Bacterial diversity in various coastal mariculture ponds in Southeast China and in diseased eels as revealed by culture and culture-independent molecular techniques

Zeng, Yonghui; Ma, Ying; Wei, Chaoling; Jiao, Nianzhi; Tang, Kunxian; Wu, Zhaofei; Jian, Jichang

doi:10.1111/j.1365-2109.2010.02499.x

Cited by 26 publications

(20 citation statements)

References 36 publications

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“…The discrepancy determined in the bacterial community analysed by culturedependent and culture-independent methods in the present study is a finding that previously has been reported in various ecosystems (Tamaki et al, 2005;Michaud et al, 2009;Huang et al, 2010;Zeng et al, 2010;Szabo et al, 2011). By using culture-dependent methods to analyze the bacterial community of an ecosystem, it is widely recognized that only 0.001 to 15% of the total cell counts can be cultured (Amann et al, 1995).…”

Section: Discussionmentioning

confidence: 44%

Bacterial Community of Koumiss from Mongolia Investigated by Culture and Culture-Independent Methods

et al. 2014

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The bacterial community of fermented horse milk (koumiss) from Mongolia was studied using three methods: cultivation, direct identification by 16S rRNA clone library and denaturing gradient gel electrophoresis (DGGE). Ninety-eight strains were isolated by traditional cultivation and 61 of those were randomly selected for further identification by 16S rRNA gene sequencing. The strains were dominated by lactic acid bacteria (LAB; six different lactobacilli), Acinetobacter, Bacillus and Psychrobacter. Construction of the clone library analysis revealed that 16S sequences of 220 clones, genus Lactobacillus was dominant, but Streptococcus thermophilus, Acetobacter pasteurianus and uncultured clones were also detected. Ten unique bands were sequenced from the DGGE and revealed: Lactococcus lactis, Lactococcus lactis subsp. lactis, Clostridium acidurici, Acinetobacter johnsonii, Dickeya sp., Enterobacter sp., Pseudomonas sp., Raoultella sp., and Ruminococcus sp.. In vitro growth inhibition of three human pathogens, Escherichia coli, Enterobacter sakazakii and Staphylococcus aureus by 14 culturable bacteria displayed that only three of the isolates tested inhibit growth of E. sakazakii while most of the other bacteria delayed growth of the target bacteria.

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Section: Discussionmentioning

confidence: 44%

Bacterial Community of Koumiss from Mongolia Investigated by Culture and Culture-Independent Methods

et al. 2014

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“…During the past few decades many articles have been published in which the bacteria of aquatic environments were identified by culture-dependent and culture-independent techniques (Arias et al 2006;AlHarbi & Uddin 2008;Huang et al 2008;Zeng et al 2010;Niu et al 2011). Nevertheless, the cultured species account for less than 5% of the total bacteria in environmental samples (Amann et al 1995).…”

Section: Introductionmentioning

confidence: 99%

“…Nevertheless, the cultured species account for less than 5% of the total bacteria in environmental samples (Amann et al 1995). Recently, a geneclone-library-based culture-independent technique has been frequently used to determine the complex microbial community in natural aquatic environments (Arias et al 2006;Huang et al 2008;Zeng et al 2010;Niu et al 2011), because it provides more information on bacterial diversity than culture-dependent and some of culture-independent techniques. However, to our knowledge, previous studies have not used culture-independent techniques to investigate 728 J.Q.…”

Section: Introductionmentioning

confidence: 99%

“…With the rapid development of common carp culture, many ponds used in culture are changing these pond environments. The increased nutrient materials, such as uneaten feed and faecal matter in culture ponds may lead to eutrophication and affect the biogeochemical process and bacterial communities of ponds (Sara 2007;Zeng et al 2010); thus, the bacterial communities in ponds have become an important research area.…”

Section: Introductionmentioning

confidence: 99%

“…They have critical effects on productivity, nutrient cycling, and water quality in ponds (Moriarty 1997;Cotner & Biddanda 2002). Aquatic microorganisms also provide a reservoir of harmful and pathogenic bacteria to aquaculture animals, and thus their diversity may provide a bioindicator of healthy aquatic ecosystem or disease outbreak (Arias et al 2006;Zeng et al 2010).…”

