Bacterial communities in paddy soil and ditch sediment under rice-crab co-culture system

Abstract

As an important form of sustainable agriculture, rice-crab (Eriocheir sinensis) co-culture is rapid developing worldwide. However, the knowledge on the bacterial communities of the different components of the system is limited. In this study, we investigated the bacterial community structure in paddy soil and ditch sediment by using high-throughput sequencing technology. The results showed that compared with the ditch sediment, the content of NH4+-N in paddy soil decreased by 62.31%, and the content of AP (available phosphorus) increased by 172.02% (P < 0.05). The most abundant phyla in paddy soil and ditch sediment were Proteobacteria, Bacteroidetes and Chloroflexi, whose relative abundance was above 65%. Among the dominant genera, the relative abundance of an uncultured bacterium genus of Saprospiraceae and an uncultured bacterium genus of Lentimicrobiaceae in paddy soil was significantly lower than ditch sediment (P < 0.05). Alpha diversity indicated that the bacterial diversity of paddy soil and ditch sediment was similar. The bacterial community structure was affected by the relative abundance of bacteria, not the species of bacteria. Redundancy analysis (RDA) showed that the bacterial communities in paddy soil and ditch sediment were correlated with physicochemical properties. Our findings showed that the bacterial community structure was distinct in paddy soil and ditch sediment under rice-crab co-culture probably due to their different management patterns. These results can provide theoretical support for improving rice-crab co-culture technology.

Soil Microbial Diversity and Community Composition in Rice–Fish Co-Culture and Rice Monoculture Farming System

“…Even though the alpha diversity indices, which present observed richness, Shannon’s, and Simpson’s indices, differed between the two sites, the differences were minor and did not reveal a significant difference. This result is consistent with previous studies on other rice co-culture fields, including rice–frog (Yi et al, 2019), rice–crab [ 19 ], and rice–fish fields [ 7 , 45 ]. Whilst Zhao et al [ 7 ] reported that microbial diversity in rice–fish co-culture fields was similar to those in monoculture rice fields in the first year of cultivation and substantially changed after 5 years, Li et al [ 45 ] found that it took up to 12 years to see the differences in rice–fish–turtle fields.…”

“…Meanwhile, all alpha diversity indices showed no significant difference between the two sites. This is consistent with the study of Jiang et al [ 19 ], who found that the most abundant phyla in paddy soil and ditch sediment under the rice–crab co-culture system were Proteobacteria, Bacteroidetes, and Chloroflexi, while alpha diversity of bacterial diversity in paddy soil and ditch sediment was similar. The phylum Actinobacteria, which contributes to the turnover of the complex biopolymers and plant residue decomposition [ 51 , 52 ] by producing various carbon cycling enzymes [ 53 ], was the most dominant taxa in both RF and MC sites.…”

“…These promote the suitable condition for the abundant and diversified population of soil microorganisms, especially bacteria that play a crucial role in soil carbon and nitrogen mineralization. Proteobacteria, Bacteroidetes, Acidobacteria, and Chloroflexi were generally dominant phyla in the paddy soil [ 17 , 18 , 19 ], which play important roles in soil nutrient cycles [ 20 , 21 ]. Thus, soil microbial communities can be used as an indicator to explain soil health [ 22 ].…”

Bacterial communities in co-cultured fish intestines and rice field soil irrigated with aquaculture wastewater

“…In this study, no significant differences in Cyanobacteria abundances were found between intestinal and soil bacteria. Members of another phylum, Chloroflexi , were found to be dominant in rice field soil, especially at the mature stage (Sohn et al 2016 ), and in soil from rice-crab co-culture fields (Jiang et al 2021 ). In our study, Chloroflexi was the top phylum in rice field soil, and the relative abundances were significantly higher in the soil than in fish intestines.…”

Effects of stocking density on the growth performance, mitophagy, endocytosis and metabolism of Cherax quadricarinatus in integrated rice–crayfish farming systems

“…It has been reported that rice-aquatic animals co-culture system has higher ecosystem service value compared with rice monoculture ( Liu et al, 2020 ). In farming practice, various aquatic animals, such as common carp ( Cyprinus carpio ) ( Liu et al, 2022 ), Chinese mitten crab ( Eriocheir sinensis ) ( Jiang et al, 2021 ), red swamp crayfish ( Procambarus clarkia ) ( Si et al, 2018 ) and Chinese soft-shelled turtle ( Trionyx sinensis ) ( Wu et al, 2021 ), have been co-cultured with rice. It is worth noting that existing research majorly focuses on the assessment of ecological and economic values, microbial diversity and soil nutrition in the integrated rice-aquatic animals farming system ( Si et al, 2018 ; Liu et al, 2020 ), but the suitable stocking density of aquatic animals and the effects of stoking density on physiological function are rarely evaluated.…”