Journal of Microbiology

Journal Articles

Temporal and spatial impact of Spartina alterniflora invasion on methanogens community in Chongming Island, China: Xue Ping Chen , Jing Sun , Yi Wang , Heng Yang Zhang , Chi Quan He , Xiao Yan Liu , Nai Shun Bu , Xi-En Long; J. Microbiol. 2018;56(7):507-515. Published online June 14, 2018; DOI: https://doi.org/10.1007/s12275-018-8062-y

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Methane production by methanogens in wetland is recognized as a significant contributor to global warming. Spartina alterniflora (S. alterniflora), which is an invasion plant in China’s wetland, was reported to have enormous effects on methane production. But studies on shifts in the methanogen community in response to S. alterniflora invasion at temporal and spatial scales in the initial invasion years are rare. Sediments derived from the invasive species S. alterniflora and the native species Phragmites australis (P. australis) in pairwise sites and an invasion chronosequence patch (4 years) were analyzed to investigate the abundance and community structure of methanogens using quantitative real-time PCR (qPCR) and Denaturing gradient gel electrophoresis (DGGE) cloning of the methyl-coenzyme M reductase A (mcrA) gene. For the pairwise sites, the abundance of methanogens in S. alterniflora soils was lower than that of P. australis soils. For the chronosequence patch, the abundance and diversity of methanogens was highest in the soil subjected to two years invasion, in which we detected some rare groups including Methanocellales and Methanococcales. These results indicated a priming effect at the initial invasion stages of S. alterniflora for microorganisms in the soil, which was also supported by the diverse root exudates. The shifts of methanogen communities after S. alterniflora invasion were due to changes in pH, salinity and sulfate. The results indicate that root exudates from S. alterniflora have a priming effect on methanogens in the initial years after invasion, and the predominate methylotrophic groups (Methanosarcinales) may adapt to the availability of diverse substrates and reflects the potential for high methane production after invasion by S. alterniflora.

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Stronger increase of methane emissions from coastal wetlands by non‐native Spartina alterniflora than non‐native Phragmites australis
Andrea Fuchs, Ian C. Davidson, J. Patrick Megonigal, John L. Devaney, Christina Simkanin, Genevieve L. Noyce, Meng Lu, Grace M. Cott
PLANTS, PEOPLE, PLANET.2025; 7(1): 62. CrossRef
Predictions of Spartina alterniflora leaf functional traits based on hyperspectral data and machine learning models
Wei Li, Xueyan Zuo, Zhijun Liu, Leichao Nie, Huazhe Li, Junjie Wang, Zhiguo Dou, Yang Cai, Xiajie Zhai, Lijuan Cui
European Journal of Remote Sensing.2024;[Epub] CrossRef
Salt marsh soil organic carbon is regulated by drivers of microbial activity
Hailey Erb, Ashley Keiser, Kristen M DeAngelis
Sustainable Microbiology.2024;[Epub] CrossRef
Asymmetric responses of functional microbes in methane and nitrous oxide emissions to plant invasion: A meta-analysis
Yanzhong Yao, Youtao Song, Pinjie Su, Jing Wang, Congke Miao, Yifu Luo, Qiqi Sun, Jiale Wang, Guohui Zhang, Naishun Bu, Zhaolei Li
Soil Biology and Biochemistry.2023; 178: 108931. CrossRef
Increasing coastal reclamation by Invasive alien plants and coastal armoring threatens the ecological sustainability of coastal wetlands
Jian Li, Zhanrui Leng, Taitiya Kenneth Yuguda, Lili Wei, Jiaojiao Xia, Chongyu Zhuo, Ziying Nie, Daolin Du
Frontiers in Marine Science.2023;[Epub] CrossRef
Spartina alterniflora Invaded Coastal Wetlands by Raising Soil Sulfur Contents: A Meta-Analysis
Zhenzhen Zhao, Liyu Cheng, Chiquan He, Feifei Wang, Jialin Liu, Yuanhang Li, Xueping Chen, Xiaoyan Liu, Gaoming Lv, Daoyuan Wang
Water.2022; 14(10): 1633. CrossRef
Exogenous nitrogen from riverine exports promotes soil methane production in saltmarshes in China
Chenhao Zhou, Yan Zhang, Songshuo Li, Qiuyue Jiang, Hongyang Chen, Ting Zhu, Xiao Xu, Hao Liu, Shiyun Qiu, Jihua Wu, Ming Nie, Bo Li
Science of The Total Environment.2022; 838: 156203. CrossRef
Exogenous Nitrogen from Riverine Exports Promotes Soil Methane Production in Saltmarshes in China
Chenhao Zhou, Yan Zhang, Songshuo Li, Qiuyue Jiang, Hongyang Chen, Ting Zhu, Xiao Xu, Hao Liu, Shi-Yun Qiu, Jihua Wu, Ming Nie, Bo Li
SSRN Electronic Journal .2021;[Epub] CrossRef
Spartina alterniflora raised soil sulfide content by regulating sulfur cycle-associated bacteria in the Jiuduansha Wetland of China
Chiquan He, Liyu Cheng, Daoyuan Wang, Zhenzhen Zhao, Zhengyu Wang, Feifei Wang, Xiaoxi Wang, Pu Zhang, Xueping Chen, Xiaoyan Liu
Plant and Soil.2021; 469(1-2): 107. CrossRef
The linkage between methane production activity and prokaryotic community structure in the soil within a shale gas field in China
Yan-Qin Wang, Guang-Quan Xiao, Yong-Yi Cheng, Ming-Xia Wang, Bo-Ya Sun, Zhi-Feng Zhou
Environmental Science and Pollution Research.2020; 27(7): 7453. CrossRef

