Search Results (43)

The genus Xanthomonas (family Xanthomonadaceae) comprises 39 validly published species and is associated with a broad host range, infecting hundreds of monocot and dicot plants worldwide. While many Xanthomonas species are notorious for causing leaf spot and blight diseases in major agricultural crops, less attention has been given to their impact on ornamental plants. In Hawaii and other key production regions, xanthomonads have posed persistent threats to popular ornamentals in the Araceae and Araliaceae families. This review synthesizes the evolving phylogenetic and taxonomic framework of Xanthomonas strains isolated from Araceae and Araliaceae, highlighting recent advances enabled by multilocus sequence analysis and whole genome sequencing. We discuss the reclassification of key pathovars, unresolved phylogenetic placements, and the challenges of pathovar delineation within these plant families. Additionally, we examine current knowledge of molecular determinants of pathogenicity, including gene clusters involved in exopolysaccharide and lipopolysaccharide biosynthesis, flagellar assembly, cell-wall-degrading enzymes, and secretion systems (types II, III, and VI). Comparative genomics and functional studies reveal that significant gaps remain in our understanding of the genetic basis of host adaptation and virulence in these xanthomonads. Addressing these knowledge gaps will be crucial for developing effective diagnostics and management strategies for bacterial diseases in ornamental crops. Full article

Soil carbon dynamics and microbial communities are critical to soil health. However, the specific effects of mulching on soil microbial community and carbon dynamics in semi-arid rainfed regions remain insufficiently understood. This study aims to identify optimal mulching practices that promote soil carbon sequestration and enhance soil microbial functionality. Mulching treatments were applied in furrows before maize sowing, including black plastic film (TB), white plastic film (TW), straw mulching without sowing (TC), and straw mulching with sowing (TG), and were compared with flat sowing without mulching (TN). Results revealed that TG treatment promoted soil carbon dynamics by increasing total carbon (9%), organic carbon (19%), microbial biomass carbon (100%), easily oxidized carbon (10%), particulate-associated carbon (77%), carbon stability index (7%), active carbon fraction (45%), dissolved carbon proportion (30%), and microbial quotient (34%) compared to TN. A higher abundance and composition of bacterial communities were observed compared to fungal communities. The highest bacterial abundance of Kaistobacter, iii1_15, Sinobacteraceae, and Xanthomonadaceae, and fungal abundance of unspecified fungi, Laiosphaeriaceae, and Sordariomycetes, with the dominant aerobic respiration metabolic pathway involved in organic matter decomposition, were observed in TG and TC. The results indicated that TG treatment most effectively promoted carbon fractions and microbial activity that could strengthen soil health. Full article

Kazakhstan’s rich biodiversity includes diverse apple populations, notably the wild apple tree (Malus sieversii) prized for traits like disease resistance and adaptability, potentially aiding breeding programs. Analyzing their microbiomes offers insights into bacterial diversity and how it influences apple tree development, making it a reliable method for understanding ecological interactions. In this research, 334 apple tree samples were collected from different mountain ranges in southeastern Kazakhstan. An analysis using nanopore-based 16S rRNA sequencing showed a distinct similarity in the microbiome compositions of samples from the Zhongar and Ile Alatau mountain ranges, with a predominance of Pseudomonadaceae, Enterobacteriaceae, and Microbacteriaceae. In contrast, samples from Ketmen ridge showed a higher prevalence of Enterobacteriaceae. Alongside the less represented Pseudomonadaceae family, in the Ketmen ridge region, bacteria of the Xanthomonadaceae, Alcaligenaceae, and Brucellaceae families were also present. Across all regions, beneficial plant-associated bacteria were identified, such as Pseudomonas veronii, Stenotrophomonas geniculata, and Kocuria rhizophila, potentially enhancing plant resilience. However, opportunistic phytopathogens were also detected, including Pseudomonas viridiflava and Serratia marcescens, particularly in the Ile Alatau region. These findings highlight the complex microbial interactions in M. sieversii, thus offering key insights into host—microbe relationships that can inform apple breeding and ecological preservation efforts. Full article

