Journal of Microbiology

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Delineating the Acquired Genetic Diversity and Multidrug Resistance in Alcaligenes from Poultry Farms and Nearby Soil: Abhilash Bhattacharjee, Anil Kumar Singh; J. Microbiol. 2024;62(7):511-523. Published online June 21, 2024; DOI: https://doi.org/10.1007/s12275-024-00129-w

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Abstract: Alcaligenes faecalis is one of the most important and clinically significant environmental pathogens, increasing in importance due to its isolation from soil and nosocomial environments. The Gram-negative soil bacterium is associated with skin endocarditis, bacteremia, dysentery, meningitis, endophthalmitis, urinary tract infections, and pneumonia in patients. With emerging antibiotic resistance in A. faecalis, it has become crucial to understand the origin of such resistance genes within this clinically significant environmental and gut bacterium. In this research, we studied the impact of antibiotic overuse in poultry and its effect on developing resistance in A. faecalis. We sampled soil and faecal materials from five poultry farms, performed whole genome sequencing & analysis and identified four strains of A. faecalis. Furthermore, we characterized the genes in the genomic islands of A. faecalis isolates. We found four multidrug-resistant A. faecalis strains that showed resistance against vancomycin (MIC >1000 μg/ml), ceftazidime (50 μg/ml), colistin (50 μg/ml) and ciprofloxacin (50 μg/ml). From whole genome comparative analysis, we found more than 180 resistance genes compared to the reference sequence. Parts of our assembled contigs were found to be similar to different bacteria which included pbp1A and pbp2 imparting resistance to amoxicillin originally a part of Helicobacter and Bordetella pertussis. We also found the Mycobacterial insertion element IS6110 in the genomic islands of all four genomes. This prominent insertion element can be transferred and induce resistance to other bacterial genomes. The results thus are crucial in understanding the transfer of resistance genes in the environment and can help in developing regimes for antibiotic use in the food and poultry industry.

Relationship Between Mycotoxin Production and Gene Expression in Fusarium graminearum Species Complex Strains Under Various Environmental Conditions: Wenwen Huang , Ping Zhou , Guanghui Shen , Tao Gao , Xin Liu , Jianrong Shi , Jianhong Xu , Jianbo Qiu; J. Microbiol. 2023;61(5):525-542. Published online May 2, 2023; DOI: https://doi.org/10.1007/s12275-023-00046-4

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The Fusarium graminearum species complex (FGSC) can produce various mycotoxins and is a major concern for food quantity and quality worldwide. In this study, we determined the effects of water activity ( aw), temperature, incubation time and their interactions on mycotoxin accumulation and the expression levels of biosynthetic genes in FGSC strains from maize samples in China. The highest deoxynivalenol (DON), 3-acetyldeoxynivalenol(3ADON) and 15-acetyldeoxynivalenol (15ADON) levels of the F. boothii and F. graminearum strains were observed at 0.98 aw/ 30 °C or 0.99 aw/ 25 °C. F. asiaticum and F. meridionale reached maximum nivalenol (NIV) and 4-acetylnivalenol (4ANIV) contents at 0.99 aw and 30 °C. With the extension of the incubation time, the concentrations of DON and NIV gradually increased, while those of their derivatives decreased. F. boothii, F. meridionale and one F. asiaticum strain had the highest zearalenone (ZEN) values at 0.95 aw and 25 °C, while the optimum conditions for the other F. asiaticum strain and F. graminearum were 0.99 aw and 30 °C. Four genes associated with trichothecene and zearalenone synthesis were significantly induced under higher water stress in the early stage of production. The results indicated independence of mycotoxin production and gene expression, as maximum amounts of these toxic metabolites were observed at higher aw in most cases. This study provides useful information for the monitoring and prevention of such toxins entering the maize production chain.

