Journal of Microbiology

Journal Articles

Different distribution patterns of microorganisms between aquaculture pond sediment and water: Lili Dai , Chengqing Liu , Liang Peng , Chaofeng Song , Xiaoli Li , Ling Tao; J. Microbiol. 2021;59(4):376-388. Published online February 25, 2021; DOI: https://doi.org/10.1007/s12275-021-0635-5

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Aquatic microorganisms in the sediment and water column are closely related; however, their distribution patterns between these two habitats still remain largely unknown. In this study, we compared sediment and water microeukaryotic and bacterial microorganisms in aquaculture ponds from different areas in China, and analyzed the influencing environmental factors as well as the inter-taxa relationships. We found that bacteria were significantly more abundant than fungi in both sediment and water, and the bacterial richness and diversity in sediment were higher than in water in all the sampling areas, but no significant differences were found between the two habitats for microeukaryotes. Bacterial taxa could be clearly separated through cluster analysis between the sediment and water, while eukaryotic taxa at all classification levels could not. Spirochaetea, Deltaproteobacteria, Nitrospirae, Ignavibacteriae, Firmicutes, Chloroflexi, and Lentimicrobiaceae were more abundantly distributed in sediment, while Betaproteobacteria, Alphaproteobacter, Cyanobacteria, Roseiflexaceae, Dinghuibacter, Cryomorphaceae, and Actinobacteria were more abundant in water samples. For eukaryotes, only Cryptomonadales were found to be distributed differently between the two habitats. Microorganisms in sediment were mainly correlated with enzymes related to organic matter decomposition, while water temperature, pH, dissolved oxygen, and nutrient levels all showed significant correlation with the microbial communities in pond water. Intensive interspecific relationships were also found among eukaryotes and bacteria. Together, our results indicated that eukaryotic microorganisms are distributed less differently between sediment and water in aquaculture ponds compared to bacteria. This study provides valuable data for evaluating microbial distributions in aquatic environments, which may also be of practical use in aquaculture pond management.

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International Journal of Environmental Studies.2024; 81(4): 1836. CrossRef
Metagenomic Insight into the Effect of Probiotics on Nitrogen Cycle in the Coilia nasus Aquaculture Pond Water
Qi Mang, Jun Gao, Quanjie Li, Yi Sun, Gangchun Xu, Pao Xu
Microorganisms.2024; 12(3): 627. CrossRef
Carbon and Nutrient Limitations of Microbial Metabolism in Xingkai Lake, China: Abiotic and Biotic Drivers
Xingting Chen, Weizhen Zhang, Mengdie Geng, Ji Shen, Jianjun Wang
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Biofilm formation and chlorine resistance of microbial communities in household drinking water system: Preliminary idea of using bacteria to control bacteria
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Yan Zhang, Tiejun Li, Guangzhi Li, Tao Yuan, Yao Zhang, Lei Jin
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Anwar Hossain, Md Al Zahid, Santonu Kumar Sanyal, Md Inja-Mamun Haque, Md Habibullah-Al-Mamun, Shankar Chandra Mandal, Kozo Watanabe
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Sara Vettorazzo, Adriano Boscaini, Leonardo Cerasino, Nico Salmaso
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Minhai Liu, Zhongneng Yan, Chengwei Huang, Zhihua Lin, Zhilan Peng, Chenxi Zhao, Xiafei Zheng
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Ngoc Minh Ngan Bui, Jasmine Heyse, Jérôme Delamare-Deboutteville, Tom Defoirdt, Ruben Props, Colin Shelley
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Saurabh Chatterjee, Madhura More
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Chaohua Wang, Zhiyuan Yao, Pingping Zhan, Xianghua Yi, Jiong Chen, Jinbo Xiong
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Antonia Bruno, Alessandra Cafiso, Anna Sandionigi, Andrea Galimberti, Davide Magnani, Amedeo Manfrin, Giulio Petroni, Maurizio Casiraghi, Chiara Bazzocchi
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Antibiotic resistance gene-free probiont administration to tilapia for growth performance and Streptococcus agalactiae resistance
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Analysis of the structure and function of microbial community in late-stage of grass carp (Ctenopharyngodon idella) farming ponds
Shuhui Niu, Kai Zhang, Zhifei Li, Jun Xie, Guangjun Wang, Hongyan Li, Ermeng Yu, Yun Xia, Jingjing Tian, Wangbao Gong
Aquaculture Reports.2023; 30: 101556. CrossRef
Case study on the aptness of in-pond raceways for pikeperch, Sander lucioperca, grow-out
Zoltán Nagy, László Ardó, Ferenc Demény, Dénes Gál, Zsuzsanna J. Sándor, Uroš Ljubobratović
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Structural and functional comparisons of the environmental microbiota of pond and tank environments at different locations for the commercial aquaculture of American shad
J. Du, Q.H. Liu, J.S. Liu, K.-Q. Zhang, W.F. Huang
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Hongyu Feng, Yajun Qiao, Lu Xia, Wen Yang, Yongqiang Zhao, Nasreen Jeelani, Shuqing An
Plant and Soil.2022; 477(1-2): 439. CrossRef
Improvement of fish production and water quality in a recirculating aquaculture pond enhanced with bacteria-microalgae association
Chu Wang, Cancan Jiang, Tianming Gao, Xiawei Peng, Shuanglong Ma, Qian Sun, Bing Xia, Xiangming Xie, Zhihui Bai, Shengjun Xu, Xuliang Zhuang
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Xuemei Li, Lu Liu, Yongjiu Zhu, Tingbing Zhu, Xingbing Wu, Deguo Yang
Water.2021; 13(21): 3089. CrossRef

