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The relationship between bacterial diversity and organic carbon mineralization in soft rock and sand compound soil
Zhen Guo , Juan Li , Lei Ge , Chenxi Yang , Jichang Han
J. Microbiol. 2020;58(9):750-760.   Published online July 24, 2020
DOI: https://doi.org/10.1007/s12275-020-0130-4
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AbstractAbstract
The soil organic carbon (SOC) mineralization rate in sandy soil plays an important role in improving soil quality, and a research is needed to determine management practices that optimize the mineralization rate. When sandy soil is improved by adding soft rock, the specific promotion process of bacterium to SOC mineralization remain unclear. To investigate these mechanisms, we selected four treatments with soft rock to sand volume ratios of 0:1 (CK), 1:5 (C1), 1:2 (C2) and 1:1 (C3) to study. The mineralization rate of organic carbon was measured using the lye absorption method. Highthroughput sequencing and scanning electron microscopy were used to determine the bacterial community structure and soil microstructure, respectively. The results showed that the organic carbon content of the sandy soil increased significantly (182.22–276.43%) after using the soft rock treatments. The SOC mineralization rate could be divided into two stages: a rapid decline during days 1–8 and a slow decline during days 8–60. With increased incubation time, the intensity of the cumulative release of organic carbon gradually weakened. Compared with the CK treatment, the SOC mineralization accumulation (Ct) and the potential mineralizable organic carbon content (C0) in the C1, C2, and C3 treatments increased significantly, by 106.98–225.94% and 112.22– 254.08%, respectively. The cumulative mineralization rate (Cr) was 18.11% and 21.38% smaller with treatments C2 and C3, respectively. The SOC mineralization rate constant (k) decreased significantly after the addition of soft rock, while the half-turnover period (Th) changed inversely with k. Compared with the CK treatment, the number of gene copies of the soil bacteria increased by 15.38–272.53% after adding soft rock, with the most significant increase in treatment C3. The bacterial diversity index also increased significantly under treatment C3. The three dominant bacteria were Proteobacteria, Actinobacteria, and Chloroflexi. The correlation between Cr and one of the non-dominant bacteria, Firmicutes, was large, and the bacteria had a significant positive correlation with k. At the same time, the abundance of Firmicutes under treatments C2 and C3 was small. As the proportion of soft rock increased, the soil particles changed from point contact to surface contact, and the adhesion on the surface of the particles gradually increased. Results from this study show that the retention time of SOC can be increased and the carbon sequestration effect is better when the ratio of soft rock to sand is set to 1:2.

Citations

Citations to this article as recorded by  
  • Siltation of check dams alters microbial communities and thus limits organic carbon mineralization
    Xiaojun Liu, Yi Zhang, Peng Li, Lie Xiao
    Soil and Tillage Research.2024; 236: 105949.     CrossRef
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    Wen-Qing Li, Zi-Jun Wu, Ying-Ying Zong, G. Geoff Wang, Fu-Sheng Chen, Yuan-Qiu Liu, Jian-Jun Li, Xiang-Min Fang
    Forest Ecology and Management.2022; 516: 120238.     CrossRef
  • Response of soil structure and crop yield to soft rock in Mu Us sandy land, China
    Jian Zhang, Zhen Guo
    Scientific Reports.2022;[Epub]     CrossRef
Reviews
MINIREVIEW] Bacterial persistence: Fundamentals and clinical importance
Sung-Hee Jung , Choong-Min Ryu , Jun-Seob Kim
J. Microbiol. 2019;57(10):829-835.   Published online August 28, 2019
DOI: https://doi.org/10.1007/s12275-019-9218-0
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AbstractAbstract
The threat of antibiotic-resistant bacteria is increasing worldwide. Bacteria utilize persistence and resistance to survive antibiotic stress. For a long time, persistence has been studied only under laboratory conditions. Hence, studies of bacterial persistence are limited. Recently, however, the high incidence of infection relapses caused by persister cells in immunocompromised patients has emphasized the importance of persister research. Furthermore, persister pathogens are one of the causes of chronic infectious diseases, leading to the overuse of antibiotics and the emergence of antibiotic-resistant bacteria. Therefore, understanding the precise mechanism of persister formation is important for continued use of available antibiotics. In this review, we aimed to provide an overview of the persister studies published to date and the current knowledge of persister formation mechanisms. Recent studies of the features and mechanisms of persister formation are analyzed from the perspective of the nature of the persister cell.