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Application of MOX Sensors to Determine the Emission of Volatile Compounds in Corn Groats as a Function of Vertical Pressure in the Silo and Moisture Content of the Bed
Robert Rusinek, Aleksandra Żytek, Mateusz Stasiak, Joanna Wiącek, Marek Gancarz
Sensors.2024; 24(7): 2187. CrossRef

Description of Fervidibacillus gen. nov. with Two Species, Fervidibacillus albus sp. nov., and Fervidibacillus halotolerans sp. nov., Isolated from Tidal Flat Sediments and Emendation of Misclassificed Taxa in the Genus Caldibacillus: Sung&# , Mi&# , Hyun&# , Kae Kyoung Kwon; J. Microbiol. 2023;61(2):175-187. Published online February 17, 2023; DOI: https://doi.org/10.1007/s12275-023-00022-y

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Abstract

Two Gram-stain-positive, motile, endospore-forming, facultatively anaerobic strains, designated MEBiC13591T and MEBiC13594T, were isolated from tidal flat sediment of the Incheon City on the west coast of Korea. Growth of both novel strains was observed at pH 5–9 (optimum, pH 7–7.5), and in 0–8% NaCl (optimum, 2% for MEBiC13591T and 3% for MEBiC13594T). Strains MEBiC13591T and MEBiC13594T grew optimally at 50 °C, (37.5–56.1 °C) and 44 °C (20.7–50.7 °C), respectively. The main cellular fatty acids of strain MEBiC13591T were iso-C15: 0, anteiso-C15: 0, iso-C16: 0, iso-C17: 0 and anteiso-C17: 0, while those for strain MEBiC13594T were C14: 0, iso-C14: 0, iso-C15: 0, anteiso-C15: 0 and C16: 0. In both taxa, the major isoprenoid was MK-7. The genomic DNA G + C contents were 34.1 and 37.0 mol% for MEBiC13591T and MEBiC13594T, respectively. A 16S rRNA gene sequence analysis revealed that the novel strains showed high similarity with members of the genera Aeribacillus (95.0%) and Caldibacillus (93.5–94.5%); however, showed lower than 90% with Caldibacillus debilis TfT. Phylogenetic and Phylogenomic analysis revealed that two novel strains comprised distinct phyletic line with members formerly assigned to Caldibacillus. Based on genomic indices, such as AAI and ANI, members formerly affiliated with Caldibacillus and Bacillus as well as the novel strains should be classified into five independent genera. Based on the phenotypic, genomic and biochemical data, strains MEBiC13591T and MEBiC13594T represent two novel species in the novel genus, for which the names Fervidibacillus albus gen. nov., sp. nov. ( MEBiC13591T [= KCCM 43317T = KCTC 43181T = JCM 33662T = MCCC 1K04565T]), and Fervidibacillus halotolerans sp. nov. ( MEBiC13594T [= KCTC 43182T = JCM 34001T]) are proposed. Three additional genera Caldifermentibacillus, Palidibacillus, and Perspicuibacillus are also proposed by reclassification of the several species with valid names that formerly affiliated with the genera Caldibacillus.

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An update on novel taxa and revised taxonomic status of bacteria isolated from domestic companion and agricultural animals described in 2023
Sara D. Lawhon, Claire R. Burbick, Trinity Krueger, Elena Ruiz-Reyes, Erik Munson, Romney M. Humphries
Journal of Clinical Microbiology.2024;[Epub] CrossRef
Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter
Hyeonsu Tak, Miri S. Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho
Journal of Microbiology.2024; 62(9): 739. CrossRef
Validation List no. 213. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef

Variations in bacterial and fungal communities through soil depth profiles in a Betula albosinensis forest: Can Du , Zengchao Geng , Qiang Wang , Tongtong Zhang , Wenxiang He , Lin Hou , Yueling Wang; J. Microbiol. 2017;55(9):684-693. Published online September 2, 2017; DOI: https://doi.org/10.1007/s12275-017-6466-8

