Complete genome sequence of Planococcus donghaensis JH1T, a pectin-degrading bacterium

See-Too, Wah-Seng; Chua, Kek Heng; Lim, Yan-Lue; Chen, Jian-Woon; Convey, Peter; Mohidin, Taznim Begam Mohd; Yin, Wai‐Fong; Chan, Kok‐Gan

doi:10.1016/j.jbiotec.2017.05.005

Cited by 13 publications

(10 citation statements)

References 28 publications

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“…As many endophytes and bacteria colonizing root surfaces have beneficial effects, such as nitrogen fixation, phytohormone production, nutrient supply and pathogen suppression (Rosenblueth & Martinez-Romero, 2006; Hardoim, van Overbeek & van Elsas, 2008), they typically promote plant growth and can alleviate salt stress in halophytes (Ali et al, 2015). Some Microbulbifer and Planococcus species have the ability to degrade complex hydrocarbons (See-Too et al, 2017). Meanwhile, Bacillus , Exiguobacterium , Halomonas , Planococcus and Pseudomonas can generate 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase to convert the ethylene precursor ACC into ammonia and α-ketobutyrate; this has the effect of lowering the ethylene concentration within plant tissues, reducing its constraining effect on root elongation and general plant growth (Siddikee et al, 2010).…”

Section: Discussionmentioning

confidence: 99%

Rhizobacterial communities of five co-occurring desert halophytes

Kong

Teng

et al. 2018

PeerJ

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BackgroundRecently, researches have begun to investigate the microbial communities associated with halophytes. Both rhizobacterial community composition and the environmental drivers of community assembly have been addressed. However, few studies have explored the structure of rhizobacterial communities associated with halophytic plants that are co-occurring in arid, salinized areas.MethodsFive halophytes were selected for study: these co-occurred in saline soils in the Ebinur Lake Nature Reserve, located at the western margin of the Gurbantunggut Desert of Northwestern China. Halophyte-associated bacterial communities were sampled, and the bacterial 16S rDNA V3–V4 region amplified and sequenced using the Illumina Miseq platform. The bacterial community diversity and structure were compared between the rhizosphere and bulk soils, as well as among the rhizosphere samples. The effects of plant species identity and soil properties on the bacterial communities were also analyzed.ResultsSignificant differences were observed between the rhizosphere and bulk soil bacterial communities. Diversity was higher in the rhizosphere than in the bulk soils. Abundant taxonomic groups (from phylum to genus) in the rhizosphere were much more diverse than in bulk soils. Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Planctomycetes were the most abundant phyla in the rhizosphere, while Proteobacteria and Firmicutes were common in bulk soils. Overall, the bacterial community composition were not significantly differentiated between the bulk soils of the five plants, but community diversity and structure differed significantly in the rhizosphere. The diversity of Halostachys caspica, Halocnemum strobilaceum and Kalidium foliatum associated bacterial communities was lower than that of Limonium gmelinii and Lycium ruthenicum communities. Furthermore, the composition of the bacterial communities of Halostachys caspica and Halocnemum strobilaceum was very different from those of Limonium gmelinii and Lycium ruthenicum. The diversity and community structure were influenced by soil EC, pH and nutrient content (TOC, SOM, TON and AP); of these, the effects of EC on bacterial community composition were less important than those of soil nutrients.DiscussionHalophytic plant species played an important role in shaping associated rhizosphere bacterial communities. When salinity levels were constant, soil nutrients emerged as key factors structuring bacterial communities, while EC played only a minor role. Pairwise differences among the rhizobacterial communities associated with different plant species were not significant, despite some evidence of differentiation. Further studies involving more halophyte species, and individuals per species, are necessary to elucidate plant species identity effects on the rhizosphere for co-occurring halophytes.

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Section: Discussionmentioning

confidence: 99%

Rhizobacterial communities of five co-occurring desert halophytes

Kong

Teng

et al. 2018

PeerJ

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“…Moreover, two PL1s and one PL9 were annotated to degrade pectin. Pectate lyase (EC 4.2.2.2) usually has (1 → 4)-α-d-galacturonan cleavage function, causing oligosaccharides present at the end [40] (Table 2). AA4, AA6, AA7 and AA10 were included in the genome.…”

Section: Carbohydrate-active Enzyme (Cazyme) Annotationmentioning

confidence: 99%

Genome sequencing of gut symbiotic Bacillus velezensis LC1 for bioethanol production from bamboo shoots

