First Report of Leaf Spot on Cucumis melo L. Caused by Arcopilus aureus in China.

Cucumis melo L. is an important fruit with widespread consumption and commercial value. However, an undescribed disease affecting Hami melon (Cucumis melo L. var. Luhoutian) plants has consistently emerged in the Qihe region of Dezhou, Shandong Province of China since 2021. The disease can occur in both seedling and mature stages of Hami melon plants, and in severely diseased areas, the incidence rate was seen as 40 to 80%. During the seedling stage, the initial symptom is the appearance of water-soaked spots on the leaves. As the disease progresses, the leaves develop necrotic spots, and severely affected plants may exhibit stem rot and decay. In the mature stage, the disease primarily affects the leaves, causing necrotic spots and chlorosis. Under conditions of high humidity, black mold can be observed in the affected areas. Small pieces of symptomatic leaves from six different infected plants were collected and surface-sterilized with 5% NaClO for 3 min and 75% alcohol for 30 s for pathogen isolation (Wang et al., 2020). After rinsing with sterile water and blotted on sterile filter paper, the tissues were established on potato dextrose agar (PDA) media and incubated at 28℃ for 3-4 days. Pure isolates showed up at PDA were obtained through single-spore isolation. Colonies of all 16 isolates obtained by single-spore isolation had similar morphological characteristics on the PDA medium, the mycelium of the isolate appears dense and yellowish-brown on the PDA medium, and also secretes a brownish-red pigment on PDA. Under the opticalmicroscope, the perithecia from PDA media are subglobose spherical in shape, 80-100 µm in diameter, brownish by reflected light, wholly and densely hairy. Terminal hairs are very dense, greyish by reflected light, olive brown to reddish brown by transmitted light, thick-walled, arcuate, circinate, or spirally coiled at the apex. The ascospores within the perithecia are elliptical or droplet-shaped, initially colorless hyaline but later becoming subhyaline slightly gray, with dimensions of 7-9 µm × 4-5 µm. The morphological characteristics of the isolates were consistent with the description of Arcopilus aureus (Wang et.al. 2016). The internal transcribed spacer (ITS) region and ß-tubulin genes of three randomly selected isolates were PCR amplified and sequenced using primers ITS4/ITS5 and Bt2a/Bt2b. The sequences of ITS and ß-tubulin genes were submitted to NCBI with GenBank Accession No. OR539527 and OR640972, respectively. Based on morphological features and phylogenetic analysis, we concluded that the isolates belonged to A. aureus. Pathogenicity tests were conducted by placing agar plugs-containing fungal mycelia and agar blocks (control) on leaves of Hami melon seedlings (n=12) grown at 28°C with 60% humidity in a greenhouse, the assay was repeated three times. Symptoms appeared on the pathogen-inoculated leaves seven days after inoculation, whereas the control treatment remained symptomless. The pathogens were reisolated from diseased leaves and identified as A. aureus based on morphological, and molecular phylogenetic analysis, while Koch'sostulate was used to confirm its life mode. To the best of our knowledge, this is the first report of leaf spot caused by A. aureus on Cucumis melo L. in China.

Fine-Scale Structuring of Planktonic Vibrio spp. in the Chinese Marginal Seas.