Taxonomic description and draft genome of Pseudomonas sediminis sp. nov., isolated from the rhizospheric sediment of Phragmites karka: Pratiksha Behera , Madhusmita Mahapatra , Arman Seuylemezian , Parag Vaishampayan , V. Venkata Ramana , Neetha Joseph , Amaraja Joshi , Yogesh Shouche , Mrutyunjay Suar , Ajit K. Pattnaik , Gurdeep Rastogi; J. Microbiol. 2018;56(7):458-466. Published online June 14, 2018; DOI: https://doi.org/10.1007/s12275-018-7549-x

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Abstract

The taxonomic position of a Gram-stain-negative, rod-shaped bacterial strain, designated PI11T , isolated from the rhizospheric sediment of Phragmites karka was characterized using a polyphasic approach. Strain PI11T could grow optimally at 1.0% NaCl concentration with pH 7.0 at 30°C and was positive for oxidase and catalase but negative for hydrolysis of starch, casein, and esculin ferric citrate. Phylogenetic analysis of 16S rRNA gene sequences indicated that the strain PI11T belonged to the genus Pseudomonas sharing the highest sequence similarities with Pseudomonas indoloxydans JCM 14246T (99.72%), followed by, Pseudomonas oleovorans subsp. oleovorans DSM 1045T (99.29%), Pseudomonas toyotomiensis JCM 15604T (99.15%), Pseudomonas chengduensis DSM 26382T (99.08%), Pseudomonas oleovorans subsp. lubricantis DSM 21016T (99.08%), and Pseudomonas alcaliphila JCM 10630T (99.01%). Experimental DNA-DNA relatedness between strain PI11T and P. indoloxydans JCM 14246T was 49.4%. The draft genome of strain PI11T consisted of 4,884,839 bp. Average nucleotide identity between the genome of strain PI11T and other closely related type strains ranged between 77.25–90.74%. The polar lipid pattern comprised of phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylcholine. The major (> 10%) cellular fatty acids were C18:1 ω6c/ω7c, C16:1 ω6c/ω7c, and C16:0. The DNA G + C content of strain PI11T was 62.4 mol%. Based on the results of polyphasic analysis, strain PI11T was delineated from other closely related type strains. It is proposed that strain PI11T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas sediminis sp. nov. is proposed. The type strain is PI11T (= KCTC 42576T = DSMZ 100245T).

