Seasonal changes and diversity of bacteria in Bohai Bay by RFLP analysis of PCR-amplified 16S rDNA gene fragments

Sun, Jiufeng; Guo, Fei; Geng, Xin; Jun-li, Wei; Li, Xiang; Li, Jingjing

doi:10.1007/s11274-010-0456-x

Cited by 12 publications

(2 citation statements)

References 36 publications

(20 reference statements)

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“…Subsequently, filtration was carried out with a nitrocellulose membrane filter with a pore size of 0.22 µm and a diameter of 47 mm (Merck KGaA) to trap bacteria on the membrane surface. Membrane filters were cut into small pieces, and total genomic DNA after filtration was extracted with a modified phenol‐chloroform method in accordance with previously described methods (Molina et al, (2007); Zhang et al, (2008); Jinsheng et al, (2011)). Genomic DNA extraction from sediment was conducted by mixing 5 g of sediment sample with 5 ml of lysis buffer (100 mM Tris HCl 1 M [pH 8], 100 mM NaCl, 50 mM EDTA [pH 8], and 2% SDS), 0.6 g of glass bead, 30 μl of proteinase‐K (20 mg ml −1 ), 50 μl of lysozyme (1 mg ml −1 ), 750 μl of CTAB and 1.5 ml of 20% SDS in a 15 ml conical tube.…”

Section: Methodsmentioning

confidence: 99%

Dynamic change in bacterial communities in the integrated rice–fish farming system in Sleman, Yogyakarta, Indonesia

Herlambang

Murwantoko

Istiqomah

2021

Aquaculture Research

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An integrated rice-fish farming system is an efficient technique used to maintain water quality and rice/fish productivity. In addition to fish and rice plants that have mutually beneficial ecological roles, bacteria play important roles in maintaining water quality and soil fertility. Therefore, this study investigated the diversity and dynamic change in the bacterial community composition of water and sediment in an integrated ricefish farming system using a high-throughput sequencing approach. The 16S rRNA gene of bacteria was amplified, and the IonS5™XL sequencing platform was used to identify bacterial community during the cultivation period. The results demonstrated that fishpond, rice field and trench sediment samples were dominated by the phyla Proteobacteria (60.9%-64.4%), Acidobacteria (8.7%) and Chloroflexi (6.3%), whereas water samples were dominated by the phyla Proteobacteria (65.7%), Bacteroidetes (17.1%) and Actinobacteria (8.5%). The dynamics of the bacterial community composition of the water and sediment samples were clearly observed at phylum and genus levels respectively. Water temperature (34.67°C) and ammonia-nitrogen content (0.38 mg L −1 ) at the early stage of cultivation correlated with the abundances of Actinobacteia and Cyanobacteria at the phylum level and Acinetobacter at the genus level. Furthermore, several bacterial genera could potentially contribute to the biogeochemical cycle. In particular, Sorangium was involved in organic matter degradation, Methylophilus was implicated in nitrification, Novosphingobium and Methylotenera were essential for denitrification, and Desulfobacca was important for sulfate reduction. This study improved our understanding of the bacterial community in the integrated rice-fish farming system and provided data for further development.

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Section: Methodsmentioning

confidence: 99%

Dynamic change in bacterial communities in the integrated rice–fish farming system in Sleman, Yogyakarta, Indonesia

Herlambang

Murwantoko

Istiqomah

2021

Aquaculture Research

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“…The Bohai Sea, in the northwestern Pacific Ocean, is an economically important marine ecosystem for fish, shrimp and crab in China (Sun et al 2010). It is also rich in crude oil and surrounded by a string of industrial zones known as the Bohai Sea Economic Rim (BER).…”

Section: Introductionmentioning

confidence: 99%

Bacterial communities and their hydrocarbon bioremediation potential in the Bohai Sea, China

Yang¹,

Yang²,

Deng³

et al. 2015

Mar. Ecol. Prog. Ser.