Vibrio is ubiquitous in marine environments with high metabolism flexibility and genome plasticity. Studies have investigated the ecological distribution of Vibrio spp. in several narrow zones, but a broad scale pattern of distribution and community assembly is still lacking. Here, we elucidated the distribution of Vibrio spp. in seawater along the Chinese marginal seas with a high spatial range. Comparison of Vibrio abundance between 3- and 0.2-µm-pore-size membranes showed distinction in preferential lifestyle. Vibrio spp. in the Yellow Sea (YS) was low in abundance and adopted a particle-associated lifestyle, whereas that in the East China Sea (ECS) and South China Sea (SCS) was more abundant and was likely in a temporary free-living state as a strategy to cope with nutrient limitation. Vibrio community compositions were also separated by sampling area, with different dominant groups in YS (Vibrio chagasii and Vibrio harveyi), ECS and SCS (Vibrio japonicus and V. chagasii). The community niche breadth was significantly wider in ECS and SCS than that of YS. Among species, V. chagasii and V. harveyi had the largest niche breadths likely reflecting strong competitive positions. Stochastic processes played important roles in shaping the geographical pattern of the vibrionic community. Environmental selection (e.g., temperature, salinity, and dissolved oxygen) had a much greater impact on the community in surface than in bottom water. The large proportions of unexplained variations (78.9%) imply complex mechanisms in their community assembly. Our study provides insights into the spatial distribution patterns and underlying assembly mechanisms of Vibrio at a broad spatial scale. IMPORTANCE Vibrio spp. may exert large impacts on biogeochemical cycling in coastal habitats, and their ecological importance has drawn increasing attention. Here, we investigated the spatial distribution pattern and community assembly of Vibrio populations along the Chinese marginal seas, spanning a wide spatial scale. Our results showed that the abundances of the Vibrio population increased with decreasing latitude and their preferential lifestyle differed among adjacent coastal areas. The compositions of Vibrio spp. were also separated by geographical location, which was mainly attributable to stochastic processes. Overall, this work contributes to the understanding of the ecological distribution patterns and the community assembly mechanisms of marine vibrios at a high spatial range. The large proportion of unexplained variations indicates the existence of complex mechanisms in the assembly of vibrionic community which should be considered comprehensively in future.

Genomic Analysis Reveals Adaptation of Vibrio campbellii to the Hadal Ocean.

The genus Vibrio is characterized by high metabolic flexibility and genome plasticity and is widely distributed in the ocean from euphotic layers to deep-sea environments. The relationship between genome features and environmental adaptation strategies of Vibrio has been extensively investigated in coastal environments, yet very little is known about their survival strategies in oligotrophic deep-sea. In this study, we compared genomes of five Vibrio campbellii strains isolated from the Mariana and Yap Trenches at different water depths, including two epipelagic strains and three hadopelagic strains, to identify genomic characteristics that facilitate survival in the deep sea. Genome streamlining is found in pelagic strains, such as smaller genome sizes, lower G+C contents, and higher gene densities, which might be caused by long-term residence in an oligotrophic environment. Phylogenetic results showed that these five Vibrio strains are clustered into two clades according to their collection depth. Indeed, hadopelagic isolates harbor more genes involved in amino acid metabolism and transport, cell wall/membrane/envelope biogenesis, and inorganic ion transport and metabolism through comparative genomics analysis. Specific macrolide export gene and more tellurite resistance genes present in hadopelagic strains by the annotation of antibiotic and metal resistance genes. In addition, several genes related to substrate degradation are enriched in hadopelagic strains, such as chitinase genes, neopullulanase genes, and biopolymer transporter genes. In contrast, epipelagic strains are unique in their capacity for assimilatory nitrate reduction. The genomic characteristics investigated here provide insights into how Vibrio adapts to the deep-sea environment through genomic evolution. IMPORTANCE With the development of deep-sea sampling technology, an increasing number of deep-sea Vibrio strains have been isolated, but the adaptation mechanism of these eutrophic Vibrio strains to the deep-sea environment is unclear. Here, our results show that the genome of pelagic Vibrio is streamlined to adapt to a long-term oligotrophic environment. Through a phylogenomic analysis, we find that genomic changes in marine Vibrio campbellii strains are related to water depth. Our data suggest that an increase in genes related to antibiotic resistance, degradation of macromolecular and refractory substrates, and utilization of rare ions is related to the adaptation of V. campbellii strains to adapt to hadal environments, and most of the increased genes were acquired by horizontal gene transfer. These findings may deepen our understanding of adaptation strategies of marine bacteria to the extreme environment in hadal zones.

Spatiotemporal distribution of bacterial dimethylsulfoniopropionate producing and catabolic genes in the Changjiang Estuary.