Soil pH critically regulates microbial community structure and activity, thereby influencing carbon transformation processes in terrestrial ecosystems. However, the mechanisms underlying pH-mediated shifts in microbial metabolic functions and cellulose-degrading functional genes remain poorly understood. This study investigated the responses of bacterial communities, metabolic profiles, and the abundance of cellobiohydrolase I (cbhI) and glycoside hydrolase family 48 (GH48) genes to varying pH levels in fluvo-aquic and red soils. High-throughput sequencing, PICRUSt-based metabolic prediction, and quantitative PCR were employed to analyze microbial composition, functional traits, and gene dynamics. Network analysis clarified linkages between functional genes, pathways, and taxa. The results revealed that elevated pH significantly increased CO₂ emissions and dissolved organic carbon (DOC) content in both soils. Dominant taxa, including Alphaproteobacteria, Bacteroidetes, Xanthomonadaceae, and Mycoplasma, exhibited pH-dependent enrichment. Metabolic predictions indicated that pH positively influenced genes linked to biodegradation and xenobiotic metabolism in fluvo-aquic soil but suppressed energy-metabolism-related genes. Contrastingly, in red soil, cbhI and GH48 gene abundance declined with rising pH, suggesting that acidic conditions favor cellulolytic activity. Network analysis identified strong positive correlations between CO₂ emissions and Caulobacteraceae, while cbhI and GH48 genes were closely associated with taxa such as Xanthomonadaceae, Comamonadaceae, and Micromonosporaceae, which drive organic matter decomposition. These findings underscore pH as a pivotal regulator of microbial community structure and functional gene expression, with soil-specific responses highlighting the need for tailored strategies to optimize carbon cycling and sequestration in agricultural ecosystems. Full article

Bacterial canker of kiwifruit is the most destructive bacterial disease caused by Pseudomonas syringae pv. actinidiae. Bacteriophages are regarded as promising biocontrol agents against kiwifruit bacterial pathogens due to their exceptional host specificity and environmentally friendly nature. However, the underlying mechanism of phages in the control of kiwifruit bacterial canker disease remains elusive. In this study, the field trial results showed that phage cocktail could significantly reduce the incidence of bacterial canker in kiwifruit. The high throughput sequencing results showed that the phage cocktail regulated the impact of pathogen invasion on branch endophytic communities, adjusted the diversity of the bacterial community structure, regulated the composition of rare taxa and abundant taxa, and increased the proportion of deterministic processes in community assembly processes. The phage cocktail significantly reduced the relative abundance of Pseudomonadaceae, Pectobacteriaceae, and Yersiniacea. Furthermore, the application of the phage cocktail resulted in an increase in the relative abundance of Beijerinckiaceae, Sphingomonadaceae, and Xanthomonadaceae, most of which are abundant taxa of the corresponding microbial communities. Additionally, the composition of rare taxa was also altered under the influence of phages. These findings offer perspectives on the phage-mediated biocontrol of kiwifruit bacterial canker and provide practical backing for the implementation of phage cocktails in sustainable agriculture. Full article

The white poplar (Populus alba) is a dioecious woody plant with significant potential for the phytoremediation of soils. To realize this potential, it is necessary to utilize growth-promoting microorganisms. One potential source of such beneficial microorganisms is the rhizosphere community of wild-growing trees. However, the structure, dynamics, and metabolism of the rhizosphere community of wild-growing white poplar remain poorly understood. To ascertain seasonal dynamics, species diversity, and metabolic potential, we sequenced 16S rRNA genes in metagenomes derived from 165 soil samples collected in spring and autumn from the root surfaces of 102 trees situated in disparate geographical locations. The three most prevalent phyla across all samples are Proteobacteria, Actinobacteriota, and Acidobacteriota. At the order level, the most prevalent orders are Sphingomonadales and Rhizobiales. Accordingly, the families Sphingomonadaceae and Rhizobiaceae were identified as dominant. The rhizospheric microbiome exhibited substantial inter-seasonal variation. Six families, including Caulobacteraceae, Xanthomonadaceae, Chitinophagaceae, Chthoniobacteraceae, Sphingomonadaceae, and Rhizobiaceae, exhibited alterations (spring-to-autumn) across all geographical locations under study. Members of the Rhizobiaceae family, which includes nitrogen-fixing bacteria, can provide poplar with plant-available forms of nitrogen such as nitrate and ammonium. The rhizosphere microbiome may facilitate the conversion of inorganic sulfur into sulfur-containing amino acids, cysteine and methionine, that are bioavailable to plants. Furthermore, the rhizosphere microbiome is capable of synthesizing amino acids, organic acids (including Krebs cycle acids), and some lipids and sugars. Consequently, the rhizosphere community can stimulate poplar growth by providing it with readily available forms of nitrogen and sulfur, as well as building blocks for the synthesis of proteins, nucleic acids, and other macromolecules. Many of these pathways, including nitrogen fixation, were subjected to seasonal changes. Full article