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Abstract

Microbial communities in subsurface soil are specialized for their environment, which is distinct from that of the surface communities. However, little is known about the microbial communities (bacteria and fungi) that exist in the deeper soil horizons. Vertical changes in microbial alpha-diversity (Chao1 and Shannon indices) and community composition were investigated at four soil depths (0–10, 10–20, 20–40, and 40–60 cm) in a natural secondary forest of Betula albosinensis by high-throughput sequencing of the 16S and internal transcribed spacer rDNA regions. The numbers of operational taxonomic units (OTUs), and the Chao1 and Shannon indices decreased in the deeper soil layers. Each soil layer contained both mutual and specific OTUs. In the 40–60 cm soil layer, 175 and 235 specific bacterial and fungal OTUs were identified, respectively. Acidobacteria was the most dominant bacterial group in all four soil layers, but reached its maximum at 40–60 cm (62.88%). In particular, the 40–60 cm soil layer typically showed the highest abundance of the fungal genus Inocybe (47.46%). The Chao1 and Shannon indices were significantly correlated with the soil organic carbon content. Redundancy analysis indicated that the bacterial communities were closely correlated with soil organic carbon content (P = 0.001). Collectively, these results indicate that soil nutrients alter the microbial diversity and relative abundance and affect the microbial composition.