The osmolyte dimethylsulfoniopropionate (DMSP) is produced in petagram amounts by marine microorganisms. Estuaries provide natural gradients in salinity and nutrients, factors known to regulate DMSP production; yet there have been no molecular studies of DMSP production and cycling across these gradients. Here, we study the abundance, distribution and transcription of key DMSP synthesis (e.g. dsyB and mmtN) and catabolic (e.g. dddP and dmdA) genes along the salinity gradient of the Changjiang Estuary. DMSP levels did not correlate with Chl a across the salinity gradient. In contrast, DMSP concentration, abundance of bacterial DMSP producers and their dsyB and mmtN transcripts were lowest in the freshwater samples and increased abruptly with salinity in the transitional and seawater samples. Metagenomics analysis suggests bacterial DMSP-producers were more abundant than their algal equivalents and were more prominent in summer than winter samples. Bacterial DMSP catabolic genes and their transcripts followed the same trend of being greatly enhanced in transitional and seawater samples with higher DMSP levels than freshwater samples. DMSP cleavage was likely the dominant catabolic pathway, with DMSP lyase genes being ~4.3-fold more abundant than the demethylase gene dmdA. This is an exemplar study for future research on microbial DMSP cycling in estuary environments.

Spatiotemporal dynamics of the total and active Vibrio spp. populations throughout the Changjiang estuary in China.

Vibrio is ubiquitously distributed in marine environments and is the most extensively characterized group within Gammaproteobacteria. Studies have investigated Vibrio spp. worldwide, but mostly focused on pathogenic vibrios and based on cultivation methods. Here, using a combination of molecular and culturing methods, we investigated the dynamics of the total and active Vibrio spp. throughout the Changjiang estuary in China. The total Vibrio abundance was higher in summer (~6.59 × 103 copies ml-1) than in winter (~1.85 × 103 copies ml-1) and increased from freshwater to saltwater (e.g. 8.04 × 101 to 9.39 × 103 copies ml-1 in summer). The ratio of active to total Vibrio (Va/Vt) revealed a high activity of vibrios, with remarkable differences between freshwater and saltwater (p < 0.05). Based on the community compositions of the culturable, total and active Vibrio, Vibrio atlanticus and Vibrio owensii were the dominant and active species in winter and summer, respectively. The distribution of Vibrio was governed by the effects of diverse environmental factors, such as temperature, salinity, pH, dissolved oxygen and SiO3 2-. Our study clearly demonstrates the spatiotemporal dynamics of total and active Vibrio spp. and lays a foundation for fully understanding the ecological roles of marine Vibrio.

Vibrio ouci sp. nov. and Vibrio aquaticus sp. nov., two marine bacteria isolated from the East China Sea.

Two Gram-stain-negative, catalase- and oxidase-positive, facultative anaerobic and rod-shaped motile bacteria, designated strains BEI176T and BEI207T, were isolated from seawater collected in the East China Sea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains BEI176T and BEI207T belonged to the genus Vibrio and were closely related to each other with 98.18 % similarity. The closest phylogenetic relatives of strain BEI176T were Vibrio alginolyticus LMG 4409T (98.85 %) and Vibrio campbellii LMG 11216T (98.81 %), whereas the closest relative of strain BEI207T was Vibrio hepatarius LMG 20362T (98.64 %). The two strains showed growth at different conditions; while strain BEI176T grew at 16-37 °C, pH 5.0-9.5 and 0-7.0 % (w/v) NaCl, the growth of strain BEI207T occurred at 10-37 °C, pH 6.0-9.5 and 1.0-7.0 % (w/v) NaCl. Both strains shared the same major fatty acid components of summed feature 3 (C16 : 1ω7c or C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω6c or C18 : 1ω7c). The DNA G+C contents of the assembled genomic sequences were 44.73 and 45.06 mol% for strains BEI176T and BEI207T, respectively. Average nucleotide identity values between the two strains and their reference species were lower than the threshold for species delineation (95-96 %); in silico DNA-DNA hybridization further showed that the two strains had less than 70 % similarity to their relatives. Therefore, two novel Vibrio species are proposed to accommodate them: Vibrioouci sp. nov. (type strain, BEI176T=MCCC 1K03515T=JCM 32690T= KCTC 62616T) and Vibrioaquaticus sp. nov. (type strain, BEI207T=MCCC 1K03516T=JCM 32691T=KCTC 62617T).

Vibrio sinensis sp. nov. and Vibrio viridaestus sp. nov., two marine bacteria isolated from the East China Sea.

