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

Abstract

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.

Bacterial community in the rumen of Tibetan sheep and Gansu alpine fine-wool sheep grazing on the Qinghai-Tibetan Plateau, China

“…where n is the number of unique OTUs that occurred only once in the clone library, and N is the total number of clones in the library (Huang et al, 2014). The frequency (F) was calculated as follows: F = (m/N) ¥ 100, where m is the number of clones of an OTU in a library and N is the total number of clones in the same library.…”

“…The frequency (F) was calculated as follows: F = (m/N) ¥ 100, where m is the number of clones of an OTU in a library and N is the total number of clones in the same library. Rarefaction curves were used to determine phylotype diversity, and the sampling efficiency of the library was constructed using Analytic Rarefaction (Huang et al, 2014). Diversity (Shannon-Weiner H and Simpson D) and evenness (J) indices were calculated for each library.…”

Bacterial composition, abundance and diversity in fish polyculture and mussel-fish integrated cultured ponds in China

“…The microbial composition has been studied in the water column and sediment of shrimp ponds (Li, Zhang, Juck, Fortin, Greer & Tang ; Tang, Tao, Tan, Mu, Peng, Yang, Tong & Chen ; Zhang, Sun, Liu, Xuan, Jiang, Pan, Zhang, Gong, Lu, Yu, Kumar, Hu, Cao, Xue & Gong ), freshwater crab ponds (Liu, Zhou, He, Yao & Ringo ), seawater fish ponds (Zeng, Ma, Wei, Jiao, Tang, Wu & Jian ; Pereira, Salvador, Arrojado, Silva, Santos, Cunha, Gomes & Almeida ) and lobster tanks (Bourne, Young, Webster, Payne, Salmon, Demel & Hall ; Payne, Hall, Sly & Bourne ). However, knowledge in bacterial diversity in freshwater polyculture and integrated ponds is scarce (Zhou, Wang, Tang & Dai ; Huang, Liu, Li & Wang ).…”

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

“…Cyanobacteria, which are usually found in eutrophic freshwater, were significantly enriched in the aquaculture ponds during the months of July and August, which may explain the increase in pH. The bacterial blooms and toxins produced by Microcystis and Synechococcus have been shown to be harmful to aquatic animals and humans (Huang, Liu, Li, & Wang, ). Therefore, genera within Actinobacteria and Cyanobacteria that may be potentially associated with CyHV‐2 infection, require further investigation.…”