Lü

Zheng

et al. 2020

Biotechnol Biofuels

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Background: Bamboo, a lignocellulosic feedstock, is considered as a potentially excellent raw material and evaluated for lignocellulose degradation and bioethanol production, with a focus on using physical and chemical pre-treatment. However, studies reporting the biodegradation of bamboo lignocellulose using microbes such as bacteria and fungi are scarce. Results:In the present study, Bacillus velezensis LC1 was isolated from Cyrtotrachelus buqueti, in which the symbiotic bacteria exhibited lignocellulose degradation ability and cellulase activities. We performed genome sequencing of B. velezensis LC1, which has a 3929,782-bp ring chromosome and 46.5% GC content. The total gene length was 3,502,596 bp using gene prediction, and the GC contents were 47.29% and 40.04% in the gene and intergene regions, respectively. The genome contains 4018 coding DNA sequences, and all have been assigned predicted functions. Carbohydrate-active enzyme annotation identified 136 genes annotated to CAZy families, including GH, GTs, CEs, PLs, AAs and CBMs. Genes involved in lignocellulose degradation were identified. After a 6-day treatment, the bamboo shoot cellulose degradation efficiency reached 39.32%, and the hydrolysate was subjected to ethanol fermentation with Saccharomyces cerevisiae and Escherichia coli KO11, yielding 7.2 g/L of ethanol at 96 h. Conclusions:These findings provide an insight for B. velezensis strains in converting lignocellulose into ethanol. B. velezensis LC1, a symbiotic bacteria, can potentially degrade bamboo lignocellulose components and further transformation to ethanol, and expand the bamboo lignocellulosic bioethanol production.

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“…Brega et al (1990) documented the presence of this particular phenolic compound in human urine even though the presence was not linked to this bacterium. This bacterium was previously isolated in the human gut, sea water, clamp prawns and the marine environment (Seck et al 2016; Too et al 2017). The ability to survive in different environments may be related to their presence in the fermenting urine of mammals where they are associated with the production of o-cresol as established in this study.…”

Section: Discussionmentioning

confidence: 98%

16S rRNA gene profiling of bacterial communities mediating production of tsetse attractive phenols in mammalian urine

Musonye

Njeru

Hassanali

et al. 2019

Onderstepoort Journal of Veterinary Research

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Several types of odours are involved in the location of host animals by tsetse (Diptera: Glossinidae), a vector of animal African trypanosomiasis. Host animals’ ageing urine has been shown to be the source of a phenolic blend attractive to the tsetse. Nevertheless, limited research has been performed on the microbial communities’ role in the production of phenols. This study aimed at profiling bacterial communities mediating the production of tsetse attractive phenols in mammalian urine. Urine samples were collected from African buffalo ( Syncerus caffer ), cattle ( Bos taurus ) and eland ( Taurotragus oryx ) at Kongoni Game Valley Ranch and Kenyatta University in Kenya. Urine samples, of each animal species, were pooled and left open to age in ambient conditions. Bacteriological and phenols analyses were then carried out, at 4 days ageing intervals, for 24 days. Phenols analysis revealed nine volatile phenols: 4-cresol, ortho-cresol, 3-cresol, phenol, 3-ethylphenol, 3-propylphenol, 2-methyloxyphenol, 4-ethylphenol and 4-propylphenol. Eight out of 19 bacterial isolates from the ageing urine revealed the potential to mediate production of phenols. 16S rRNA gene characterisation of the isolates closely resembled Enterococcus faecalis KUB3006, Psychrobacter alimentarius PAMC 27887, Streptococcus agalactiae 2603V, Morganella morganii sub.sp. morganii KT, Micrococcus luteus NCTC2665, Planococcus massiliensis strain ES2, Ochrobactrum pituitosum AA2 and Enterococcus faecalis OGIRF. This study established that some of the phenols emitted from mammalian urine, which influence the tsetse‘s host-seeking behaviour, are well characterised by certain bacteria. These results may allow the development of biotechnological models in vector control that combines the use of these bacteria in the controlled release of semiochemicals.

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Complete genome sequence of Planococcus donghaensis JH1T, a pectin-degrading bacterium

Cited by 13 publications

References 28 publications

Rhizobacterial communities of five co-occurring desert halophytes

Rhizobacterial communities of five co-occurring desert halophytes

Genome sequencing of gut symbiotic Bacillus velezensis LC1 for bioethanol production from bamboo shoots

16S rRNA gene profiling of bacterial communities mediating production of tsetse attractive phenols in mammalian urine

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