Diversity and assembly of active bacteria and their potential function along soil aggregates in a paddy field

Ding, Chenxiao; Xu, Xinji; Liu, Yaowei; Huang, Xing; Xi, MengYuan; Liu, Haiyang; Dumont, Marc G.; Di, Hongjie; Hernández, Marcela; Xu, Jianming; Li, Yong

doi:10.1016/j.scitotenv.2022.161360

Cited by 5 publications

(3 citation statements)

References 136 publications

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“…The amplification of the cry 1 gene was observed in all B. thuringiensis spiked water and soil samples with Ct values ranging from 28 to 31. The lower assay efficiency in paddy field soil (89.3%) was observed as compared to the river water (103.6%) which could be due to the presence of PCR inhibitors in soil samples such as humic substances [ 36 , 38 ]. Moreover, no amplification was observed with total DNA isolated from unspiked water and soil which are the primary habitats of many micro and macroorganisms showing the high degree of specificity of developed multiplex assay S664 [ 39 , 40 ].…”

Section: Discussionmentioning

confidence: 99%

Development of a novel sequence based real-time PCR assay for specific and sensitive detection of Burkholderia pseudomallei in clinical and environmental matrices

Yadav,

Singh,

Paul

et al. 2024

Ann Clin Microbiol Antimicrob

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Background Melioidosis, caused by the category B biothreat agent Burkholderia pseudomallei, is a disease with a high mortality rate and requires an immediate culture-independent diagnosis for effective disease management. In this study, we developed a highly sensitive qPCR assay for specific detection of Burkholderia pseudomallei and melioidosis disease diagnosis based on a novel target sequence. Methods An extensive in-silico analysis was done to identify a novel and highly conserved sequence for developing a qPCR assay. The specificity of the developed assay was analyzed with 65 different bacterial cultures, and the analytical sensitivity of the assay was determined with the purified genomic DNA of B. pseudomallei. The applicability of the assay for B. pseudomallei detection in clinical and environmental matrices was evaluated by spiking B. pseudomallei cells in the blood, urine, soil, and water along with suitable internal controls. Results A novel 85-nucleotide-long sequence was identified using in-silico tools and employed for the development of the highly sensitive and specific quantitative real-time PCR assay S664. The assay S664 was found to be highly specific when evaluated with 65 different bacterial cultures related and non-related to B. pseudomallei. The assay was found to be highly sensitive, with a detection limit of 3 B. pseudomallei genome equivalent copies per qPCR reaction. The detection limit in clinical matrices was found to be 5 × 102 CFU/mL for both human blood and urine. In environmental matrices, the detection limit was found to be 5 × 101 CFU/mL of river water and 2 × 103 CFU/gm of paddy field soil. Conclusions The findings of the present study suggest that the developed assay S664 along with suitable internal controls has a huge diagnostic potential and can be successfully employed for specific, sensitive, and rapid molecular detection of B. pseudomallei in various clinical and environmental matrices.

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Section: Discussionmentioning

confidence: 99%

Development of a novel sequence based real-time PCR assay for specific and sensitive detection of Burkholderia pseudomallei in clinical and environmental matrices

Yadav,

Singh,

Paul

et al. 2024

Ann Clin Microbiol Antimicrob

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“…In actuality, soil microbes have been clocked with doubling times only as low as 7.2 h in the rhizosphere [33] and 14 to 45 days in bulk soil [34] (depicted in Figure 4 as rate of change per h). This suggests that reactivation of 42% [10] 55% [11] 91% [12] 25% [13] dormant cells largely contributed to the increase in active cells. With the same reasoning of a high rate of increase in active cells, dormant microbes were likely reactivating in the water treatment between 2-12 h (Figure 4).…”

Section: Glucose Amendment Reactivated Dormant Cellsmentioning

confidence: 93%

“…Early studies enumerating redox-active soil bacterial cells report active fractions of 5-20% or as low as 1% [7,4,8,9]. More recently, however, other methods have found over 40% [10], 50% [11], or 90% [12] active bacteria in soil samples. In a laboratory incubation study, transcriptionally active soil bacterial fraction increased from near zero to 15% after 48 h [13].…”