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Deciphering mycobiota and its functional dynamics in root hairs of Rhododendron campanulatum D. Don through Next-gen sequencing
Nafeesa Farooq Khan, Sheikh Sajad Ahmed, Mukhtar Iderawumi Abdulraheem, Zafar Ahmad Reshi, Abdul Wahab, Gholamreza Abdi
Scientific Reports.2024;[Epub] CrossRef
Fungal diversity and key functional gene abundance in Iowa bioretention cells: implications for stormwater remediation potential
Erica A. Wiener, Jessica M. Ewald, Gregory H. LeFevre
Environmental Science: Processes & Impacts.2024; 26(10): 1796. CrossRef
Lifting the Profile of Deep Forest Soil Carbon
Loretta G. Garrett, Alexa K. Byers, Kathryn Wigley, Katherine A. Heckman, Jeff A. Hatten, Steve A. Wakelin
Soil Systems.2024; 8(4): 105. CrossRef
Interactions of soil nutrients and microbial communities during root decomposition of gramineous and leguminous forages
Can Ma, Xiuru Wang, Jianjia Wang, Xiaoyue Zhu, Chao Qin, Ye Zeng, Wenlong Zhen, Yan Fang, Zhouping Shangguan
Land Degradation & Development.2023; 34(11): 3250. CrossRef
Distribution of microbial communities in seasonally frozen soil layers on the Tibetan Plateau and the driving environmental factors
Xiaojie Wang, Zhiqiang Yu, Guofeng Shen, Hefa Cheng, Shu Tao
Environmental Science and Pollution Research.2023; 30(1): 1919. CrossRef
Vertical Distribution of Soil Bacterial Communities in Different Forest Types Along an Elevation Gradient
Qiuxiang Tian, Qinghu Jiang, Lin Huang, Dong Li, Qiaoling Lin, Zhiyao Tang, Feng Liu
Microbial Ecology.2023; 85(2): 628. CrossRef
Rhizobacterial compositions and their relationships with soil properties and medicinal bioactive ingredients in Cinnamomum migao
Lixia Li, Xuedong Yang, Bingli Tong, Deng Wang, Xiu Tian, Jiming Liu, Jingzhong Chen, Xuefeng Xiao, Shu Wang
Frontiers in Microbiology.2023;[Epub] CrossRef
The vertical distribution and control factor of microbial biomass and bacterial community at macroecological scales
Libing He, Xiangyang Sun, Suyan Li, Wenzhi Zhou, Zhe Chen, Xueting Bai
Science of The Total Environment.2023; 869: 161754. CrossRef
Distribution of soil microorganisms in different complex soil layers in Mu Us sandy land
Zhen Guo, Haiou Zhang, Juan Li, Tianqing Chen, Huanyuan Wang, Yang Zhang, Tunira Bhadauria
PLOS ONE.2023; 18(4): e0283341. CrossRef
Diversity and structure of soil fungal communities unveil the building history of a burial mound of ancient Japan (Tobiotsuka Kofun, Okayama Prefecture)
Samuele Voyron, Chiara Tonon, Laura Guglielmone, Luisella Celi, Cesare Comina, Hajime Ikeda, Naoko Matsumoto, Daniele Petrella, Joseph Ryan, Kazuhiro Sato, Akira Seike, Ivan Varriale, Jun Yamashita, Sergio E. Favero-Longo, Eleonora Bonifacio
Journal of Archaeological Science.2022; 146: 105656. CrossRef
Variations of rhizosphere and bulk soil microbial community in successive planting of Chinese fir (Cunninghamia lanceolata)
Jiachen Chen, Zhifang Deng, Zheng Jiang, Jin Sun, Fangfang Meng, Xiaodong Zuo, Linkun Wu, Guangqiu Cao, Shijiang Cao
Frontiers in Plant Science.2022;[Epub] CrossRef
Soil Fungal Community and Potential Function in Different Forest Ecosystems
Xiaoli Li, Zhaolei Qu, Yuemei Zhang, Yan Ge, Hui Sun
Diversity.2022; 14(7): 520. CrossRef
Interactions of Soil Nutrients and Soil Microbial Communities During Root Decomposition of Gramineous and Leguminous Forages
Can Ma, Xiaoyue Zhu, Xiuru Wang, Jianjia Wang, Chao Qin, Zeng Ye, Wenlong Zhen, Yan Fang, Zhouping Shangguan
SSRN Electronic Journal .2022;[Epub] CrossRef
Effects of soft rock on soil properties and bacterial community in Mu Us Sandy Land, China
Zhen Guo, Wei Hui, Juan Li, Chenxi Yang, Haiou Zhang, Huanyuan Wang
PeerJ.2022; 10: e13561. CrossRef
Diversity of root-associated mycobiome of Betula utilis D. Don: a treeline species in Kashmir Himalaya
Nafeesa Farooq Khan, Zafar Ahmad Reshi
Tropical Ecology.2022; 63(4): 531. CrossRef
The divergent vertical pattern and assembly of soil bacterial and fungal communities in response to short-term warming in an alpine peatland
