Scale-Dependent Effects of Growth Stage and Elevational Gradient on Rice Phyllosphere Bacterial and Fungal Microbial Patterns in the Terrace Field

The variation of phyllosphere bacterial and fungal communities along elevation gradients may provide a potential link with temperature, which corresponds to an elevation over short geographic distances. At the same time, the plant growth stage is also an important factor affecting phyllosphere microorganisms. Understanding microbiological diversity over changes in elevation and among plant growth stages is important for developing crop growth ecological theories. Thus, we investigated variations in the composition of the rice phyllosphere bacterial and fungal communities at five sites along an elevation gradient from 580 to 980 m above sea level (asl) in the Ziquejie Mountain at the seedling, heading, and mature stages, using high-throughput Illumina sequencing methods. The results revealed that the dominant bacterial phyla were Proteobacteria, Actinobacteria, and Bacteroidetes, and the dominant fungal phyla were Ascomycota and Basidiomycota, which varied significantly at different elevation sites and growth stages. Elevation had a greater effect on the α diversity of phyllosphere bacteria than on that phyllosphere fungi. Meanwhile, the growth stage had a great effect on the α diversity of both phyllosphere bacteria and fungi. Our results also showed that the composition of bacterial and fungal communities varied significantly along elevation within the different growth stages, in terms of both changes in the relative abundance of species, and that the variations in bacterial and fungal composition were well correlated with variations in the average elevation. A total of 18 bacterial and 24 fungal genera were significantly correlated with elevational gradient, displaying large differences at the various growth stages. Soluble protein (SP) shared a strong positive correlation with bacterial and fungal communities (p < 0.05) and had a strong significant negative correlation with Serratia, Passalora, unclassified_Trichosphaeriales, and antioxidant enzymes (R > 0.5, p < 0.05), and significant positive correlation with the fungal genera Xylaria, Gibberella, and Penicillium (R > 0.5, p < 0.05). Therefore, it suggests that elevation and growth stage might alter both the diversity and abundance of phyllosphere bacterial and fungal populations.

The Role of Phyllosphere Bacteria in Improving Cotton Growth and Yield Under Drought Conditions

Cotton is a valuable fiber and cash crop in Telangana, India. This study examines how crop growth and fiber yield are affected by the uneven distribution of rainfall. Cotton phyllosphere bacterial isolates were gathered from the Rangareddy and Warangal Districts of Telangana, and in total, 31 phyllosphere bacterial isolates were obtained. These isolates were screened for drought tolerance and it was found that fifteen suitable isolates grew at −1.25 Mpa stress level with copious amounts of exopolysaccharides production. These isolates were further screened for ACC deaminase production and we observed 0.13–0.40 mM of α-ketobutyrate per milligram of cellular protein per hour. Five efficient bacterial isolates, namely Pseudomonas stutzeri, Acinetobacter sp., Bacillus mojavensis, Pseudomonas chlororaphis, and Enterobacter asburiae were found to produce ACC deaminase and were able to grow at −1.25 Mpa stress level. The cotton variety ADB-542 (drought susceptible) was treated with drought-tolerant five isolates. Acinetobacter sp. treated seeds had the highest seed germination and seedling vigor of 76.67 and 45.81%, respectively. The nutrient status of inoculated plots was considerably improved. The root length, fresh weight, proline content, and the number of bolls were increased by 28.52, 41.9, 28.78, and 12.99%, respectively, with the inoculation of Acinetobacter sp., to plants at −0.75 Mpa water potential. Overall the performance of cotton was improved significantly with the inoculation of phyllosphere bacteria to seeds; hence they can be recommended for the application of field crops as bio-inoculants.

Comparative Bacterial Metagenomics of Cnidoscolus aconitifolius (Mill.) I. M. Johnston and Other Leafy Vegetables

Aims: Vegetables provide a favourable habitat for diverse populations of microorganisms. Some vegetables, especially the ones used in salads are ready-to-eat food products and some phyllosphere bacteria might contribute to the prolonged presence of human food-borne pathogens in these vegetables. Methodology: Phyllosphere bacteria associated with Cnidoscolus aconitifolius were evaluated using a culture-independent approach, Illumina MiSeq platform of 16S rRNA gene sequencing and then compared with publicly available data obtained from Spinacia oleracea (spinach) and Lactuca sativa (lettuce) on GenBank. Results: The results from this study showed that the three vegetables harbor diverse bacterial organisms. Eighty-three (83) Operational Taxonomic Units (OTUs) assigned to five phyla were obtained from C. aconitifolius phyllosphere. The most predominant phyla across studied vegetables were: Proteobacteria (74.79%), Actinobacteria (8.69%) and Firmicutes (7.37%). Potential human pathogenic species such as Bacillus spp., Enterococcus spp., Staphylococcus spp., Klebsiella spp., and Pseudomonas spp. were also present in lettuce and spinach. Bacteria with potential for antibiotic production, anti-microbial and antibiotic resistant genes belong to the families Bacillaceae, Streptomycetaceae, Pseudomonaceae, Enterobacteriaceae, Staphylococcaceae, Enterococcaceae and Streptococcaceae. The most abundant taxa obtained from this study were Pseudomonas, Erwinia, Brachybacterium, Megasphaera, Janthinobacterium, Sphingomonas and Lactobacillus. Conclusion: Our result successfully determined the relative abundance of potential human and plant pathogens in the leafy vegetables and also showed the bacterial community structure in the studied vegetables.