Colonization study of gfp-tagged Achromobacter marplatensis strain in sugar beet: YingWu Shi , Chun Li Li , HongMei Yang , Tao Zhang , Yan Gao , Min Chu , Jun Zeng , Qing Lin , OuTiKu Er , YuGuo Li , Xiangdong Huo , Kai Lou; J. Microbiol. 2017;55(4):267-272. Published online January 26, 2017; DOI: https://doi.org/10.1007/s12275-017-6371-1

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Abstract

This study details the introduction of a gfp marker into an endophytic bacterial strain (Achromobacter marplatensis strain 17, isolated from sugar beet) to monitor its coloniza-tion of sugar beet (Beta. vulgaris L.). Stability of the plasmid encoding the gfp was confirmed in vitro for at least 72 h of bacterial growth and after the colonization of tissues, under nonselective conditions. The colonization was observed us-ing fluorescence microscopy and enumeration of culturable endophytes in inoculated sugar beet plants that grew for 10 or 20 days. gfp-Expressing strains were re-isolated from the inner tissues of surface-sterilized roots and stems of inocu-lated plants, and the survival of the Achromobacter marpla-tensis 17:gfp strain in plants 20 days after inoculation, even in the absence of selective pressure, suggests that it is good colonizer. These results also suggest that this strain could be a useful tool for the delivery of enzymes or other proteins into plants. In addition, the study highlights that sugar beet plants can be used effectively for detailed in vitro studies on the interactions between A. marplatensis strain 17 and its host, particularly if a gfp-tagged strain of the pathogen is used.

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Understanding the sugar beet holobiont for sustainable agriculture
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Mengting He, Zengyuan Tian, Qianqian Liu, Yuqi Guo
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Research Support, Non-U.S. Gov'ts

Characterization of Cellulases of Fungal Endophytes Isolated from Espeletia spp.: Luisa Cabezas , Carolina Calderon , Luis Miguel Medina , Isabela Bahamon , Martha Cardenas , Adriana Jimena Bernal , Andrés Gonzalez , Silvia Restrepo; J. Microbiol. 2012;50(6):1009-1013. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2130-5

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Abstract: Endophytes are microorganisms that asymptomatically invade plant tissues. They can stimulate plant growth and/or provide defense against pathogen attacks through the production of secondary metabolites. Most endophyte species are still unknown, and because they may have several applications, the study of their metabolic capabilities is essential. We characterized 100 endophytes isolated from Espeletia spp., a genus unique to the paramo ecosystem, an extreme environment in the Andean mountain range. We evaluated the cellulolytic potential of these endophytes on the saccharification of the oil palm empty fruit bunch (OPEFB). The total cellulolytic activity was measured for each endophyte on filter paper (FPA). In addition, the specific carboxymethyl cellulase (CMCase), exoglucanase, and β-glucosidase activities were determined. We found four fungi positive for cellulases. Of these fungi, Penicillium glabrum had the highest cellulolytic activity after partial purification, with maximal CMCase, exoglucanase and β-glucosidase enzyme activities of 44.5, 48.3, and 0.45 U/ml, respectively. Our data showed that the bioprospection of fungi and the characterization of their enzymes may facilitate the process of biofuel production.

