• Title/Summary/Keyword: soil microbiology

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Report of Eight Unrecorded Fungi from the Fire Blight Burial Control Soil in Korea (과수화상병 매몰방재지 토양에서 분리된 8종의 국내 미기록 진균 보고)

  • Hyeongjin Noh;Huiju Seo;Seong Hwan Kim
    • The Korean Journal of Mycology
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    • v.51 no.4
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    • pp.447-460
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    • 2023
  • Fire blight, a plant disease caused by Erwinia amylovora, continues to cause considerable damage to fruit-bearing trees belonging to the Rosaceae family, such as apples and pears. In Korea, to hinder its rapid spread diseased apple and pear trees have been buried since its first occurrence. To determine the safety of this control method, the buried plant materials and adjacent soil have been investigated. In the process of investigating the microbiota of the buried soil, Bisifusarium allantoides, Botryotrichum domesticum, Microascus verrucosus, Paraphoma pye, Phaeosphaeria culmorum, Ramophialophora globispora, Sordaria tomentoalba, and Striaticonidium brachysporum were identified as unrecorded species in Korea. To report the above eight species as Korean unrecorded species, we report their morphological and molecular features in this study.

Changes in Resident Soil Bacterial Communities in Response to Inoculation of Soil with Beneficial Bacillus spp. (유용한 바실러스의 토양 접종에 따른 토착 세균 군집의 변화)

  • Kim, Yiseul;Kim, Sang Yoon;An, Ju Hee;Sang, Mee Kyung;Weon, Hang-Yeon;Song, Jaekyeong
    • Microbiology and Biotechnology Letters
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    • v.46 no.3
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    • pp.253-260
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    • 2018
  • Beneficial microorganisms are widely used in the forestry, livestock, and, in particular, agricultural sectors to control soilborne diseases and promote plant growth. However, the industrial utilization of these microorganisms is very limited, mainly due to uncertainty concerning their ability to colonize and persist in soil. In this study, the survival of beneficial microorganisms in field soil microcosms was investigated for 13 days using quantitative PCR with B. subtilis group-specific primers. Bacterial community dynamics of the treated soils were analyzed using 16S ribosomal RNA (rRNA) gene amplicon sequencing on the Illumina MiSeq platform. The average 16S rRNA gene copy number per g dry soil of Bacillus spp. was $4.37{\times}10^6$ after treatment, which was 1,000 times higher than that of the control. The gene copy number was generally maintained for a week and was reduced thereafter, but remained 100 times higher than that of the control. Bacterial community analysis indicated that Acidobacteria ($26.3{\pm}0.9%$), Proteobacteria ($24.2{\pm}0.5%$), Chloroflexi ($11.1{\pm}0.4%$), and Actinobacteria ($9.7{\pm}2.5%$) were abundant phyla in both treated and non-treated soils. In the treated soils, the relative abundance of Actinobacteria was lower, whereas those of Bacteroidetes and Firmicutes were higher compared to the control. Differences in total relative abundances of operational taxonomic units belonging to several genera were observed between the treated and non-treated soils, suggesting that inoculation of soil with the Bacillus strains influenced the relative abundances of certain groups of bacteria and, therefore, the dynamics of resident bacterial communities. These changes in resident soil bacterial communities in response to inoculation of soil with beneficial Bacillus spp. provide important information for the use of beneficial microorganisms in soil for sustainable agriculture.

Isolation and Identification of Opportunist Mycobacteria and Nocardia from Soil Specimens of School Ground in Seoul City (서울시내(布內) 초중고등학교(初中高等學校) 토양(土壤)으로부터 비정형(非定型) Mycobacteria와 Nocardia의 분리(分離) 및 생화학적(生化學的) 동정(同定))