Two Gram-staining-negative, facultatively anaerobic, motile, short clavate and flagellated marine bacteria, designated strains BEI233T and LJC006T, were isolated from the East China Sea. On the basis of the results of 16S rRNA gene sequencing and multilocus sequence analysis, BEI233T and LJC006T should be assigned to the genus Vibrio. The closest phylogenetic relatives of BEI233T are Vibrio scophthalmi LMG 19158T (98.7 % 16S rRNA gene sequence pairwise similarity), Vibrio ichthyoenteri DSM 14397T (98.5 %), Vibrio renipiscarius KCTC 42287T (97.7 %), Vibrio aestuarianus ATCC 35048T (97.3 %) and Vibrio thalassae MD16T (96.5 %), whereas for LJC006T they were Vibrio furnissii CAIM 518T (97.1 %), Vibrio fluvialis LMG 7894T (97.0%), Vibrio tritonius JCM 16456T (96.9 %) and Vibrio xuii LMG 21346T (96.1 %). The growth of BEI233T occurred at 10-37 °C, pH 5.0-8.0 and with 1-7 % (w/v) NaCl, while the growth of LJC006T occurred at 10-37 °C, pH 6.0-9.0, and 0-8 % (w/v) NaCl. The predominant fatty acids (>10 %) were summed feature 3 (C16 : 1ω7c or/and C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω7c or/and C18 : 1ω6c), with different proportions. The DNA G+C contents of BEI233T and LJC006T are 42.41 mol% and 41.88 mol%, respectively. On the basis of the results of polyphasic analysis, BEI233T and LJC006T are considered to represent novel species of the genus Vibrio, for which the names Vibrio sinensis sp. nov. and Vibrio viridaestus sp. nov. are proposed. The type strains are BEI233T (=JCM 32692T=KCTC 62618T) and LJC006T (=JCM 32693T=KCTC 62620T), respectively.

Spatial Heterogeneity of Vibrio spp. in Sediments of Chinese Marginal Seas.

Vibrio spp. are ubiquitous marine bacteria with high metabolism flexibility and genome plasticity. Previous studies have revealed the dynamics of planktonic vibrios in relation to environmental forces, such as temperature and salinity. However, little is known about Vibrio ecology in benthic environments. Here, we elucidate the abundance, diversity, and spatial distribution of Vibrio spp. in sediments of the Chinese marginal seas, with a wide spatial range from north to south covering the Yellow Sea (YS), East China Sea (ECS), and South China Sea (SCS). Quantitative analysis showed that Vibrio spp. were most abundant in the SCS (∼9.04 × 105 copies/g) compared to the YS (∼1.00 × 105 copies/g) and ECS (∼8.86 × 105 copies/g). Vibrio community compositions derived from Illumina sequencing of Vibrio-specific 16S rRNA genes varied significantly between sampling areas, which was reflected by a strong distance-decay pattern. The spatial distribution of Vibrio was governed by a joint effect of spatial and environmental factors (especially temperature, salinity, and SiO32-), and their respective pure effects explained only a small fraction of the community variation. Moreover, we identified the most prominent operational taxonomic units (OTUs) that were partitioned in these sea areas. Whereas Vibrionaceae OTU20 and Photobacterium lipolyticum were prevalent in the YS, Vibrio gigantis and Photobacterium piscicola, and P. piscicola, Photobacterium lutimaris, and Photobacterium alginatilyticum were prevalent in the ECS and SCS, respectively. Our study demonstrated clear spatial heterogeneity of Vibrio spp. in sediments of the Chinese marginal seas, laying a foundation for fully understanding the marine Vibrio ecology and the ecological roles of the species.IMPORTANCEVibrio is an important component of natural marine microbial populations in terms of pathogenicity and roles in carbon cycling. Compared to the marine pelagic environment, our knowledge of the diversity and distribution pattern of Vibrio spp. in sediment is limited. Here, we show higher Vibrio abundance in Chinese marginal seas than in other studied sediments. There was a clear spatial differentiation of Vibrio abundance and community composition in different sea areas. The benthic Vibrio community displayed a strong distance-decay pattern across a wide spatial range, which was formed under the combined effects of spatial and environmental factors. These results provide deep insights into the ecological dynamics of Vibrio and its environmental controls, facilitating a more comprehensive understanding of the marine Vibrio ecology.