Enhancement of Anti-candidal Activity of Endophytic Fungus Phomopsis sp. ED2, Isolated from Orthosiphon stamineus Benth, by Incorporation of Host Plant Extract in Culture Medium: Tong Woei Yenn , Chong Chai Lee , Darah Ibrahim , Latiffah Zakaria; J. Microbiol. 2012;50(4):581-585. Published online July 21, 2012; DOI: https://doi.org/10.1007/s12275-012-2083-8

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Abstract: This study examined the effect of host extract in the culture medium on anti-candidal activity of Phomopsis sp. ED2, previously isolated from the medicinal herb Orthosiphon stamineus Benth. Interestingly, upon addition of aqueous host extract to the culture medium, the ethyl acetate extract prepared from fermentative broth exhibited moderate anticandidal activity in a disc diffusion assay. The minimal inhibitory concentration of this extract was 62.5 μg/ml and it only exhibited fungistatic activity against C. albicans. In the time-kill study, a 50% growth reduction of C. albicans was observed at 31.4 h for extract from the culture incorporating host extract. In the bioautography assay, only one single spot (Rf 0.59) developed from the extract exhibited anti-candidal activity. A spot with the a similar Rf was not detected for the crude extract from YES broth without host extract. This indicated that the terpenoid anti-candidal compound was only produced when the host extract was introduced into the medium. The study concluded that the incorporation of aqueous extract of the host plant into the culture medium significantly enhanced the anti-candidal activity of Phomopsis sp. ED2.

Endophytic Fungus Trichothecium roseum LZ93 Antagonizing Pathogenic Fungi In Vitro and Its Secondary Metabolites: XiaoMei Zhang , GuoHong Li , Juan Ma , Ying Zeng , WeiGuang Ma , PeiJi Zhao; J. Microbiol. 2010;48(6):784-790. Published online January 9, 2011; DOI: https://doi.org/10.1007/s12275-010-0173-z

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Abstract: The endophytic fungus Trichothecium roseum LZ93 from Maytenus hookeri was found to antagonize other pathogenic fungi in vitro. To identify which compound contributed substantially to the antagonism, we fermented the strain and purified its fermentation products. Eleven compounds were obtained, including two trichothecenes, five rosenonolactones, two cardiotonic cyclodepsipeptides, and two sterols. Compound 11β-hydroxyrosenonolactone (1) was assigned according to 1D and 2D-NMR data for the first time. At the same time, the 1H and 13C-NMR assignments for 6β-hydroxyrosenonolactone (2) were revised. Of all of them, only trichothecin (6) showed strong antifungal activity. Based on our observations of the antagonistic activity and the other experimental results, we suggest that the antifungal compound trichothecin was the main contributor to the antagonistic action of T. roseum LZ93.

Endophytic Fungi Diversity of Aquatic/Riparian Plants and Their Antifungal Activity In Vitro: Hai-Yan Li , Chun-An Zhao , Chen-Jian Liu , Xiao-Fei Xu; J. Microbiol. 2010;48(1):1-6. Published online March 11, 2010; DOI: https://doi.org/10.1007/s12275-009-0163-1

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Abstract

Two hundred and fourteen endophytic fungi were isolated from 500 segments of aquatic/riparian plants Ottelia acuminata, Myriophyllum verticillatum, Equisetum arvense, Cardamine multijuga, and Impatiens chinensis. They were identified to 31 taxa in which Cladosporium, Fusarium, and Geotrichum were the dominant genera. Among all isolates, 169 (79%) were anamorphic fungi, 1 (0.5%) was an teleomorphic ascomycete and 44 (21%) were sterile mycelia. There were significant differences in the colonization frequency of endophytes between the five plant species (X~2=51.128, P<0.001, Chi-square test). The riparian plants harboured more endophytes than the submerged plants. The antifungal activity of these isolates against Fusarium solani and Phytophthora nicotianae in vitro were tested and 28 (13.1%) isolates showed antifungal activities with more than 30% growth inhibition rate against the two pathogens.