Although organic amendment has been widely accepted to be capable of facilitating soil agglomeration in coastal salt-affected soils, quantitative characterization with respect to how abiotic and biotic components drive the formation and stabilization of soil aggregates remains largely unexplored and poorly understood. In the current study, wet-sieving, Miseq sequencing, etc., were employed to study the impacts of different application amounts of sewage sludge on soil aggregates, physicochemical properties, enzyme activities, and microbial core microbiomes in coastal saline soils. The results indicated that sewage sludge was conducive to soil agglomeration, abiotic constraint alleviation, microbial activity enhancement, and bacterial and fungal community stabilization and functionalization. The results derived from variation partitioning analysis and the structural equation model showed that elevated soil organic carbon and mitigated salinization were dominant abiotic factors that directly drove the stabilization and functionalization of bacterial and fungal microbiomes. In addition, bacterial families (e.g., Xanthomonadaceae, Rhodospirillaceae, and Micrococcaceae) and fungal genera (e.g., Trichoderma, Cephaliophora, Mortierella, and Penicillium) were potential functional microbial populations related to soil agglomeration in organic amended coastal salt-affected soils. Together, these abiotic and biotic agents jointly drove soil agglomeration and totally explained 87% of the variations in soil aggregates. Collectively, this study highlighted the approach and effectiveness of the impacts of organic amendment on soil agglomeration in coastal salt-affected land based on qualitative and quantitative analysis, which would enhance our knowledge with respect to coastal salt-affected soil quality indication and development. Full article

Morchella mushroom is a nutritionally rich and rare edible fungus. The traditional cultivation model, which relies on expanding the cultivation area to meet market demand, is no longer sufficient to address the rapidly growing market demand. Enhancing the yield and quality of Morchella without increasing the cultivation area is an intractable challenge in the development of the Morchella mushroom industry. Against this backdrop, this study investigates the effects of different amounts of wood ash (WA) application on the yield and quality of Morchella, and conducts an in-depth analysis in conjunction with soil physicochemical properties and microbial communities. The results indicate that the application of WA improves both the yield and quality of Morchella, with the highest yield increase observed in the WA2 treatment (4000 kg/hm²), which showed a 118.36% increase compared to the control group (CK). The application of WA also modified the physicochemical properties of the soil, significantly improving the integrated fertility index of the soil (IFI, p < 0.05). The soil microbial community structure was altered by the addition of WA. Redundancy analysis (RDA) revealed that pH and total potassium (TK) were the main environmental factors influencing the bacterial community, while pH, TK, and total nitrogen (TN) were the main factors influencing the fungal community structure. In addition, bacterial community diversity tended to increase with higher WA application rates, whereas fungal community diversity generally showed a decreasing trend. Furthermore, the relative abundance of beneficial microbial communities, such as Acidobacteriota, which promote the growth of Morchella, increased with higher WA application, while the relative abundance of detrimental microbial communities, such as Xanthomonadaceae, decreased. Partial least squares path model (PLS-PM) analysis of external factors affecting Morchella yield and quality indicated that WA application can alter soil physicochemical properties and soil microbial communities, thereby improving Morchella yield and quality. Among these factors, soil fertility was identified as the most important determinant of Morchella yield and quality. Full article

Animals form functional units with their microbial communities, termed metaorganisms. Despite extensive research on some model animals, microbial diversity in many species remains unexplored. Here, we describe the taxonomic profile of the microbes from the outer gut mucus layer from the Northeast Arctic cod using a shotgun DNA sequencing approach. We focused on the mucus to determine if its microbial composition differs from that of the fecal microbiota, which could reveal unique microbial interactions and functions. Metagenomes from six individuals were analyzed, revealing three different taxonomic profiles: Type I is dominated in numbers by Pseudomonadaceae (44%) and Xanthomonadaceae (13%), Type II by Vibrionaceae (65%), and Type III by Enterobacteriaceae (76%). This stands in sharp contrast to the bacterial diversity of the transient gut content (i.e., feces). Additionally, binning of assembled reads followed by phylogenomic analyses place a high-completeness bin of Type I within the Pseudomonas fluorescens group, Type II within the Photobacterium phosphoreum clade, and Type III within the Escherichia/Shigella group. In conclusion, we describe the adherent bacterial diversity in the Northeast Arctic cod’s intestine using shotgun sequencing, revealing different taxonomic profiles compared to the more homogenous transient microbiota. This suggests that the intestine contains two separate and distinct microbial populations. Full article

