Comparable Ecological Processes Govern the Temporal Succession of Gut Bacteria and Microeukaryotes as Shrimp Aged

Xiong, Jinbo; Li, Xiaohui; Yan, Maocang; Lü, Jiaqi; Qiu, Qiongfen; Chen, Jiong

doi:10.1007/s00248-020-01533-6

Cited by 27 publications

(20 citation statements)

References 55 publications

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“…As the Pacific white shrimp is a typical benthos that takes in feed debris or sediment from the pond bottom, some culture operations in the Aquamimicry system, such as removal the feed from the bottom and using multiple oxygen increasing device to agitate the water thoroughly, can effectively reduce shrimp's intake of debris, which might weaken the effect of the environmental harmful factors on shrimp. As previously reported, shrimp sourced little of their intestinal microbiota from their rearing water, whereas the successions of intestinal microbiota were significantly correlated with host age (Xiong et al 2019(Xiong et al , 2020. In the present study, the culture stages were more pronounced than environmental factors in microbial variations (Additional file 1.…”

Section: Discussionsupporting

confidence: 70%

“…This expertise has been presented to a large number of shrimp producers, and is now adapted in many countries, such as Australia, Bangladesh, Brazil, Brunei, China, Ecuador, Egypt, India, Korea, Malaysia, Mexico, Peru, Singapore, Sri Lanka, USA, and, Vietnam. As part of this novel shrimp culture technique, the microbial communities of the shrimp intestine and surrounding environment must be studied. Previous studies indicated that shrimp sourced little of their intestinal microbiota from their rearing water, whereas the successions of intestinal microbiota were significantly correlated with host age (Xiong et al 2019(Xiong et al , 2020. Indeed, identification of the microbial community present in the shrimp and nearby environment at different culture stages could facilitate our understanding of the main and important microbial groups which will help to prevent disease outbreaks and maintain good water quality condition during the culture period.…”

Section: Introductionmentioning

confidence: 99%

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Dissimilarity of microbial diversity of pond water, shrimp intestine and sediment in Aquamimicry system

et al. 2020

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The Pacific white shrimp, with the largest production in shrimp industry, has suffered from multiple severe viral and bacterial diseases, which calls for a more reliable and environmentally friendly system to promote shrimp culture. The “Aquamimicry system”, mimicking the nature of aquatic ecosystems for the well-being of aquatic animals, has effectively increased shrimp production and been adapted in many countries. However, the microbial communities in the shrimp intestine and surrounding environment that act as an essential component in Aquamimicry remain largely unknown. In this study, the microbial composition and diversity alteration in shrimp intestine, surrounding water and sediment at different culture stages were investigated by high throughput sequencing of 16S rRNA gene, obtaining 13,562 operational taxonomic units (OTUs). Results showed that the microbial communities in shrimp intestine and surrounding environment were significantly distinct from each other, and 23 distinguished taxa for each habitat were further characterized. The microbial communities differed significantly at different culture stages, confirmed by a great number of OTUs dramatically altered during the culture period. A small part of these altered OTUs were shared between shrimp intestine and surrounding environment, suggesting that the microbial alteration of intestine was not consistent with that of water and sediment. Regarding the high production of Aquamimicry farm used as a case in this study, the dissimilarity between intestinal and surrounding microbiota might be considered as a potential indicator for healthy status of shrimp farming, which provided hints on the appropriate culture practices to improve shrimp production.

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Section: Discussionsupporting

confidence: 70%

Section: Introductionmentioning

confidence: 99%

Dissimilarity of microbial diversity of pond water, shrimp intestine and sediment in Aquamimicry system

et al. 2020

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“…In the present study, the homogeneous selection correlated with the general positive correlation of the microbial interactions because of homogeneous abiotic and biotic environmental conditions facilitated by continuing additive nutrient settlement (Zhou and Ning, 2017). This result coincided with recent findings that bacterial and eukaryotic communities are governed by homogeneous selection in shrimp gut with age (Xiong et al, 2020). However, the correlation between the assembly and positive interactions were not significant.…”

