Whole genome sequencing and identification of host-interactive genes in the rice endophytic Leifsonia sp. ku-ls

Battu, Latha; Ulaganathan, Kandasamy

doi:10.1007/s10142-019-00713-z

Cited by 15 publications

(7 citation statements)

References 56 publications

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“…Considering the use of a lipid-rich waste as a substrate for the PHAs accumulation, it is necessary for the hydrolysis of triglycerides into free fatty acids before their subsequent transformation to PHAs [ 98 ]. The bacteria that were potentially able to accumulate PHAs with a lipolytic activity were Acidovorax [ 99 ], Acinetobacter [ 100 ], Azospirillum [ 101 ], Chryseobacterium [ 102 ], Comamonas [ 103 ], Corynebacterium [ 104 ], Devosia [ 105 ], Dokdonella [ 106 ], Dyella [ 107 ], Ferruginibacter [ 108 ], Flavobacterium [ 109 ], Gemmobacter [ 77 ], Gordonia [ 110 ], Leifsonia [ 111 ], Lysobacter [ 112 ], Niveispirillum [ 113 ], Novosphingobium [ 114 ], Pandoraea [ 115 ], Polynucleobacter [ 83 ], Pseudomonas [ 98 ], Qipengyuania [ 116 ], Rhizobium [ 117 ], Stenotrophomonas [ 118 ], Taibaiella [ 119 ], Thermomonas [ 120 ], and Tsukamurella [ 121 ].…”

Section: Resultsmentioning

confidence: 99%

Dynamics of PHA-Accumulating Bacterial Communities Fed with Lipid-Rich Liquid Effluents from Fish-Canning Industries

et al. 2022

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The biosynthesis of polyhydroxyalkanoates (PHAs) from industrial wastes by mixed microbial cultures (MMCs) enriched in PHA-accumulating bacteria is a promising technology to replace petroleum-based plastics. However, the populations’ dynamics in the PHA-accumulating MMCs are not well known. Therefore, the main objective of this study was to address the shifts in the size and structure of the bacterial communities in two lab-scale sequencing batch reactors (SBRs) fed with fish-canning effluents and operated under non-saline (SBR-N, 0.5 g NaCl/L) or saline (SBR-S, 10 g NaCl/L) conditions, by using a combination of quantitative PCR and Illumina sequencing of bacterial 16S rRNA genes. A double growth limitation (DGL) strategy, in which nitrogen availability was limited and uncoupled to carbon addition, strongly modulated the relative abundances of the PHA-accumulating bacteria, leading to an increase in the accumulation of PHAs, independently of the saline conditions (average 9.04 wt% and 11.69 wt%, maximum yields 22.03 wt% and 26.33% SBR-N and SBR-S, respectively). On the other hand, no correlations were found among the PHAs accumulation yields and the absolute abundances of total Bacteria, which decreased through time in the SBR-N and did not present statistical differences in the SBR-S. Acinetobacter, Calothrix, Dyella, Flavobacterium, Novosphingobium, Qipengyuania, and Tsukamurella were key PHA-accumulating genera in both SBRs under the DGL strategy, which was revealed as a successful tool to obtain a PHA-enriched MMC using fish-canning effluents.

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Section: Resultsmentioning

confidence: 99%

Dynamics of PHA-Accumulating Bacterial Communities Fed with Lipid-Rich Liquid Effluents from Fish-Canning Industries

et al. 2022

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“…is considered an asymptomatic endophyte as it is often found in natural grass fields [38]. Commercial monocots, such as corn and rice have a neutral and, in some cases, beneficial role for the host [39][40][41]. However, in susceptible sugarcane cultivars, the strain Leifsonia xyli subsp.…”