The formation of mineral-protected organic carbon (MPOC) is a vital process for soil organic carbon (SOC) accumulation and stabilization, influenced by factors such as exogenous carbon (C) input and soil microorganisms. However, the dynamics of MPOC and soil microorganisms following exogenous C input, and the key microorganisms driving MPOC formation, remain poorly understood. To address this, we conducted exogenous C addition culture experiments to investigate changes in MPOC and soil microorganisms and identify the primary microorganisms influencing MPOC formation. We observed that the MPOC content in treated soils increased over time, ranging from 0.43 to 2.06 g kg⁻¹. MPOC showed a significant positive correlation with soil bacterial diversity and a significant negative correlation with fungal diversity. Soil samples contained 248 bacterial families and 189 fungal genera, with Oxalobacteraceae (7.42%) and unclassified_k__Fungi (24.82%) being the most abundant, respectively. Using FAPROTAX and FunGuild ecological function prediction methods, we analyzed soil bacteria and fungi functional profiles and abundances. We identified the main bacterial families influencing MPOC formation as Microbacteriaceae, Mycobacteriaceae, Pseudomonadaceae, Streptomycetaceae, and Xanthomonadaceae. The primary fungal genera were Cylindrocarpon, Leohumicola, Metarhizium, Neobulgaria, Neopestalotiopsis, Olpidium, and Tetracladium. These findings provide theoretical support for understanding microbial regulation mechanisms in soil C sequestration and emission reduction. Full article

This study investigated the phenology and population dynamics of potential insect vectors of Xylella fastidiosa Wells et al. and other Auchenorrhyncha species in olive and citrus groves of Chania province, Crete, Greece. Although X. fastidiosa has not been reported in Greece, its introduction could cause serious diseases in many crops, including olives and citrus. Olive groves of Olea europaea L. ‘Koroneiki’ were sampled systematically using sweep net and Malaise traps over 24 months. One citrus grove was sampled for one year using a Malaise trap. Sweep net samples were taken from the herbaceous cover, tree canopy, and field borders of olive groves. Auchenorrhyncha were more abundant on the herbaceous cover compared to the canopy and field margins. Aphrophoridae species were mostly found on the herbaceous cover and in low numbers during fall (October–December) and spring (April–May). Cicadellidae species, such as Euscelis spp., were frequently found on the herbaceous cover of both olive and citrus groves. One Aphrophoridae and several Cicadellidae species were recorded in the citrus grove. Altitude was found to influence the population abundance of some Auchenorrhyncha species in olive groves. These results provide information for effective integrated management of insect vectors and their vector-borne pathogens. Full article

The objectives of the current study were to evaluate the fluctuations in production performance, rumen fermentation, and microbial community in lactating dairy cows fed a high-grain diet (HG). In this study, 16 healthy Holstein lactating dairy cattle with similar milk yields of 16.80 ± 4.30 kg/d, days in milk 171.44 ± 23.25 days, and parity 2.2 ± 1.5 times were selected and randomly allocated into two groups. One group was fed a low-grain diet (LG; 40% concentrate, DM basis; n = 8), and the other group was fed a high-grain diet (HG; 60% concentrate, DM basis; n = 8). The experiment lasted 6 weeks, including 1 week for adaptation. The experimental results showed that the milk fat content in the milk of lactating cows in the HG group was significantly reduced (p < 0.05), and the milk urea nitrogen (MUN) content showed an increasing trend (0.05 < p < 0.10) compared with the LG group. Compared with the LG group, rumen fluid pH was significantly decreased after feeding a high-grain diet, and contents of total volatile fatty acids (TVFA), acetate, propionate, and butyrate were significantly increased (p < 0.05). The acetate/propionate significantly decreased (p < 0.05). HG group significantly increased the abundance of Prevotella and Bacteroides in rumen fluid while significantly reducing the abundance of Methanobrevibacter and Lachnospiraceae ND3007_group (p < 0.05). Microorganisms with LDA scores > 2 were defined as unique, with the bacterial genus Anaerorhabdus_furcosa_group identified as a biomarker for the LG group, and the unique bacterial genus in the HG group were Prevotella, Stenotrophomonas, and Xanthomonadaceae. The prediction results of microbial function showed that a total of 18 KEGG differential pathways were generated between the two treatment groups, mainly manifested in metabolic pathways, signal transduction, and the immune system. In conclusion, the HG group promoted rumen fermentation by altering the microbial composition of lactating cows. Our findings provide a theoretical basis for the rational use of high-grain diets to achieve high yields in intensive dairy farming. Full article