Section: Discussionsupporting

confidence: 92%

Bacterial and eukaryotic community interactions might contribute to shrimp culture pond soil ecosystem at different culture stages

et al. 2021

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Sedimentary bacterial and eukaryotic communities are major components of the aquatic ecosystem. Revealing the linkages between their community structure and interactions is crucial to understand the diversity and functions of aquatic and soil ecosystems. However, how their diversity and assembly contribute to their interactions on time scale is unclear. This study examined sedimentary bacterial and eukaryotic communities in shrimp culture ponds at different culture stages. The most abundant bacteria were Proteobacteria (38.27%), whereas the most abundant eukaryotes were Chytridiomycota (27.48%). Bacterial and eukaryotic diversities were correlated (P < 0.05), implying the strong interactions between bacteria and eukaryotes. Results showed that the bacterial and eukaryotic communities became increasingly similar on a local scale along with the shrimp culture. Only the eukaryotic community significantly increased in similarity along with the shrimp culture (P < 0.05), suggesting that the sedimentary eukaryotic community structure is sensitive under shrimp culture. Co-occurrence network modeling indicated that positive microbial interactions were dominant. The homogeneous selection was the major driver of community assembly. Bacterial diversity negatively correlated with operational taxonomic units and positive links in networks (P < 0.05), whereas eukaryotic diversities positively correlated with positive links in networks (P < 0.05). This study broadens our knowledge about sedimentary microbial diversity, community assembly, and interaction patterns on time scale, providing a reference for the sustainable management in aquaculture production.

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“…6 A). In a given microbial community, some microbe exhibited broad environmental adaptations (generalists), while others showed specific and narrow environmental tolerances (specialists) (Xiong et al 2020 ). Consistently, the rhizosphere microbial community exhibited significantly widest niche breadths among all microbial communities (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…The community assembly mechanism was calculated using phylogenetic bin-based null model analysis (iCAMP) (Ning et al 2020 ). Niche breadth was calculated using Levins’ niche breadth index (B) equation, (Xiong et al 2020 ). The B value representing the community level (Bcom) was calculated as the average of B values from all taxa occurring in one community.…”

Section: Methodsmentioning

confidence: 99%

Strategies and Structure Feature of the Aboveground and Belowground Microbial Community Respond to Drought in Wild Rice (Oryza longistaminata)

Xie

Wang

et al. 2021

Rice

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Background Drought is global environmental stress that limits crop yields. Plant-associated microbiomes play a crucial role in determining plant fitness in response to drought, yet the fundamental mechanisms for maintaining microbial community stability under drought disturbances in wild rice are poorly understood. We make explicit comparisons of leaf, stem, root and rhizosphere microbiomes from the drought-tolerant wild rice (Oryza longistaminata) in response to drought stress. Results We find that the response of the wild rice microbiome to drought was divided into aboveground–underground patterns. Drought reduced the leaf and stem microbial community diversity and networks stability, but not that of the roots and rhizospheres. Contrary to the aboveground microbial networks, the drought-negative response taxa exhibited much closer interconnections than the drought-positive response taxa and were the dominant network hubs of belowground co-occurrence networks, which may contribute to the stability of the belowground network. Notably, drought induces enrichment of Actinobacteria in belowground compartments, but not the aboveground compartment. Additionally, the rhizosphere microbiome exhibited a higher proportion of generalists and broader habitat niche breadth than the microbiome at other compartments, and drought enhanced the proportion of specialists in all compartments. Null model analysis revealed that both the aboveground and belowground-community were governed primarily by the stochastic assembly process, moreover, drought decreased ‘dispersal limitation’, and enhanced ‘drift’. Conclusions Our results provide new insight into the different strategies and assembly mechanisms of the above and belowground microbial community in response to drought, including enrichment of taxonomic groups, and highlight the important role of the stochastic assembly process in shaping microbial community under drought stress.

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Comparable Ecological Processes Govern the Temporal Succession of Gut Bacteria and Microeukaryotes as Shrimp Aged

Cited by 27 publications

References 55 publications

Dissimilarity of microbial diversity of pond water, shrimp intestine and sediment in Aquamimicry system

Dissimilarity of microbial diversity of pond water, shrimp intestine and sediment in Aquamimicry system

Bacterial and eukaryotic community interactions might contribute to shrimp culture pond soil ecosystem at different culture stages

Strategies and Structure Feature of the Aboveground and Belowground Microbial Community Respond to Drought in Wild Rice (Oryza longistaminata)

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