Xiaodong Wang, Yong Li, Zhongqing Yan, Yanbin Hao, Enze Kang, Xiaodong Zhang, Meng Li, Kerou Zhang, Liang Yan, Ao Yang, Yuechuan Niu, Xiaoming Kang
Frontiers in Plant Science.2022;[Epub] CrossRef
Trends in Microbial Community Composition and Function by Soil Depth
Dan Naylor, Ryan McClure, Janet Jansson
Microorganisms.2022; 10(3): 540. CrossRef
Effects of Tree Composition and Soil Depth on Structure and Functionality of Belowground Microbial Communities in Temperate European Forests
Luis Daniel Prada-Salcedo, Juan Pablo Prada-Salcedo, Anna Heintz-Buschart, François Buscot, Kezia Goldmann
Frontiers in Microbiology.2022;[Epub] CrossRef
Responses of N-Cycling Enzyme Activities and Functional Diversity of Soil Microorganisms to Soil Depth, Pedogenic Processes and Cultivated Plants
Anna Piotrowska-Długosz, Jacek Długosz, Agata Gryta, Magdalena Frąc
Agronomy.2022; 12(2): 264. CrossRef
Characteristics of water extractable organic carbon fractions in the soil profiles of Picea asperata and Betula albosinensis forests
Zhikang Wang, Jiawei Ren, Chenyang Xu, Zengchao Geng, Xuguang Du, Yan Li
Journal of Soils and Sediments.2021; 21(11): 3580. CrossRef
Soil depth matters: shift in composition and inter-kingdom co-occurrence patterns of microorganisms in forest soils
Sunil Mundra, O Janne Kjønaas, Luis N Morgado, Anders Kristian Krabberød, Yngvild Ransedokken, Håvard Kauserud
FEMS Microbiology Ecology.2021;[Epub] CrossRef
Undisturbed Soil Pedon under Birch Forest: Characterization of Microbiome in Genetic Horizons
Natalia B. Naumova, Ivan P. Belanov, Tatiana Y. Alikina, Marsel R. Kabilov
Soil Systems.2021; 5(1): 14. CrossRef
Soil microbial communities and their relationships to soil properties at different depths in an alpine meadow and desert grassland in the Qilian mountain range of China
Baotian Kang, Saman Bowatte, Fujiang Hou
Journal of Arid Environments.2021; 184: 104316. CrossRef
Soil pH and Organic Carbon Properties Drive Soil Bacterial Communities in Surface and Deep Layers Along an Elevational Gradient
Qiuxiang Tian, Ying Jiang, Yanan Tang, Yu Wu, Zhiyao Tang, Feng Liu
Frontiers in Microbiology.2021;[Epub] CrossRef
Dynamics of Soil Nutrients, Microbial Community Structure, Enzymatic Activity, and Their Relationships along a Chronosequence of Pinus massoniana Plantations
Jinwen Pan, Qiqiang Guo, Huie Li, Siqiong Luo, Yaqin Zhang, Shan Yao, Xin Fan, Xueguang Sun, Yujiao Qi
Forests.2021; 12(3): 376. CrossRef
Fungal Community Composition and Diversity Vary With Soil Horizons in a Subtropical Forest
Xia Luo, Kezhong Liu, Yuyu Shen, Guojing Yao, Wenguang Yang, Peter E. Mortimer, Heng Gui
Frontiers in Microbiology.2021;[Epub] CrossRef
Deep Soil Layers of Drought-Exposed Forests Harbor Poorly Known Bacterial and Fungal Communities
Beat Frey, Lorenz Walthert, Carla Perez-Mon, Beat Stierli, Roger Köchli, Alexander Dharmarajah, Ivano Brunner
Frontiers in Microbiology.2021;[Epub] CrossRef
Root associated fungi respond more strongly than rhizosphere soil fungi to N fertilization in a boreal forest
Srisailam Marupakula, Shahid Mahmood, Karina E. Clemmensen, Staffan Jacobson, Lars Högbom, Roger D. Finlay
Science of The Total Environment.2021; 766: 142597. CrossRef
Soil microbiome after nine years of fly ash dump spontaneous revegetation
Natalia Naumova, Ivan Belanov, Tatiana Alikina, Marsel Kabilov
Soil Research.2021; 59(7): 673. CrossRef
Vertical changes in bacterial community composition down to a depth of 20 m on the degraded Loess Plateau in China
Guiyao Liu, Lili Chen, Qiang Deng, Xinrong Shi, Thomas Ryan Lock, Robert L. Kallenbach, Zhiyou Yuan
Land Degradation & Development.2020; 31(10): 1300. CrossRef
Microbial communities and soil chemical features associated with commercial production of the medicinal mushroom Ganoderma lingzhi in soil
Le-Qin Ke, Pu-Dong Li, Jian-Ping Xu, Qiu-Shuang Wang, Liang-Liang Wang, Hui-Ping Wen
Scientific Reports.2019;[Epub] CrossRef
Ginkgo agroforestry practices alter the fungal community structures at different soil depths in Eastern China
Jing Guo, Guibin Wang, Yaqiong Wu, Yuanbao Shi, Yu Feng, Fuliang Cao
Environmental Science and Pollution Research.2019; 26(21): 21253. CrossRef