Section: Discussionmentioning

confidence: 99%

Towards defining the core Saccharum microbiome: input from five genotypes

Ishida

Bini²,

Creste³

et al. 2022

BMC Microbiol

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Background Plant microbiome and its manipulation inaugurate a new era for plant biotechnology with the potential to benefit sustainable crop production. Here, we used the large-scale 16S rDNA sequencing analysis to unravel the dynamic, structure, and composition of exophytic and endophytic microbial communities in two hybrid commercial cultivars of sugarcane (R570 and SP80–3280), two cultivated genotypes (Saccharum officinarum and Saccharum barberi) and one wild species (Saccharum spontaneum). Results Our analysis identified 1372 amplicon sequence variants (ASVs). The microbial communities’ profiles are grouped by two, root and bulk soils and stem and leave when these four components are compared. However, PCoA-based data supports that endophytes and epiphytes communities form distinct groups, revealing an active host-derived mechanism to select the resident microbiota. A strong genotype-influence on the assembly of microbial communities in Saccharum ssp. is documented. A total of 220 ASVs persisted across plant cultivars and species. The ubiquitous bacteria are two potential beneficial bacteria, Acinetobacter ssp., and Serratia symbiotica. Conclusions The results presented support the existence of common and cultivar-specific ASVs in two commercial hybrids, two cultivated canes and one species of Saccharum across tissues (leaves, stems, and roots). Also, evidence is provided that under the experimental conditions described here, each genotype bears its microbial community with little impact from the soil conditions, except in the root system. It remains to be demonstrated which aspect, genotype, environment or both, has the most significant impact on the microbial selection in sugarcane fields.

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“…Whole‐genome sequencing of Leifsonia sp. ku‐Is, a rice endophytic bacterial strain colonizing in high numbers the stem and leaf of the high yielding and widely grown Oryza sativa indica rice cultivar RP Bio‐226, identified 3930 protein‐coding genes, 45 tRNA genes, and 3 rRNA genes [211]. Detailed analysis showed the presence of host beneficial genes, such as for hormone production, nitrogen metabolism, and stress response.…”

Section: Genetics Of Plant Growth Promotion By Endophytic Bacteriamentioning

confidence: 99%

“…Whole-genome sequencing of Leifsonia sp., an endophytic bacterial strain colonizing in high numbers the stem and leaf, showed the presence of host beneficial genes, including genes associated with defense against oxidative stress that could mitigate plant oxidative stress resulting from disease or abiotic stress [211]. Paenibacillus sp.…”

Section: Genetics Of Plant Growth Promotion By Mitigating the Abiotic Stress Of Plants By Endophytic Bacteriamentioning

confidence: 99%

Bacterial endophytes: Molecular interactions with their hosts

et al. 2021

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Plant growth promotion has been found associated with plants on the surface (epiphytic), inside (endophytic), or close to the plant roots (rhizospheric). Endophytic bacteria mainly have been researched for their beneficial activities in terms of nutrient availability, plant growth hormones, and control of soil‐borne and systemic pathogens. Molecular communications leading to these interactions between plants and endophytic bacteria are now being unrevealed using multidisciplinary approaches with advanced techniques such as metagenomics, metaproteomics, metatranscriptomics, metaproteogenomic, microRNAs, microarray, chips as well as the comparison of complete genome sequences. More than 400 genes in both the genomes of host plant and bacterial endophyte are up‐ or downregulated for the establishment of endophytism and plant growth‐promoting activity. The involvement of more than 20 genes for endophytism, about 50 genes for direct plant growth promotion, about 25 genes for biocontrol activity, and about 10 genes for mitigation of different stresses has been identified in various bacterial endophytes. This review summarizes the progress that has been made in recent years by these modern techniques and approaches.

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Whole genome sequencing and identification of host-interactive genes in the rice endophytic Leifsonia sp. ku-ls

Cited by 15 publications

References 56 publications

Dynamics of PHA-Accumulating Bacterial Communities Fed with Lipid-Rich Liquid Effluents from Fish-Canning Industries

Dynamics of PHA-Accumulating Bacterial Communities Fed with Lipid-Rich Liquid Effluents from Fish-Canning Industries

Towards defining the core Saccharum microbiome: input from five genotypes

Bacterial endophytes: Molecular interactions with their hosts

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