Environmental Factors Influencing Phyllosphere Bacterial Communities in Giant Pandas’ Staple Food Bamboos

The giant panda has developed a series of evolutionary strategies to adapt to a bamboo diet. The abundance and diversity of the phyllosphere microbiome change dramatically depending on the season, host species, location, etc., which may, in turn, affect the growth and health of host plants. However, few studies have investigated the factors that influence phyllosphere bacteria in bamboo, a staple food source of the giant panda. Amplicon sequencing of the 16S rRNA gene was used to explore the abundance and diversity of phyllosphere bacteria in three bamboo species (Arundinaria spanostachya, Yushania lineolate, and Fargesia ferax) over different seasons (spring vs. autumn), elevation, distance from water, etc., in Liziping National Nature Reserve (Liziping NR), China. And whole-genome shotgun sequencing uncovered the differences in biological functions (KEGG and Carbohydrate-Active enzymes functions) of A. spanostachya phyllosphere bacteria between spring and autumn. The results showed that the abundance and diversity of F. ferax phyllosphere bacteria were greater than that of the other two bamboo species in both seasons. And three kinds of bamboo phyllosphere bacteria in autumn were significantly higher than in spring. The season was a more important factor than host bamboo species in determining the community structure of phyllosphere bacteria based on the (un)weighted UniFrac distance matrix. The composition, diversity, and community structure of phyllosphere bacteria in bamboo were primarily affected by the season, species, altitude, tree layer, and shrub layer. Different bacterial communities perform different functions in different bamboo species, and long-term low temperatures may shape more varied and complex KEGG and Carbohydrate-Active enzymes functions in spring. Our study presented a deeper understanding of factors influencing the bacterial community in the bamboo phyllosphere. These integrated results offer an original insight into bamboo, which can provide a reference for the restoration and management of giant panda bamboo food resources in the Xiaoxiangling mountains.

Quantification of anti-quorum sensing and antibiofilm activity of Phyllosphere bacteria against food spoilage bacteria

Food spoilage and microbial contamination require attention during the food production process since the presence of these bacteria can create problems including the formation of biofilms produced by these bacteria. Biofilm formations are initiated through cell-to-cell communication which is called quorum sensing mechanism. Hence, inhibition of this communication mechanism could be one of the solutions to inhibit biofilm formation. Therefore, exploration of bioactive compounds from various sources including hyllosphere bacteria with anti-quorum sensing inhibition activities is important. Phyllosphere bacteria are a community of bacteria found on the surface of plant leaves at a very large population. These bacteria can produce bioactive compounds that can inhibit quorum sensing mechanism. In this study, 54 phyllosphere bacteria isolates were tested, 8 bacterial isolates had potential effect to inhibit quorum sensing. From biofilm inhibition assay, the highest percentages were showed by ifferent phyllosphere isolates against each pathogen. Whereas, for biofilm destruction assay, JB 8F isolate had the highest percentage of destruction biofilm activity against biofilm formed by Bacillus cereus and Shewanella putrefaciens. Eight isolates of phyllosphere bacteria had the potential as quorum quencher and anti-biofilm agents, both for inhibition and destruction of biofilm.

Comparative Analyses of Phyllosphere Bacterial Communities and Metabolomes in Newly Developed Needles of Cunninghamia lanceolata (Lamb.) Hook. at Four Stages of Stand Growth