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REVIEW] Ribosome dependence of persister cell formation and resuscitation
Thomas K. Wood , Sooyeon Song , Ryota Yamasaki
J. Microbiol. 2019;57(3):213-219.   Published online February 26, 2019
DOI: https://doi.org/10.1007/s12275-019-8629-2
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  • 34 Web of Science
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AbstractAbstract
Since most bacterial cells are starving, they must enter a resting stage. Persister is the term used for metabolically-dormant cells that are not spores, and these cells arise from stress such as that from antibiotics as well as that from starvation. Because of their lack of metabolism, persister cells survive exposure to multiple stresses without undergoing genetic change; i.e., they have no inherited phenotype and behave as wild-type cells once the stress is removed and nutrients are presented. In contrast, mutations allow resistant bacteria to grow in the presence of antibiotics and slow growth allows tolerant cells to withstand higher concentrations of antibiotics; hence, there are three closely-related phenotypes: persistent, resistant, and tolerant. In addition, since dormancy is so prevalent, persister cells must have a means for resuscitating (since so many cells should obtain this resting state). In this review, we focus on what is known about the formation and resuscitation of persister cells.

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Journal Article
Metagenomic analysis reveals the prevalence and persistence of antibiotic- and heavy metal-resistance genes in wastewater treatment plant
Sachin Kumar Gupta , Hanseob Shin , Dukki Han , Hor-Gil Hur , Tatsuya Unno
J. Microbiol. 2018;56(6):408-415.   Published online June 1, 2018
DOI: https://doi.org/10.1007/s12275-018-8195-z
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AbstractAbstract
The increased antibiotic resistance among microorganisms has resulted into growing interest for investigating the wastewater treatment plants (WWTPs) as they are reported to be the major source in the dissemination of antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) in the environment. In this study, we investigated the prevalence and persistence of ARGs and HMRGs as well as bacterial diversity and mobile genetic elements (MGEs) in influent and effluent at the WWTP in Gwangju, South Korea, using high-throughput sequencing based metagenomic approach. A good number of broad-spectrum of resistance genes (both ARG and HMRG) were prevalent and likely persistent, although large portion of them were successfully removed at the wastewater treatment process. The relative abundance of ARGs and MGEs was higher in effluent as compared to that of influent. Our results suggest that the resistance genes with high abundance and bacteria harbouring ARGs and MGEs are likely to persist more through the treatment process. On analyzing the microbial community, the phylum Proteobacteria, especially potentially pathogenic species belonging to the genus Acinetobacter, dominated in WWTP. Overall, our study demonstrates that many ARGs and HMRGs may persist the treatment processes in WWTPs and their association to MGEs may contribute to the dissemination of resistance genes among microorganisms in the environment.

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Effect of Temperature on Persistence of Recombinant Plasmid pCU103 in Different Waters
Kwak, Myong Ja , Kim, Chi Kyung , Kim, Young Chang , Lim, Jae Yun , Kim, Young Soo , Lee, Ki Sung , Min, Kyung Hee
J. Microbiol. 1995;33(3):178-183.
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AbstractAbstract
The recombinant plasmid of pCU103 constructed by cloning pcbCD genes in pBluescript SK(+) was studied for the effect of temperature on its persistence in different waters by the methods of electrophoresis, Southern hybridization, quantification, and transformation. The plasmid was very rapidly degraded out in non-sterile FW water without regards to water temperature, probably due to the effect of biochemical factor such as nucleases. The pCU103 was most persistent at 4℃ in any water environments, moderately persistant at 15℃, but least stable at 30℃ such results could be explained by the facts that hydrogen bonds in double-stranded plasmid DNAs become unstable and that nucleases are activated by increasing temperature. The intact structure of pCU1-3 was generally observed by gel electrophoresis under the conditions which the plasmid should be 2.0 ng/㎕ or higher in concentration and that about 10² CFU/ml or more transformant cells should be recovered.
Structural and functional stability of the genetic recombinant plasmid pCU103 in different water environments
Kim, Chi Kyung , Kwak, Myoung Ja , Lee, Sung Gie
J. Microbiol. 1996;34(3):241-247.
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AbstractAbstract
The stbility of the genetically engineered microorganisms and their recombinant plasmids released in natural environments has been regarded as one of the molecular ecological topics. In this study, the recombinant plasmids pCU103 in which the pcbCD genes involved in biodegradation of biphenyl and 4-chlorobiphenyl were cloned in pBluescript SK(+) vector, were examined for their structural and functional stability in different waters at 15℃ by the methods of electrophoresis, Southern hybridization, quantification with fluorescent dye, and transformation. The recombinant plamids maintained their stabilities for about 30 days in sterilized distilled water (SDW), 15 days in autoclaved creek water (AW), 25 days in filtered and autoclaved non-sterible creek water (FAW), 4 days in Luria-Bertani (LB) broth, and less than one day in filtered non-sterile creek water (FW). The covalently closed circular (CCC) form of the plasmid was decreased and open circular (OC) form was increased as a function of incubation time, and then linear (L) form was produced to be ultimately degraded out. The degradation rates of the plasmid were proportionally correlated to trophic level of the water, and the biological factor such as DNases was found to be one of the most critical factors affecting structural and functional stability of the plasmid in non-sterile natural water.

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