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Phylogenomics studies and molecular markers reliably demarcate genus Pseudomonas sensu stricto and twelve other Pseudomonadaceae species clades representing novel and emended genera
Bashudev Rudra, Radhey S. Gupta
Frontiers in Microbiology.2024;[Epub] CrossRef
Plant growth-promoting characteristics of halotolerant endophytic bacteria isolated from Sporobolus specatus (Vahr) Kunth and Cyperus laevigatus L. of Ethiopian rift valley lakes
Solomon Enquahone, Guido van Marle, Addis Simachew
Archives of Microbiology.2022;[Epub] CrossRef
Haloferax litoreum sp. nov., Haloferax marinisediminis sp. nov., and Haloferax marinum sp. nov., low salt-tolerant haloarchaea isolated from seawater and sediment
Eui-Sang Cho, In-Tae Cha, Seong Woon Roh, Myung-Ji Seo
Antonie van Leeuwenhoek.2021; 114(12): 2065. CrossRef
Pseudomonas carbonaria sp. nov., isolated from charcoal
Peter Kämpfer, S. P. Glaeser, John A. McInroy, Dominique Clermont, Alexis Criscuolo, Hans-Jürgen Busse
International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef
Haloplanus rubicundus sp. nov., an extremely halophilic archaeon isolated from solar salt
Yeon Bee Kim, Joon Yong Kim, Hye Seon Song, Se Hee Lee, Na-Ri Shin, Jin-Woo Bae, Jinjong Myoung, Ki-Eun Lee, In-Tae Cha, Jin-Kyu Rhee, Seong Woon Roh
Systematic and Applied Microbiology.2020; 43(3): 126085. CrossRef
Salicibibacter halophilus sp. nov., a moderately halophilic bacterium isolated from kimchi
Young Joon Oh, Joon Yong Kim, Hyo Kyeong Park, Ja-Young Jang, Seul Ki Lim, Min-Sung Kwon, Hak-Jong Choi
Journal of Microbiology.2019; 57(11): 997. CrossRef

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

Reductive Divergence of Enterobacterial Repetitive Intergenic Consensus Sequences among Gammaproteobacteria Genomes: Young-Gun Zo; J. Microbiol. 2011;49(1):35-45. Published online March 3, 2011; DOI: https://doi.org/10.1007/s12275-011-1024-2

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Abstract: Enterobacterial repetitive intergenic consensus (ERIC) sequence is a transcription-modulating, nonautonomous, miniature inverted-repeat transposable element. Its origin and the mechanism of highly varying incidences, limited to Enterobacteriaceae and Vibrionaceae, have not been identified. In this study, distribution and divergence of ERICs along bacterial taxonomic units were analyzed. ERICs were found among five families of gammaproteobacteria, with the copy numbers varying with exponential increments. The variability was explained by genus (45%) and species (36%) affiliations, indicating that copy numbers are specific to subfamily taxa. ERICs were interspersed in genomes with considerable divergences. Locations of ERICs in a genome appeared to be strongly conserved in a strain, moderately in a species or a genus, and weakly in a family. ERICs in different species of a genus were from the identical population of sequences while ERICs in different genera of a family were nearly identical. However, ERICs in different families formed distinct monophylectic groups, implying vertical transmission of diverging population of sequences. In spite of large difference in copy numbers, overall intra-genome evolutionary distances among ERICs were similar among different species, except for a few genomes. The exceptions substantiated hypotheses of genetic drifts and horizontal gene transfers of mobility capacity. Therefore, the confined, variable distribution of ERIC could be explained as a two-step evolution: introduction and proliferation of ERIC in one of the progenitors of gammaproteobacteria, followed by vertical transmission under negative selection. Deterioration of sequences and reduction in copy number were concluded to be the predominant patterns in the evolution of ERIC loci.

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