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

Abstract

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.

The dynamics of bacterial community in a polyculture aquaculture system of Penaeus chinensis , Rhopilema esculenta and Sinonovacula constricta

“…A lot of studies have been done to analyse the composition of bacterial communities in aquaculture environment. For example, in a polyculture pond of shrimp, crab and shellfish, the dominant communities in the water were Proteobacteria, Chloroflexi, Actinobacteria, Firmicutes and Acidobacteria (Li, Yan, et al, ). Proteobacteria, Gemmatimonadetes and Actinobacteria were the top three phyla in the sediment of shrimp ponds in Mexico (Cornejogranados et al, ).…”

“…On the other hand, more diverse phyla were detected in sediment samples by the order of Bacteroidetes, Actinobacteria, Chloroflexi, Firmicutes, Acidobacteria, Cyanobacteria and Fusobacteria, which occupied 19.2%, 7.7%, 4.7%, 3.7%, 2.1%, 1.9% and 1.1% of total bacterial Chloroflexi, Actinobacteria, Firmicutes and Acidobacteria (Li, Yan, et al, 2016b). Proteobacteria, Gemmatimonadetes and Actinobacteria were the top three phyla in the sediment of shrimp ponds in Mexico (Cornejogranados et al, 2017).…”

“…Other microorganisms in aquaculture systems can transform the damaging substances for cultural species, such as ammonia, nitrite and hydrogen sulphide, into low‐toxic substances (Su, Li, Pan, & Xue, ; Su, Li, Pan, & Zhang, ). Moreover, various pathogens have been observed from aquaculture environment, which resulted in the death of breeding species and caused enormous losses (Li, Yan, Li, Xu, & An, ; Munang'Andu, ). Consequently, investigating the variation of bacterial communities and their regulatory factors during the aquaculture activities is extremely vital for the rational management and development of aquaculture industry.…”

“…Other microorganisms in aquaculture systems can transform the damaging substances for cultural species, such as ammonia, nitrite and hydrogen sulphide, into low-toxic substances (Su, Li, Pan, & Xue, 2016a;Su, Li, Pan, & Zhang, 2016b). Moreover, various pathogens have been observed from aquaculture environment, which resulted in the death of breeding species and caused enormous losses (Li, Yan, Li, Xu, & An, 2016b;Munang'Andu, 2016).…”

Impact of polyculture ecosystems of Ctenopharyngodon idellus with Eriocheir sinensis on bacterial communities in the sediments of Dongping Lake in China: Focus on optimization of polyculture modes

“…Due to the detrimental impacts of intensive aquaculture farming on environments, the development of ecofriendly polyculture systems is necessary for the sustainability of aquaculture practices although it may also alter the environments and, as a result, affect microbes. A previous study by Li, Yan, Li, Xu, and An () suggested the great influence of polyculture of shrimp, crab and shellfish on the seawater bacterial communities in pond by comparing with a non‐cultured treatment. In this study, the varying effects of polyculture systems with different biomass of fish–crab on the sediments were tested by comparing with each other and with a non‐cultured control treatment in the Dongping lake.…”