Section: Introductionmentioning

confidence: 99%

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Bacterial diversity in saline-alkali ponds rearing common carp (Cyprinus carpio) as revealed by 16S rRNA gene sequences

Huang

Liu

et al. 2014

Biologia

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The bacterial diversity in saline-alkali ponds rearing common carp was investigated using the 16S rRNA gene clone library technique. Phylogenetic analysis of the most common and dominant sequences recovered indicated that these sequences fell into the following major lineages, including Proteobacteria (α-, β-, γ-), Actinobacteria, Cyanobacteria, Planctomycetes, Fibrobacteres, Bacteroidetes, Chloroflexi, and unclassified bacteria. Sequence analysis showed that the bacterial diversity was abundant, and the sequences belonging to β-Proteobacteria, α-Proteobacteria and Actinobacteria were predominant. The most sequences in the saline-alkali rearing ponds exhibited low similarity with known bacterial 16S rRNA genes, suggesting that these sequences may represent novel bacteria. In addition, the majority of our sequences were most closely affiliated with sequences retrieved from inland waters of China. These results suggest that the saline-alkali ponds rearing common carp are specific ecologic niches and the distribution of the bacteria may be influenced by geographical factors. This study reports the bacterial diversity in saline-alkali ponds rearing common carp by the culture-independent technique for the first time; therefore, it provides important information for understanding the microbial ecology in salinealkali rearing ponds and managing the microbial community composition to promote and maintain the health of aquaculture environments.

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Investigation of bacterial diversity and pathogen abundances in gibel carp (Carassius auratus gibelio) ponds during a cyprinid herpesvirus 2 outbreak

et al. 2019

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Cyprinid herpesvirus 2 (CyHV‐2) infection is detrimental to gibel carp health and may result in severe economic loss in freshwater aquaculture. However, information regarding the interaction of this pathogen with the aquatic environment is scarce. In this study, quantitative polymerase chain reaction (qPCR) and high‐throughput sequencing were used to determine the abundances of pathogens and bacterial community compositions in two aquaculture ponds in Jiangsu Province, China. The results indicate that the concentrations of six selected pathogens were higher in the water than in the sediment and that these concentrations peaked during disease outbreak. In total, 8,326 and 18,244 operational taxonomic units were identified from water and sediment samples, respectively. The dominant phyla were Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes, and Chlorobi in water samples and Proteobacteria, Firmicutes, Actinobacteria, Chloroflexi, and Bacteroidetes in sediment samples. Bacterial communities were similar at the phylum level in different ponds, although significant differences were observed at the genus level. In addition, bacterial diversity was associated with environmental factors (temperature, chemical oxygen demand, NO2 −‐N, NO3 −‐N, and NH4 +‐N) in the pond where the outbreak occurred. Additionally, CyHV‐2 abundance was positively correlated with dissolved oxygen levels and Aeromonas spp. abundance in pond water (p < .01). This study provides comprehensive insight into the mechanisms of interaction between potential pathogens and the freshwater environment of aquaculture ponds during CyHV‐2 disease outbreaks. Furthermore, the results from this study can contribute to improvement of the aquatic environment and establishment of disease prevention and control measures.

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Bacterial diversity in various coastal mariculture ponds in Southeast China and in diseased eels as revealed by culture and culture-independent molecular techniques

Cited by 26 publications

References 36 publications

Bacterial Community of Koumiss from Mongolia Investigated by Culture and Culture-Independent Methods

Bacterial Community of Koumiss from Mongolia Investigated by Culture and Culture-Independent Methods

Bacterial diversity in saline-alkali ponds rearing common carp (Cyprinus carpio) as revealed by 16S rRNA gene sequences

Investigation of bacterial diversity and pathogen abundances in gibel carp (Carassius auratus gibelio) ponds during a cyprinid herpesvirus 2 outbreak

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