Role of RpoN from Labrenzia aggregata LZB033 (Rhodobacteraceae) in Formation of Flagella and Biofilms, Motility, and Environmental Adaptation.

Labrenzia aggregata LZB033 (Rhodobacteraceae), which produces dimethylsulfoniopropionate (DMSP) and reduces nitrate to nitrogen, was isolated from seawater of the East China Sea. Its genome encodes a large number of transcriptional regulators which may be important for its adaptation to diverse marine environments. The alternative σ54 factor (RpoN) is a central regulator of many bacteria, regulating the transcription of multiple genes and controlling important cellular functions. However, the exact role of RpoN in Labrenzia spp. is unknown. In this study, an in-frame rpoN deletion mutant was constructed in LZB033, and the function of RpoN was determined. To systematically identify RpoN-controlled genes, we performed a detailed analysis of gene expression differences between the wild-type strain and the ΔrpoN mutant using RNA sequencing. The expression of 175 genes was shown to be controlled by RpoN. Subsequent phenotypic assays showed that the ΔrpoN mutant was attenuated in flagellar biosynthesis and swimming motility, utilized up to 13 carbon substrates differently, lacked the ability to assimilate malic acid, and displayed markedly decreased biofilm formation. In addition, stress response assays showed that the ΔrpoN mutant was impaired in the ability to survive under different challenge conditions, including osmotic stress, oxidative stress, temperature changes, and acid stress. Moreover, both the DMSP synthesis and catabolism rates of LZB033 decreased after rpoN was knocked out. Our work provides essential insight into the regulatory function of RpoN, revealing that RpoN is a key determinant for LZB033 flagellar formation, motility, biofilm formation, and environmental fitness, as well as DMSP production and degradation.IMPORTANCE This study established an in-frame gene deletion method in the alphaproteobacterium Labrenzia aggregata LZB033 and generated an rpoN gene mutant. A comparison of the transcriptomes and phenotypic characteristics between the mutant and wild-type strains confirmed the role of RpoN in L. aggregata LZB033 flagellar formation, motility, biofilm formation, and carbon usage. Most importantly, RpoN is a key factor for survival under different environmental challenge conditions. Furthermore, the ability to synthesize and metabolize dimethylsulfoniopropionate (DMSP) was related to RpoN. These features revealed RpoN to be an important regulator of stress resistance and survival for L. aggregata LZB033 in marine environments.

Spatiotemporal Dynamics of Free-Living and Particle-Associated Vibrio Communities in the Northern Chinese Marginal Seas.

Vibrio species are associated with human health and play important roles in the carbon cycle. The interest in the Vibrio ecology in marine pelagic environments has increased in recent years, and the correlations between the Vibrio community structure and various environmental factors have been demonstrated. However, the identification of planktonic Vibrio species and their relationship with particulate matter are unclear. Here, we elucidated the spatiotemporal dynamics of Vibrio diversity and in relation to environmental factors in the northern Chinese marginal seas, which feature complex and ever-changing environmental conditions. Vibrio abundance derived from quantitative PCR analysis was higher in summer (∼1.4 × 106 copies liter-1) than in winter (∼1.9 × 105 copies liter-1). Interestingly, the average amount of free-living (on a 0.22-µm-pore-size filter membrane) Vibrio was higher (∼3.89 times) than that of particle-associated Vibrio (on a 3-µm-pore-size filter membrane), making it likely that the preferential lifestyle of the planktonic Vibrio community was free living. Shifts in Vibrio community composition identified by high-throughput amplicon sequencing of the Vibrio-specific 16S rRNA gene were observed at both spatial and temporal scales, which were mainly driven by temperature, dissolved oxygen, ammonium, salinity, nitrite, and phosphate. The most prominent operational taxonomic units in summer were closely related to Vibrio campbellii and Vibrio caribbeanicus and shifted to those affiliated with Vibrio atlanticus in winter. Our study demonstrated abundant and diverse Vibrio populations in the northern Chinese marginal seas, contributing to a better understanding of their potential ecological roles in these ecosystems.IMPORTANCE The dynamics of Vibrio communities have been shown in many marine habitats that are close to land, including estuary or harbor areas. Here, we investigated the spatiotemporal dynamics of Vibrio populations in the northern Chinese marginal seas, spanning a wide spatial scale. We showed that the abundances of the Vibrio population in the present study were higher than those in most previously studied areas and that Vibrio species are more likely to adopt a free-living lifestyle. Moreover, our results expanded upon previous results by showing a clear shift in the dominant Vibrio species from summer to winter, which was mainly attributable to the reduction in the abundance of dominant species in summer. Overall, this work contributes to the understanding of the ecology of the Vibrio communities in the marginal seas.