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Endophytic Bacterial Diversity in Grapevine (Vitis vinifera L.) Leaves Described by 16S rRNA Gene Sequence Analysis and Length Heterogeneity-PCR: Daniela Bulgari , Paola Casati , Lorenzo Brusetti , Fabio Quaglino , Milena Brasca , Daniele Daffonchio , Piero Attilio Bianco; J. Microbiol. 2009;47(4):393-401. Published online September 9, 2009; DOI: https://doi.org/10.1007/s12275-009-0082-1

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Abstract

Diversity of bacterial endophytes associated with grapevine leaf tissues was analyzed by cultivation and cultivation-independent methods. In order to identify bacterial endophytes directly from metagenome, a protocol for bacteria enrichment and DNA extraction was optimized. Sequence analysis of 16S rRNA gene libraries underscored five diverse Operational Taxonomic Units (OTUs), showing best sequence matches with gamma-Proteobacteria, family Enterobacteriaceae, with a dominance of the genus Pantoea. Bacteria isolation through cultivation revealed the presence of six OTUs, showing best sequence matches with Actinobacteria, genus Curtobacterium, and with Firmicutes genera Bacillus and Enterococcus. Length Heterogeneity-PCR (LH-PCR) electrophoretic peaks from single bacterial clones were used to setup a database representing the bacterial endophytes identified in association with grapevine tissues. Analysis of healthy and phytoplasma- infected grapevine plants showed that LH-PCR could be a useful complementary tool for examining the diversity of bacterial endophytes especially for diversity survey on a large number of samples.

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Dark Septate Endophyte (DSE) Fungi Isolated from Metal Polluted Soils: Their Taxonomic Position, Tolerance, and Accumulation of Heavy Metals In Vitro: Yujie Zhang , Yan Zhang , Maojun Liu , Xiaodong Shi , Zhiwei Zhao; J. Microbiol. 2008;46(6):624-632. Published online December 24, 2008; DOI: https://doi.org/10.1007/s12275-008-0163-6

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Abstract: To understand the possible role of the plant root associated fungi on metal tolerance, their role in the uptake of heavy metals and the potential transfer of these metal ions to the plant, three strains of dark septate endophytic (DSE) fungi were isolated from a waste smelter site in southwest China, and one strain was isolated from a non-contaminated site. According to molecular phylogenetic analysis of the ITS 1-5.8S rDNA-ITS 2 gene regions and morphological characteristics, one is identified as Exophiala pisciphila, and the other three are non-sporulating fungi under the experiment condition with the nearest phylogenetic affinities to the Thysanorea papuana strain EU041814. Tolerance and accumulation abilities of the three DSE strains for metals were investigated in liquid culture. Minimum inhibitory concentrations (MIC) of Pb, Zn, and Cd were determined. It was demonstrated that the tolerance of the DSE strains varied between metal species and strains. The E. pisciphila strain is able to accumulate lead and cadmium over 20% and 5% of dry weight of biomass, respectively. Partial of the sequestrated metals can be washed with CaCl2. Morphological and enzyme activity changes taking place in the presence of excessive Pb, Cd, and/or Zn also indicate that the mechanism of heavy metal tolerance and accumulation of the DSE strains would be a complex process. The findings indicated promising tolerance and accumulation of the DSE strains with potential values in metal cycling and restoration of soil and water system.

Diversity of Endophytic Enterobacteria Associated with Different Host Plants: Adalgisa Ribeiro Torres , Welington Luiz Araujo , Luciana Cursino , Mariangela Hungria , Fabio Plotegher , Fabio Luis Mostasso , Joao Lucio Azevedo; J. Microbiol. 2008;46(4):373-379. Published online August 31, 2008; DOI: https://doi.org/10.1007/s12275-007-0165-9

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Abstract: Fifty-three endophytic enterobacteria isolates from citrus, cocoa, eucalyptus, soybean, and sugar cane were evaluated for susceptibility to the antibiotics ampicillin and kanamycin, and cellulase production. Susceptibility was found on both tested antibiotics. However, in the case of ampicillin susceptibility changed according to the host plant, while all isolates were susceptible to kanamycin. Cellulase production also changed according to host plants. The diversity of these isolates was estimated by employing BOX-PCR genomic fingerprints and 16S rDNA sequencing. In total, twenty-three distinct operational taxonomic units (OTUs) were identified by employing a criterion of 60% fingerprint similarity as a surrogate for an OTU. The 23 OTUs belong to the Pantoea and Enterobacter genera, while their high diversity could be an indication of paraphyletic classification. Isolates representing nine different OTUs belong to Pantoea agglomerans, P. ananatis, P. stewartii, Enterobacter sp., and E. homaechei. The results of this study suggest that plant species may select endophytic bacterial genotypes. It has also become apparent that a review of the Pantoea/Enterobacter genera may be necessary.

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