Section: Introductionmentioning

confidence: 99%

Translationally active soil microorganisms during substrate-induced respiration

Camillone,

Bruns,

Román

et al. 2023

Preprint

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Soil microorganisms carry out many biological functions that are fundamental to soil ecosystems; however, less than 2% of soil bacterial cells are commonly estimated to be active at any point in time. Substrate-induced respiration (SIR) measures community-level microbial activity as the bulk soil response to carbon substrate addition. We hypothesized that this bulk respiration rate is dependent on changes in the number of active cells. We incubated subsamples of an agricultural soil with 2 carbon substrate treatments and a third water-only treatment, and we periodically monitored respiration and active cell counts for 24 h. To enumerate active bacterial cells, we applied the novel Bioorthogonal Non-canonical Amino Acid Tagging (BONCAT) method. BONCAT provides a labeled amino acid for active cells to incorporate into newly synthesized proteins, and then a fluorescent dye enables enumeration of labeled cells by flow cytometry. Both respiration rates and active cell counts increased over time and were positively correlated with each other after 6 h of incubation. After 24 h, however, increases in active cells were more than proportional to increases in respiration. Additionally, carbon-amended soils had higher respiration rates than water-only soils with similar active cell counts, suggesting differences in carbon use efficiency. Our results indicate that number of translationally active bacteria is an important but not singular contributor to observed bulk soil respiration.IMPORTANCEWhile many critical ecosystem services provided by soil are known to fundamentally rely on microbial activity, the soil microbial community largely remains a black box. This study demonstrates that substrate-induced respiration is linked to the number of active cells. Advancing knowledge in this area will both enable better interpretation of biological soil tests by land managers and inform researchers modeling contributions of soil microbial respiration to global carbon dynamics.

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Metagenomic analysis reveals the effect of revegetation types on the function of soil microorganisms in carbon and nitrogen metabolism in the open-cast mining area

Zhang,

et al. 2024

Plant Soil

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AimsVegetation type is one of the most important factors contributing to the changes in soil properties during the rehabilitation process in mining areas. There is still insu cient awareness of the relationship between soil properties and the function of soil microbes in the carbon and nitrogen cycles under different revegetation type in uences. MethodsSeven reclaimed vegetation plots which has been restored for over 30 years in the Pingshuo opencast coal mine, China were established (RP: Robinia pseudoacacia, UP: Ulmus pumila, LG: Larix gmelinii, PC: Populus simonii Carr., PT: Pinus tabuliformis, PA: Picea asperata, and PS: Pinus sylvestris). The soil properties and enzyme activity were detected, while the metagenomic approach was used to analyze the potential mechanisms of soil microorganisms work in carbon and nitrogen metabolism. ResultsTotal N was obviously highest in the PC habitat (2.347 ± 0.017%), followed by RP (2.188 ± 0.059 %). The major facilitator Superfamily COG0477 and dehydrogenase the COG2133 were signi cantly enriched in the PR habitat. The acetolactate synthase COG0028 was signi cantly enriched in RP, followed by LG and PC (P < 0.05). β-glucosidase (EC3.2.1.21) were dominated in soil microbial communities among 7 vegetation types, and signi cantly richer in RP and LG, followed by PC and PT (P < 0.05). GTs and GHswere signi cantly richer in UP and LG, respectively. ConclusionRobinia pseudoacacia and Larix gmelinii may be good species choice for improving the productivity and stability of the soil ecosystem in mining areas. Highlights• The revegetation species affect soil nutrient conditions and enzyme activities.• COG0477, COG2133 and COG0028 are abundant in R. pseudoacacia habits.• β-glucosidase genes dominate among all of the revegetation habits.• R. pseudoacacia and L. gmelinii are excellent species for reclamation in mining area.

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Diversity and assembly of active bacteria and their potential function along soil aggregates in a paddy field

Cited by 5 publications

References 136 publications

Development of a novel sequence based real-time PCR assay for specific and sensitive detection of Burkholderia pseudomallei in clinical and environmental matrices

Development of a novel sequence based real-time PCR assay for specific and sensitive detection of Burkholderia pseudomallei in clinical and environmental matrices

Translationally active soil microorganisms during substrate-induced respiration

Metagenomic analysis reveals the effect of revegetation types on the function of soil microorganisms in carbon and nitrogen metabolism in the open-cast mining area

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