Host-plant-associated bacteria affect the growth, vigor, and nutrient availability of the host plant. However, phyllosphere bacteria have received less research attention and their functions remain elusive, especially in forest ecosystems. In this study, we collected newly developed needles from sapling (age 5 years), juvenile (15 years), mature (25 years), and overmature (35 years) stands of Chinese fir [Cunninghamia lanceolata (Lamb.) Hook]. We analyzed changes in phyllosphere bacterial communities, their functional genes, and metabolic activity among different stand ages. The results showed that phyllosphere bacterial communities changed, both in relative abundance and in composition, with an increase in stand age. Community abundance predominantly changed in the orders Campylobacterales, Pseudonocardiales, Deinococcales, Gemmatimonadales, Betaproteobacteriales, Chthoniobacterales, and Propionibacteriales. Functional predictions indicated the genes of microbial communities for carbon metabolism, nitrogen metabolism, antibiotic biosynthesis, flavonoids biosynthesis, and steroid hormone biosynthesis varied; some bacteria were strongly correlated with some metabolites. A total of 112 differential metabolites, including lipids, benzenoids, and flavonoids, were identified. Trigonelline, proline, leucine, and phenylalanine concentrations increased with stand age. Flavonoids concentrations were higher in sapling stands than in other stands, but the transcript levels of genes associated with flavonoids biosynthesis in the newly developed needles of saplings were lower than those of other stands. The nutritional requirements and competition between individual trees at different growth stages shaped the phyllosphere bacterial community and host–bacteria interaction. Gene expression related to the secondary metabolism of shikimate, mevalonate, terpenoids, tocopherol, phenylpropanoids, phenols, alkaloids, carotenoids, betains, wax, and flavonoids pathways were clearly different in Chinese fir at different ages. This study provides an overview of phyllosphere bacteria, metabolism, and transcriptome in Chinese fir of different stand ages and highlights the value of an integrated approach to understand the molecular mechanisms associated with biosynthesis.

Environmental factors influencing the composition of phyllosphere bacterial communities in bamboo: A staple food source of giant pandas

Background The giant panda has developed a series of evolutionary strategies to adapt to a bamboo diet. The abundance and diversity of the phyllosphere microbiome change dramatically depending on the season, host species, location etc., which may, in turn, affect the growth and health of host plants. However, few studies have investigated the factors that influence phyllosphere bacteria in bamboo, a staple food source of the giant panda. Methods Amplicon sequencing of the 16S rRNA gene of rRNA genomic loci was used to explore the abundance and diversity of phyllosphere bacteria in three bamboo species (Arundinaria spanostachya, Yushania lineolate and Fargesia ferax) over different seasons (spring vs. autumn), elevation, distance from water, etc. in Liziping National Nature Reserve (Liziping NR), China. Results The results show that a total of 2,562 operational taxonomic units (OTUs) were obtained from all 101 samples, which belonged to 24 phyla and 608 genera. Proteobacteria was the dominant phyla, followed by Acidobacteria and Actinobacteria. The Sobs index and Shannon index of F. ferax phyllosphere bacteria were greater than that of the other two bamboo species in both seasons. The Sobs index and Shannon index of phyllosphere bacteria in all three bamboo species in autumn were significantly higher than in spring. Season was a stronger driver of community structure of phyllosphere bacteria than host bamboo species based on the (un)weighted UniFrac distance matrix. Many bacteria phyla were negatively correlated with elevation and distance from water, but positively related to mean height of bamboo and mean base diameter of bamboo. Function prediction of PICRUSt revealed the relative abundance of transporters function was highest in all three bamboo species, followed by ABC transporters. There were nine relative abundance pathways with significant differences in the 3-level KEGG pathway. The genes related to membrane transport, signal transduction and porphyrin transport in phyllosphere bacteria of F. ferax were significantly lower than in the other two species. Conclusions The composition, diversity and community structure of phyllosphere bacteria in bamboo, a staple food source of giant pandas, were primarily affected by the season, species, altitude, tree layer and shrub layer. The better the growth of bamboo forests, the richer the bacterial phyla in the bamboo phyllosphere. Our study presented a deeper understanding of factors influencing the bacterial community in the bamboo phyllosphere. These findings could provide a reference for the restoration and management of giant panda habitat and food resources in this area, especially for those small isolated populations of giant pandas in Xiaoxiangling mountains.

Extract from phyllosphere bacteria with antibiofilm and quorum quenching activity to control several fish pathogenic bacteria

Objective The objective of this research were to screen quorum quenching activity compound from phyllosphere bacteria as well as antibiofilm activity against several fish pathogen bacteria such as Aeromonas hydrophila, Streptococcus agalactiae, and Vibrio harveyi. Results We found eight phyllosphere bacteria isolates with potential quorum quenching activity to inhibit Chromobacterium violaceum as indicator bacteria. Crude extracts (20 mg/mL) showed various antibiofilm activity against fish pathogenic bacteria used in this study. Isolate JB 17B showed the highest activity to inhibit biofilm formation of A. hydrophila and V. harveyi, meanwhile isolate JB 3B showed the highest activity to inhibit biofilm of S. agalactiae. From destruction assay, isolate JB 8F showed the highest activity to disrupt biofilm of A. hydrophila isolate JB 20B showed the highest activity to disrupt biofilm of V. harveyi, isolate JB 17B also showed the highest activity to disrupt biofilm of S. agalactiae.