Winogradskyella ouciana sp. nov., isolated from the hadal seawater of the Mariana Trench.

A Gram-staining-negative, strictly aerobic, long-rod shaped with no flagellum and yellow-pigmented bacterium designated strain ZXX205T, was isolated from the hadal seawater at the depth of 7500 m in the Mariana Trench, Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences placed strain ZXX205T within the genus Winogradskyella and strain ZXX205T was most closely related to Winogradskyella flava KCTC 52348T and Winogradskyella echinorum KCTC 22026T with 96.9 % and 96.6 % sequence similarity, respectively. The sequence similarities to all other type strains were 96.3 % or less, and to the type strain Winogradskyella thalassocola LMG 22492T was 94.1 %. Growth occurred in the presence of 0-9.0 % (w/v) NaCl (optimum 3.0 %), at 4-45 °C (optimum 28 °C) and pH 6.0-9.0 (optimum pH 7.5). The sole respiratory quinone was menaquinone 6 (MK-6). The dominant cellular fatty acids (>10 %) of strain ZXX205T were iso-C15 : 0, iso-C15 : 1 G, iso-C16 : 0 3-OH and iso-C16 : 0. The polar lipids profile contained predominantly phosphatidylethanolamine, four glycolipids, four unidentified aminolipids and three unidentified lipids. The genomic DNA G+C content was 35.5 %. The DNA-DNA relatedness (DDH) values between strain ZXX205T and the most closely related species Winogradskyella flava and Winogradskyella echinorum were 21.1 and 20.4 %, respectively. Based on polyphasic taxonomic analysis, strain ZXX205T is considered to represent a novel species in the genus Winogradskyella of the family Flavobacteriaceae, for which the name Winogradskyella ouciana is proposed. The type strain is ZXX205T (=MCCC 1K03851T=JCM 33665T).

Bacterial wilt affects the structure and assembly of microbial communities along the soil-root continuum.

BACKGROUND: Beneficial root-associated microbiomes play crucial roles in enhancing plant growth and suppressing pathogenic threats, and their application for defending against pathogens has garnered increasing attention. Nonetheless, the dynamics of microbiome assembly and defense mechanisms during pathogen invasion remain largely unknown. In this study, we aimed to investigate the diversity and assembly of microbial communities within four niches (bulk soils, rhizosphere, rhizoplane, and endosphere) under the influence of the bacterial plant pathogen Ralstonia solanacearum. RESULTS: Our results revealed that healthy tobacco plants exhibited more diverse community compositions and more robust co-occurrence networks in root-associated niches compared to diseased tobacco plants. Stochastic processes (dispersal limitation and drift), rather than determinism, dominated the assembly processes, with a higher impact of drift observed in diseased plants than in healthy ones. Furthermore, during the invasion of R. solanacearum, the abundance of Fusarium genera, a known potential pathogen of Fusarium wilt, significantly increased in diseased plants. Moreover, the response strategies of the microbiomes to pathogens in diseased and healthy plants diverged. Diseased microbiomes recruited beneficial microbial taxa, such as Streptomyces and Bacilli, to mount defenses against pathogens, with an increased presence of microbial taxa negatively correlated with the pathogen. Conversely, the potential defense strategies varied across niches in healthy plants, with significant enrichments of functional genes related to biofilm formation in the rhizoplane and antibiotic biosynthesis in the endosphere. CONCLUSION: Our study revealed the varied community composition and assembly mechanism of microbial communities between healthy and diseased tobacco plants along the soil-root continuum, providing new insights into niche-specific defense mechanisms against pathogen invasions. These findings may underscore the potential utilization of different functional prebiotics to enhance plants' ability to fend off pathogens.