  • Choi, Chul-Soon;Yang, Yong-Tae
    • The Journal of the Korean Society for Microbiology
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    • v.11 no.1
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    • pp.69-78
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    • 1976
  • There have been increasing reports of mycobacterioses in man and animals caused by "atypical" or "opportunist" mycobacteria. At the presnt, "opportunist mycobacterioses" are not generally responsive to antituberculosis drugs, and therefore, create considerable problems with regard to chemotherapy and control measures. In recent years studies have been made to isolate opportunist mycobacteria from soil, house-dusts and tap-water. It seemed quite interesting to define the extent of circumstantial presence of "opportunist" mycobacteria and nocardia in the soils of school-ground of primary schools and middle-high schools. This communication is the results of pilot study to isolate and identify "opportunist" mycobacteria and nocardia from 504 soil specimens of 72 schools in Seoul City. 1. Of a total of 59 isolates from 504 soil specimens tested, 32 strains were identified as opportunist mycobacteria and 27 strains as nocardia. 2. Isolation rates of opportunist mycobacteria by the areas(of specimen collection) were as follows: 36.4% in the southern area of Han-River, 33.3% in the central area, 22.7% in the outskirt area and 16.6% in the intermediate area. There observed no apparent difference in the isolation rates both-between the areas and between primary schools and middle-high schools. However, a significant difference was noted in the isolation rates between the places of soil sampling in a given school(P<0.05), i.e., the highest was the soil of refuge heaps(15.2%), and tap-water pole area(11.1%), the school-lavatory entrance(9.7%), the school gate entrance(5.5%), and iron-bar play ground(2.7%). The soil specimens from the center of school ground and from school building entrance yielded none of mycobacterial isolates. 3. Isolation rates of nocardia by the areas were as follows: 33.3% in the central area, 31.8% in the outskirt area, 27.3% in the southern ares of Han-River and 11.1% in the intermediate area. As in the case of mycobacteral isolates, there observed no apparent differences in the isolation rates both between the areas and between primary schools and middle-high schools, but a significant difference was noted between the places of soil sampling(P<0.05), i.e., the highest was the soil of school building entrance(15.2%), and of school gate entrance(6.9%), refuge heaps(5.5,%), iron-bar play ground(4.1%), the school-lavatory entrance(2.7%) and tap-water pole area(2.7%), respectively. The soil specimens from the center of, school ground yielded none of nocardia isolates. 4. Of the 32 strains of isolated mycobacteria. 15 strains were slow-growing mycobacteria and the remaining 17 strains belonged to the rapid growers. Of the 15 slow-growers. 4 strains were M. scrofulaceum-szulgai complex, 3 M. gordonae, 4 M. terrae-triviale complex, 2 M. avium-intracellulare-xenopi complex, and 2 unclassified schotochromogens. Of the 17 strains of rapid growers, 12 were M. diernhoferi, 2 M. fortuitum-peregrinum complex, 2 M. vaccae and one M. flavescens. 5. Of the 27 strains of nocardia isolated, 11 strains were N. transvalensis, 5 N. convoluta, 5 N. erythropolis, one N. vaccinii, one N. polychromogens-paraffinae complex and 4 untypable strains of orange-pigmented nocardia spp.

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Effects of Short-Term Soil Tillage Management on Activity and Community Structure of Denitrifiers under Double-Cropping Rice Field

  • Tang, Haiming;Li, Chao;Cheng, Kaikai;Shi, Lihong;Wen, Li;Xiao, Xiaoping;Xu, Yilan;Li, Weiyan;Wang, Ke
    • Journal of Microbiology and Biotechnology
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    • v.30 no.11
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    • pp.1688-1696
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    • 2020
  • Soil physical and chemical characteristics, soil potential denitrification rates (PDR), community composition and nirK-, nirS- and nosZ-encoding denitrifiers were studied by using MiSeq sequencing, quantitative polymerase chain reaction (qPCR), and terminal restriction fragment polymorphism (T-RFLP) technologies base on short-term (5-year) tillage field experiment. The experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue retention (NT), and rotary tillage with crop residue removed as control (RTO). The results indicated that soil organic carbon, total nitrogen and NH4+-N contents were increased with CT, RT and NT treatments. Compared with RTO treatment, the copies number of nirK, nirS and nosZ in paddy soil with CT, RT and NT treatments were significantly increased. The principal coordinate analysis indicated that tillage management and crop residue returning management were the most and the second important factors for the change of denitrifying bacteria community, respectively. Meanwhile, this study indicated that activity and community composition of denitrifiers with CT, RT and NT treatments were increased, compared with RTO treatment. This result showed that nirK, nirS and nosZ-type denitrifiers communities in crop residue applied soil had higher species diversity compared with crop residue removed soil, and denitrifying bacteria community composition were dominated by Gammaproteobacteria, Deltaproteobacteria, and Betaproteobacteria. Therefore, it is a beneficial practice to increase soil PDR level, abundance and community composition of nitrogen-functional soil microorganism by combined application of tillage with crop residue management.

Bacillus subtilis as a Tool for Screening Soil Metagenomic Libraries for Antimicrobial Activities

  • Biver, Sophie;Steels, Sebastien;Portetelle, Daniel;Vandenbol, Micheline
    • Journal of Microbiology and Biotechnology
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    • v.23 no.6
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    • pp.850-855
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    • 2013
  • Finding new antimicrobial activities by functional metagenomics has been shown to depend on the heterologous host used to express the foreign DNA. Therefore, efforts are devoted to developing new tools for constructing metagenomic libraries in shuttle vectors replicatable in phylogenetically distinct hosts. Here we evaluated the use of the Escherichia coli-Bacillus subtilis shuttle vector pHT01 to construct a forest-soil metagenomic library. This library was screened in both hosts for antimicrobial activities against four opportunistic bacteria: Proteus vulgaris, Bacillus cereus, Staphylococcus epidermidis, and Micrococcus luteus. A new antibacterial activity against B. cereus was found upon screening in B. subtilis. The new antimicrobial agent, sensitive to proteinase K, was not active when the corresponding DNA fragment was expressed in E. coli. Our results validate the use of pHT01 as a shuttle vector and B. subtilis as a host to isolate new activities by functional metagenomics.