The application of beneficial microbial consortium can effectively improve plant disease resistance and its growth. Various fungi were compounded with Bacillus velezensis LJ02 and applied to watermelon plants in this paper. The results showed that the microbial consortium T2 (compounded Bacillus velezensis LJ02 with Aspergillus aculeatus 9) can effectively control gummy stem blight and powdery mildew in watermelon, while the control effect reached 83.56% and 70.93%, respectively (p < 0.05). Compound treatment improved the diversity and richness of the rhizosphere microbial community structure, and the relative abundance of Caulobacterales and Xanthomonadaceae significantly increased after applying T2 to the soil. Meanwhile, the internode length was significantly decreased 28% (p < 0.05), and the maximum leaf length increased 10.33% (p < 0.05). In addition, the microbial consortium delays the maturity of watermelon vegetables. By studying the effects of microbial consortium on watermelon seedlings, our study provides a theoretical basis for the popularization and application of the compound inoculant. Full article

The genus Xanthomonas primarily comprises phytopathogenic species. By carrying out deep phylo-taxonogenomics, we recently reported that the genera Xylella, Stenotrophomonas, and Pseudoxanthomonas are misclassified and belong to the genus Xanthomonas. Considering the importance of Xanthomonas/Xylella as plant pathogens and to further determine the taxonomic and phylogenetic breadth of this genus, we extended our earlier study by including all the reported genera and families in the order. This investigation revealed that at least four more genera belong to the genus Xanthomonas, with a notable case being Lysobacter, after which the family and order are named. Similarly, our investigation also allowed us to reveal the expanded taxonomic breadth of the related genus Rhodanobacter. This finding of a major related genus that lacks plant pathogenic species will allow for taxonomy-based comparative studies. The phylo-taxonogenomic revelations were further supported by complete 16S rRNA-based sequence boundaries proposed for genus delineation. Accordingly, we propose a taxonomic revision of these major and closely related genera along with their constituent families within the order Lysobacteraceae (Xanthomonadaceae). The identification of a major related genus lacking plant pathogenic species will be important in investigating the origin and success of pathogenic species/lineages in the genus Xanthomonas. Full article

Gut dysbiosis presents in many digestive diseases. The aim of this study is to investigate the composition of the gut microbiota and its metabolic activity in patients with diarrhea-predominant irritable bowel syndrome combined with functional dyspepsia (I + D). This study included 60 patients with I + D and 20 healthy controls. Gut microbiota composition was studied using 16S rRNA gene sequencing. The short-chain fatty acids (SCFAs) spectrum was determined via gas–liquid chromatography. Patients with I + D had an increase in the abundance of Holdemanella, Erysipelotrichaceae, Erysipelotrichales, Prevotellaceae, Agathobacter, Slackia, Lactococcus, Pseudomonadaceae, Stenotrophomonas, Xanthomonadaceae, Rhizobiaceae, Erysipelatoclostridiaceae, Lachnospiraceae, and other taxa in addition to a decrease in the abundance of Frisingicoccus, Ralstonia, Burkholderiaceae, Hungatella, Eisenbergiella, Parabacteroides, Peptostreptococcaceae, Merdibacter, Bilophila, Rikenellaceae, Tannerellaceae, Bacteroidaceae, and Flavonifractor in comparison to controls. Patients with I + D showed significantly higher total SCFA content in feces; increased absolute content of acetic acid, propionic acid, butyric acid, and isoacids; and a significant negative shift in the anaerobic index. The relative levels of the main SCFAs and isoacids in the patient group did not differ significantly from those in the control group. The fecal acetate and isoacid levels correlated with the severity of diarrhea. The fecal butyrate level correlated with the severity of flatulence. Full article