Ulva prolifera polysaccharide enhances the root colonisation by Bacillus amyloliquefaciens strain Cas02.

The application of biocontrol agent is important for the sustainable development of agriculture. Unsuccessful or limited colonisation by plant growth-promoting rhizobacteria (PGPR) has become an important constraint factor for their commercial application. Here, we report that Ulva prolifera polysaccharide (UPP) promotes root colonisation by Bacillus amyloliquefaciens strain Cas02. UPP serves as an environmental signal for bacterial biofilm formation and its glucose residue is used as a carbon source for the synthesis of the exopolysaccharides and poly-gamma-glutamate present in biofilm matrix. Greenhouse experiments demonstrated that UPP could effectively enhance the root colonisation by Cas02 in both the bacterial population and survival time under natural semiarid soil conditions. Furthermore, the microbiome analysis also indicated the promoted colonisation by Cas02, as well as the improved bacterial rhizosphere community structure, after combined treatment of UPP and Cas02. This study provides a practical approach to improve the biocontrol agent with seaweed polysaccharides.

Response of bacterial community metabolites to bacterial wilt caused by Ralstonia solanacearum: a multi-omics analysis.

The soil microbial community plays a critical role in promoting robust plant growth and serves as an effective defence mechanism against root pathogens. Current research has focused on unravelling the compositions and functions of diverse microbial taxa in plant rhizospheres invaded by Ralstonia solanacearum, however, the specific mechanisms by which key microbial groups with distinct functions exert their effects remain unclear. In this study, we employed a combination of amplicon sequencing and metabolomics analysis to investigate the principal metabolic mechanisms of key microbial taxa in plant rhizosphere soil. Compared to the healthy tobacco rhizosphere samples, the bacterial diversity and co-occurrence network of the diseased tobacco rhizosphere soil were significantly reduced. Notably, certain genera, including Gaiella, Rhodoplanes, and MND1 (Nitrosomonadaceae), were found to be significantly more abundant in the rhizosphere of healthy plants than in that of diseased plants. Eight environmental factors, including exchangeable magnesium, available phosphorus, and pH, were found to be crucial factors influencing the composition of the microbial community. Ralstonia displayed negative correlations with pH, exchangeable magnesium, and cation exchange flux, but showed a positive correlation with available iron. Furthermore, metabolomic analysis revealed that the metabolic pathways related to the synthesis of various antibacterial compounds were significantly enriched in the healthy group. The correlation analysis results indicate that the bacterial genera Polycyclovorans, Lysobacter, Pseudomonas, and Nitrosospira may participate in the synthesis of antibacterial compounds. Collectively, our findings contribute to a more in-depth understanding of disease resistance mechanisms within healthy microbial communities and provide a theoretical foundation for the development of targeted strategies using beneficial microorganisms to suppress disease occurrence.

Succession of marine bacteria in response to Ulva prolifera-derived dissolved organic matter.

Increasing macroalgal blooms as a consequence of climate warming and coastal eutrophication have profound effects on the marine environment. The outbreaks of Ulva prolifera in the Yellow Sea of China occurring every summer since 2007 to present have formed the world's largest green tide. The green tide releases huge amounts of dissolved organic matter (DOM) to the seawater, causing an organic overload. However, how marine bacteria respond to this issue and the potential impact on the marine environment are still unclear. Here, we monitored the highly temporally resolved dynamics of marine bacterial community that occur in response to Ulva prolifera-derived DOM by performing a 168-h microcosm incubation experiment. DOM inputs significantly increased bacterial abundances within 6 h, decreased bacterial diversity and triggered clear community successions during the whole period of incubation. Vibrio of Gammaproteobacteria robustly and rapidly grew over short timescales (6-24 h), with its relative abundance accounting for up to 52.5% of active bacteria. From 24 to 48 h, some genera of Flavobacteriia grew rapidly, which was more conspicuous at a higher DOM concentration than at a lower concentration. The genus Donghicola of Alphaproteobacteria was predominant at later time points (>48 h). This bacterial community succession was accompanied by significant variations in the activity of 12 different extracellular enzymes, resulting in a rapid reduction of dissolved organic carbon by 74.5% within the first 36 h. In summary, our study demonstrates rapid successions of bacterial community and extracellular enzyme activity after DOM inputs, suggesting that the bacterial response to Ulva prolifera-derived organic matter may contribute to environmental restoration and may pose a health threat due to the bloom of potential pathogenic Vibrio.