Research Support, Non-U.S. Gov't

Effects of Crude Oil on Marine Microbial Communities in Short Term Outdoor Microcosms: Seung Won Jung , Joon Sang Park , Oh Youn Kown , Jung-Hoon Kang , Won Joon Shim , Young-Ok Kim; J. Microbiol. 2010;48(5):594-600. Published online November 3, 2010; DOI: https://doi.org/10.1007/s12275-010-0199-2

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Abstract: To assess the effects of crude oil spills on marine microbial communities, 10 L outdoor microcosms were manipulated over an exposure period of 8 days. The responses of microbial organisms exposed to five crude oil concentrations in 10 to 10,000 ppm (v/v) were monitored in the microcosms. The abundance of microalgae and copepods decreased rapidly upon the addition of crude oil at concentrations over 1,000 ppm, whereas the total density of heterotrophic bacteria increased dramatically at the higher concentrations. Bacterial diversity, determined by denaturing gradient gel electrophoresis, was increased at higher concentrations. In particular, the intensity of the bands representing Jannaschia sp. and Sulfitobacter brevis increased with the addition of oil. These results indicate that crude oil spills with concentrations over 1,000 ppm seriously affected the structure of the microbial communities.

Response of sheep rumen fermentation and microbial communities to feed infected with the endophyte Epichloë gansuensis as evaluated with rumen-simulating technology: Yaling Ma , Hucheng Wang , Chunjie Li; J. Microbiol. 2021;59(8):719-728.; DOI: https://doi.org/10.1007/s12275-021-1113-9

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Abstract

Achnatherum inebrians, a perennial grass, is widely distributed in China. When infected by the endophyte Epichloë gansuensis, A. inebrians produces an abundance of alkaloids that enhance plant survival but are toxic to animals. Here we used in vitro fermentation to study the impact of endophyte- infected A. inebrians (E+) addition on rumen fermentation characteristics and on microbial community and diversity as assessed with amplicon sequencing technology. We examined E+ addition at five levels, E0, E25, E50, E75, and E100, corresponding to 0%, 25%, 50%, 75%, and 100% of the fermentation substrate, respectively. Both the fermentation characteristics and rumen microbial community structure differed significantly among treatments. E100 resulted in the highest values for pH, the Shannon index, Kiritimatiellaeota, and Lentisphaerae levels relative to the other treatments. In contrast, E25 was associated with higher levels of ammonia nitrogen, total volatile fatty acid, propionate, butyrate, isobutyrate, valerate, of the phyla Bacteroidetes and Firmicutes, and of the genus Prevotella_1, Succiniclasticum, Family_XIII_AD3011_group, Rikenellaceae_RC9_gut_group, Prevotellaceae_UCG-001, and Pyramidobacter as compared with other treatments. E50 resulted in the greatest values for the abundance-based coverage estimator (ACE) and the Chao1 index as compared with other treatments. E0 resulted in the greatest values for digestibility of dry matter, gas production, acetate, and Ruminobacter as compared with other treatments. This approach avoided animal toxicity experiments and confirmed that rumen fermentation characteristics and rumen microbiota were affected by E+ toxin. Therefore, E25 showed higher abundance in Prevotella_1, Prevotellaceae_ UCG-001, and Lachnospiraceae_XPB1014_group that implied they should play significant roles in E+ alkaloids degradation. And then, we can infer that rumen microorganisms should function as an antidote with respect to this poisoning reaction at moderate dietary percentages of E+.

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Effect of Potato Vine and Leaf Mixed Silage to Whole Corn Crops on Rumen Fermentation and the Microbe of Fatten Angus Bulls
Siyu Zhang, Jiajie Deng, Yafang Cui, Lina Wang, Yingqi Li, Xianli Wang, Shengnan Min, Huili Wang, Qianzi Zhang, Peiqi Li, Yawen Luo, Xinjun Qiu, Yang He, Binghai Cao, Huawei Su
Fermentation.2023; 9(8): 704. CrossRef
Yeast (Saccharomyces cerevisiae) Culture Promotes the Performance of Fattening Sheep by Enhancing Nutrients Digestibility and Rumen Development
Jie Wang, Guohong Zhao, Yimin Zhuang, Jianmin Chai, Naifeng Zhang
Fermentation.2022; 8(12): 719. CrossRef
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Ming Deng, Zupeng Xiao, Guangbin Liu, Baoli Sun, Yongqing Guo, Xian Zou, Dewu Liu, Zhenwei Yang, Yaokun Li
Frontiers in Microbiology.2022;[Epub] CrossRef
The Potential Use of Endophyte-Free inebrians as Sheep Feed Evaluated with In Vitro Fermentation
Yaling Ma, Hucheng Wang, Chunjie Li, Kamran Malik
Fermentation.2022; 8(9): 419. CrossRef

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