genomic dynamics of Aminobacter sp. MSH1.
Soil microbiomes, as a primary reservoir for plant colonizing fungi and bacteria, play a major role in determining plant productivity and preventing invasion by pathogenic microorganisms. The use of 16S rRNA and ITS high-throughput amplicon sequencing for analysis of complex microbial communities have increased dramatically in recent years, establishing links between wine specificity and, environmental and viticultural factors, which are framed into the elusive terroir concept. Given the diverse and complex role these factors play on microbial soil structuring of agricultural crops, the main aim of this study is to evaluate how external factors, such as vintage, vineyard location, cultivar and soil characteristics, may affect the diversity of the microbial communities present. Additionally, we aim to compare the influence these factors have on the structuring of bacterial and fungal populations associated with Malbec grapevine rhizosphere with that of the more widespread Cabernet Sauvignon grapevine cultivar. Samples were taken from Malbec and Cabernet Sauvignon cultivars from two different vineyards in the San Juan Province of Argentina. Total DNA extracts from the rhizosphere soil samples were sequenced using Illumina’s Miseq technology, targeting the V3-V4 hypervariable 16S rRNA region in prokaryotes and the ITS1 region in yeasts. The major bacterial taxa identified were Proteobacteria , Bacteroidetes and Firmicutes , while the major fungal taxa were Ascomycetes , Basidiomycetes , Mortierellomycetes and a low percentage of Glomeromycetes . Significant differences in microbial community composition were found between vintages and vineyard locations, whose soils showed variances in pH, organic matter, and content of carbon, nitrogen, and absorbable phosphorus.
The Greenland Ice Sheet is a biome primarily driven by microbial activity. Despite the harsh conditions, such as cold temperatures, low nutrient levels, high UV radiation in summer, and long dark winters, various niches can be found on the ice sheet that can support organisms capable of withstanding these challenges. During the summer, eukaryotic glacier ice algae grow in large quantities on the ice surface, accompanied by a community of bacteria, fungi, and viruses. Additionally, cryoconite holes and snow serve as habitats with their own distinct microbial communities. Nevertheless, the microbiome of supraglacial habitats remains poorly studied, leading to a lack of representative genomes from these environments. In this study, we conducted a comprehensive investigation of the supraglacial microbiome using both culturing-dependent and -independent methods. We compared genomes obtained through metagenomic sequencing (133 high-quality metagenome-assembled genomes or MAGs) and whole genome sequencing (73 bacterial isolates) to the metagenome assemblies to determine their abundance within the total environmental DNA. Interestingly, the isolates obtained in this study were not dominant taxa in their respective habitats, unlike the MAGs. Under-investigated extremophiles, such as those inhabiting the Greenland Ice Sheet, may offer an untapped reservoir of undiscovered chemical diversity. We cataloged the biosynthetic potential of these organisms by examining the presence of biosynthetic gene clusters (BGCs) in the obtained genomes. To accomplish this, we utilized tools like the Antibiotics and Secondary Metabolites Analysis Shell (AntiSMASH) and the Biosynthetic Gene Similarity Clustering and Prospecting Engine (BiG-SCAPE) to mine these genomes and subsequently analyze the resulting predicted BGCs. We identified a total of 849 BGCs, which were organized into 411 gene cluster families (GCFs). Notably, the MAGs and isolate genomes exhibited distinct pools of biosynthetic diversity, with only 5 GCFs shared between the two groups. The cryoconite genomes yielded the most unique GCFs. Furthermore, we found evidence for the capacity of these microbes to produce antimicrobials, carotenoids, and osmoprotectants. However, many of the obtained BGCs could not be matched to similar, previously described BGCs, highlighting the vastness of the undescribed biosynthetic potential present in microbes from the Greenland Ice Sheet.
Cyanobacterial blooms releasing harmful cyanotoxins, such as microcystin (MC) and cylindrosper-mopsin (CYN), are prominent threats to human and animal health. Constructed wetlands (CW) may be a nature-based solution for bioremediation of lake surface water containing cyanotoxins, due to its low-cost requirement of infrastructure and environmentally friendly operation. There is recent evi-dence that microcystin-LR (MC-LR) can efficiently be removed in CW microcosms where CYN deg-radation in CW is unknown. Likewise, the mechanistic background regarding cyanotoxins transfor-mation in CW is not yet elucidated. In the present study, the objective was to compare MC-LR and CYN degradation efficiencies by two similar microbial communities obtained from CW mesocosms, by two different experiments setup: 1) in vitro batch experiment in serum bottles with an introduced CW community, and 2) degradation in CW mesocosms. In experiment 1) MC-LR and CYN were spiked at 100 µg L-1 and in experiment 2) 200 µg L-1 were spiked. The results showed that MC-LR was degraded to ≤1 µg L-1 within seven days in both experiments, however, with a markedly higher degradation rate constant in the CW mesocosms (0.18 day-1 and 0.75 day-1, respectively). No CYN removal was detected in the in vitro incubations, whereas around 50% of the spiked CYN was re-moved in the CW mesocosms. The microbial community responded markedly to the cyanotoxin treatment, with the most prominent increase of bacteria affiliated with Methylophilaceae (order: Methylophilales, phylum: Proteobacteria). The results strongly indicate that CWs can develop an ac-tive microbial community capable of efficient removal of MC-LR and CYN. However, the CW opera-tional conditions need to be optimized to achieve a full CYN degradation. To the best of our knowledge, this study is the first to report the ability of CW mesocosms to degrade CYN.
Abstract Bacteria of Lactobacillus sp. are very useful to humans. However, the biology and genomic diversity of their (bacterio)phage enemies remains understudied. Knowledge on Lactobacillus phage diversity should broaden to develop efficient phage control strategies. To this end, organic waste samples were screened for phages against two wine-related Lactobacillus plantarum strains. Isolates were shotgun sequenced and compared against the phage database and each other by phylogenetics and comparative genomics. The new isolates had only three distant relatives from the database, but displayed a high overall degree of genomic similarity amongst them. The latter allowed for the use of one isolate as a representative to conduct transmission electron microscopy and structural protein sequencing, and to study phage adsorption and growth kinetics. The microscopy and proteomics tests confirmed the observed diversity of the new isolates and supported their classification to the family Siphoviridae and the proposal of the new phage genus “Silenusvirus”.