Insights into the Vertical Stratification of Microbial Ecological Roles across the Deepest Seawater Column on Earth.

The Earth's oceans are a huge body of water with physicochemical properties and microbial community profiles that change with depth, which in turn influences their biogeochemical cycling potential. The differences between microbial communities and their functional potential in surface to hadopelagic water samples are only beginning to be explored. Here, we used metagenomics to investigate the microbial communities and their potential to drive biogeochemical cycling in seven different water layers down the vertical profile of the Challenger Deep (0-10,500 m) in the Mariana Trench, the deepest natural point in the Earth's oceans. We recovered 726 metagenome-assembled genomes (MAGs) affiliated to 27 phyla. Overall, biodiversity increased in line with increased depth. In addition, the genome size of MAGs at ≥4000 m layers was slightly larger compared to those at 0-2000 m. As expected, surface waters were the main source of primary production, predominantly from Cyanobacteria. Intriguingly, microbes conducting an unusual form of nitrogen metabolism were identified in the deepest waters (>10,000 m), as demonstrated by an enrichment of genes encoding proteins involved in dissimilatory nitrate to ammonia conversion (DNRA), nitrogen fixation and urea transport. These likely facilitate the survival of ammonia-oxidizing archaea α lineage, which are typically present in environments with a high ammonia concentration. In addition, the microbial potential for oxidative phosphorylation and the glyoxylate shunt was enhanced in >10,000 m waters. This study provides novel insights into how microbial communities and their genetic potential for biogeochemical cycling differs through the Challenger deep water column, and into the unique adaptive lifestyle of microbes in the Earth's deepest seawater.

Novel Insights Into Bacterial Dimethylsulfoniopropionate Catabolism in the East China Sea.

The compatible solute dimethylsulfoniopropionate (DMSP), made by many marine organisms, is one of Earth's most abundant organosulfur molecules. Many marine bacteria import DMSP and can degrade it as a source of carbon and/or sulfur via DMSP cleavage or DMSP demethylation pathways, which can generate the climate active gases dimethyl sulfide (DMS) or methanthiol (MeSH), respectively. Here we used culture-dependent and -independent methods to study bacteria catabolizing DMSP in the East China Sea (ECS). Of bacterial isolates, 42.11% showed DMSP-dependent DMS (Ddd+) activity, and 12.28% produced detectable levels of MeSH. Interestingly, although most Ddd+ isolates were Alphaproteobacteria (mainly Roseobacters), many gram-positive Actinobacteria were also shown to cleave DMSP producing DMS. The mechanism by which these Actinobacteria cleave DMSP is unknown, since no known functional ddd genes have been identified in genome sequences of Ddd+ Microbacterium and Agrococcus isolates or in any other sequenced Actinobacteria genomes. Gene probes to the DMSP demethylation gene dmdA and the DMSP lyase gene dddP demonstrated that these DMSP-degrading genes are abundant and widely distributed in ECS seawaters. dmdA was present in relatively high proportions in both surface (19.53% ± 6.70%) and bottom seawater bacteria (16.00% ± 8.73%). In contrast, dddP abundance positively correlated with chlorophyll a, and gradually decreased with the distance from land, which implies that the bacterial DMSP lyase gene dddP might be from bacterial groups that closely associate with phytoplankton. Bacterial community analysis showed positive correlations between Rhodobacteraceae abundance and concentrations of DMS and DMSP, further confirming the link between this abundant bacterial class and the environmental DMSP cycling.