Complete genome sequence of Massilia sp. WG5, an efficient phenanthrene-degrading bacterium from soil

Lou, Jun; Gu, Haiping; Wang, Haizhen; An, Qianli; Xu, Jia‐Zhuang

doi:10.1016/j.jbiotec.2015.11.026

Cited by 35 publications

(24 citation statements)

References 8 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The absolute abundance of genus Massilia calculated by the iHAAQ method (5.13 × 10 8 copies (g dry wt soil) −1 ) was one order of magnitude higher than the added strain WG5 concentration (1.00 × 10 7 CFU (g dry wt soil) −1 ). After considering that one chromosome of strain WG5 has 9 copies of 16S rRNA gene ( Lou et al, 2016 ), the calculated absolute abundance of Massilia was close to the added concentration of strain WG5.…”

Section: Discussionmentioning

confidence: 85%

“…The Massilia sp. strain WG5 (CCTCC AB 2015362) was isolated from a PAHs contaminated soil from Jiangsu Province, China, which has a high phenanthrene-degrading ability ( Lou et al, 2016 ; Wang et al, 2016 ). After pre-cultured in LB medium, the strain WG5 was harvested by centrifugation at 4 °C (6,000 × g for 10 min) and washed three times with sterile deionized water.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification

Lou

Yang

Wang

et al. 2018

PeerJ

Self Cite

View full text Add to dashboard Cite

Microbial ecological studies have been remarkably promoted by the high-throughput sequencing approach with explosive information of taxonomy and relative abundance. However, relative abundance does not reflect the quantity of the microbial community and the inter-sample differences among taxa. In this study, we refined and applied an integrated high-throughput absolute abundance quantification (iHAAQ) method to better characterize soil quantitative bacterial community through combining the relative abundance (by high-throughput sequencing) and total bacterial quantities (by quantitative PCR). The proposed iHAAQ method was validated by an internal reference strain EDL933 and a laboratory strain WG5. Application of the iHAAQ method to a soil phenanthrene biodegradation study showed that for some bacterial taxa, the changes of relative and absolute abundances were coincident, while for others the changes were opposite. With the addition of a microbial activity inhibitor (NaN3), the absolute abundances of soil bacterial taxa, including several dominant genera of Bacillus, Flavobacterium, and Paenibacillus, decreased significantly, but their relative abundances increased after 28 days of incubation. We conclude that the iHAAQ method can offer more comprehensive information to reflect the dynamics of soil bacterial community with both relative and absolute abundances than the relative abundance from high-throughput sequencing alone.

show abstract

Section: Discussionmentioning

confidence: 85%

Section: Methodsmentioning

confidence: 99%

Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification

Lou

Yang

Wang

et al. 2018

PeerJ

Self Cite

View full text Add to dashboard Cite

show abstract

“…At the genus level, lime application increased beneficial microbial taxa, such as Massilia, Sphingomonas, and Pseudarthrobacter (Figure 3). Previous investigations have determined that Massilia was an efficient and environmentally friendly bioremediation material for polycyclic aromatic hydrocarbon degradation in soil [69]. Species of the Pseudarthrobacter genus can effectively degrade crude oil and multi-benzene compounds efficiently at low temperatures [70].…”

Section: Discussionmentioning

confidence: 99%

Liming Positively Modulates Microbial Community Composition and Function of Sugarcane Fields