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Petroleum exploitation causes serious pollution to the semi-enclosed Bohai Sea (China) ecosystem. However, little is known about the influence of such pollution on the αand β-diversity of the bacterial communities or the in situ hydrocarbon biodegradation potential present in the surface sediments. This was explored using 16S rRNA gene-based terminal restriction fragment length polymorphism, along with alkane hydroxylase (AlkB) and soluble di-iron monooxygenase (SDIMO) gene-based clone libraries. α-diversity (Shannon-Weaver index) was negatively correlated with the BTEX (i.e. benzene, toluene, ethylbenzene, and xylene) and total nitrogen contents. β-diversity at the phylum/class level (class level for Proteobacteria) and terminal restriction fragment (T-RF) level responded differently to the abiotic factors. At a small to intermediate scale (21.4 to 142.2 km), β-diversity at the T-RF level was closely correlated with geographic distances, while at the phylum/class level, it was significantly influenced by environment heterogeneity. In total, 72.61% of the AlkB sequences were related to Gammaproteobacteria, including Alcanivorax and Marinobacter, while the SDIMO genes were similar to Phenol-2, Mmo, ThmA, PmoC and PrmA genes, with 72% of the sequences found being novel. The high SDIMO gene diversity might be related to the complexity of the hydrocarbon pollution (a mixture of phenol, methane, tetrahydrofuran, propene and propane) and demonstrates the existence of in situ hydrocarbon biodegradation potential. Information about the diversity of bacteria and the hydroxylases is helpful to guide the in situ bioremediation of petroleum pollution and protect ecosystem function in the Bohai Sea.

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A comparison of bacterial community structure in seawater pond with shrimp, crab, and shellfish cultures and in non-cultured pond in Ganyu, Eastern China

Yan

et al. 2015

Ann Microbiol

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The aim of this study was to gain an understanding of the effects of mariculture on the bacterial communities in a co-culture pond, which is a popular culture model for shrimp, crab, and shellfish along the eastern coast of China. Six seawater samples were collected from a pond with cultures of shrimp, crab, and shellfish, and six other samples were collected from a non-cultured pond (control). The diversity of the bacterial communities in the samples was examined using the MiSeq desktop sequencer (Illumina) to amplify and sequence the V4-V5 region of the 16S ribosomal DNA analysis. The Meta-Stat computer program was used to assess the differences in the two communities. The sequences produced from all 12 samples were categorized into 1533 unique phylotypes, including 30 phyla, 81 classes, 270 families, and 414 genera. The top five dominant communities in the culture pond were Proteobacteria, Chloroflexi, Actinobacteria, Firmicutes, and Acidobacteria, while Proteobacteria, Planctomycetes, Bacteroidetes, Actinobacteria, and Cyanobacteria were the dominant communities in the control pond. Higher abundance was observed in the culture pond at the phylum, class, and genus levels, and the same result was also observed in the rarefaction curves. Elusimicrobia, Fibrobacteres, Fusobacteria, Tenericutes, MVP-21, SM2F11, and WCHB1-60 were present, whereas Deferribacteres and Lentisphaerae, as well as the candidate divisions BRC1, OD1, and OP11, disappeared from the culture pond. Moreover, abundant phylotypes (Aeromonadaceae, P s e u d o m o n a d a c e a e , E n t e r o b a c t e r i a c e a e , Bradyrhizobiaceae, Clostridiaceae, and Xanthomonadaceae) were present in the culture pond, but only rarely present in the control pond. These results suggest that mariculture contributed to the change in bacterial communities in the culture pond compared with the non-culture pond. Proteobacteria was the most dominant community in both ponds, but the second most dominant community was Planctomycetes in the control pond and Chloroflexi in the culture pond. Seven new phyla were observed, but five phyla disappeared in the culture pond. The disease-or metabolism-related members of the bacterial communities, namely, Aeromonadaceae, P s e u d o m o n a d a c e a e , E n t e ro b a c t e r i a c e a e , and Xanthomonadaceae, were abundant phylotypes in the culture pond. Our results contribute to an improved understanding of the establishment and maintenance of the bacterial community structure in a complex aquaculture ecosystem and may have practical applications in terms of improving seawater quality and early disease warning in this popular mariculture model in China.

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Seasonal changes and diversity of bacteria in Bohai Bay by RFLP analysis of PCR-amplified 16S rDNA gene fragments

Cited by 12 publications

References 36 publications

Dynamic change in bacterial communities in the integrated rice–fish farming system in Sleman, Yogyakarta, Indonesia

Dynamic change in bacterial communities in the integrated rice–fish farming system in Sleman, Yogyakarta, Indonesia

Bacterial communities and their hydrocarbon bioremediation potential in the Bohai Sea, China

A comparison of bacterial community structure in seawater pond with shrimp, crab, and shellfish cultures and in non-cultured pond in Ganyu, Eastern China

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