et al. 2019

View full text Add to dashboard Cite

Liming combined with an optimum quantity of inorganic fertilizer, as a soil amendment in intensive agriculture, is a viable agricultural practice in terms of improving soil nutrient status and productivity, as well as mitigating soil degradation. The chief benefits of this strategy are fundamentally dependent on soil microbial function. However, we have limited knowledge about lime’s effects on soil microbiomes and their functions, nor on its comprehensive influence on soil nutrient status and the productivity of sugarcane plantations. This study compares the impacts of lime application (1-year lime (L1), 2-year lime (L2), and no lime (CK) on microbial communities, their functions, soil nutrient status, and crop yield in a sugarcane cropping system. We employed Illumina sequencing and functional analysis (PICRUSt and FUNGuild) to decipher microbial communities and functions. In comparison with CK, lime application (L1 and L2) mitigated soil acidity, increased the level of base cations (Ca2+ and Mg2+), and improved soil nutrient status (especially through N and P) as well as soil microbial functions associated with nutrient cycling and that are beneficial to plants, thereby improving plant agronomic parameters and yield. Liming (L1 and L2) increased species richness and stimulated an abundance of Acidobacteria and Chloroflexi compared to CK. In comparison with CK, the two functional categories related to metabolism (amino acid and carbohydrate) increased in the L1 field, whereas cofactors and vitamin metabolites increased in the L2 field. Turning to fungi, compared to CK, liming enriched symbiotrophs (endophytes, ectomycorrhizae, and arbuscular mycorrhizae) and led to a reduction of saprotrophs (Zygomycota and wood saprotrophs) and pathotrophs. The observed benefits of liming were, in turn, ultimately reflected in improved sugarcane agronomic performance, such as increased stalk height and weight in the sugarcane planting system. However, the increase in the above-mentioned parameters was more prominent in the L2 field compared to the L1 field, suggesting consecutive liming could be a practical approach in terms of sustainable production of sugarcane.

show abstract

“…Moreover, Massilia sp. WG5 can be applied for bioremediation in PHE-contaminated soil [50]. Additionally, Maya reported that the colonization of Massilia on seed coat, radicle, or roots protected against infection by the soil-borne plant pathogen Pythium aphanidermatum at the plant developmental stage [51].…”

Section: Discussionmentioning

confidence: 99%

Changes in soil bacterial community structure as a result of incorporation of Brassica plants compared with continuous planting eggplant and chemical disinfection in greenhouses

Liu

Zheng

et al. 2017

PLoS ONE

View full text Add to dashboard Cite

Greenhouse eggplant monocropping in China has contributed to the aggravation of soil-borne diseases, reductions in crop quality and yield, and the degradation of physical and chemical soil properties. Crop rotation is one effective way of alleviating the problems of continuous cropping worldwide; however, few studies have reported changes in soil bacterial community structures and physical and chemical soil properties after Brassica vegetables had been rotated with eggplant in greenhouses. In this experiment, mustard-eggplant (BFN) and oilseed rape-eggplant (BFC) rotations were studied to identify changes in the physicochemical properties and bacterial community structure in soil that was previously subject to monocropping. Samples were taken after two types of Brassica plants incorporated into soil for 15 days to compare with continually planted eggplant (control, CN) and chemical disinfection of soil (CF) in greenhouses. MiSeq pyrosequencing was used to analyze soil bacterial diversity and structure in the four different treatments. A total of 55,129 reads were identified, and rarefaction analysis showed that the soil treatments were equally sampled. The bacterial richness of the BFC treatment and the diversity of the BFN treatment were significantly higher than those of the other treatments. Further comparison showed that the bacterial community structures of BFC and BFN treatments were also different from CN and CF treatments. The relative abundance of several dominant bacterial genera in the BFC and BFN treatments (such as Flavobacteria, Stenotrophomonas, Massilia and Cellvibrio, which played different roles in improving soil fertility and advancing plant growth) was distinctly higher than the CN or CF treatments. Additionally, the total organic matter and Olsen-P content of the BFC and BFN treatments were significantly greater than the CN treatment. We conclude that Brassica vegetables-eggplant crop rotations could provide a more effective means of solving the problems of greenhouse eggplant monocultures.

show abstract

Complete genome sequence of Massilia sp. WG5, an efficient phenanthrene-degrading bacterium from soil

Cited by 35 publications

References 8 publications

Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification

Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification

Liming Positively Modulates Microbial Community Composition and Function of Sugarcane Fields

Changes in soil bacterial community structure as a result of incorporation of Brassica plants compared with continuous planting eggplant and chemical disinfection in greenhouses

Contact Info

Product

Resources

About