Stochastic processes shape the bacterial community assembly in shrimp cultural pond sediments

Hou, Dongwei; Zhou, Rui; Zeng, Shenzheng; Wei, Dongdong; Deng, Xiaogeng; Xing, Chengguang; Weng, Shaoping; He, Jianguo; Huang, Zhijian

doi:10.1007/s00253-021-11378-9

Cited by 29 publications

(11 citation statements)

References 59 publications

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“…Considering the increased abundance of N cycling genes in the shrimp-crab-clam pond together with the significant positive contribution of water salinity and pH to the differences in the relative abundance of N cycling genes between SC and SCC, the above results indicate that the coculture of S. constricta in a shrimp-crab pond improved the salinity and pH conditions for osmoregulation, thereby exerting positive feedback on microbes and creating better physiological conditions for microbial N cycling. Sediment properties including pH, NH 4 + , and temperature regulate enzyme activities involved in N metabolism [42]. In this study, P_NH 4 + showed significant negative factors affecting the relative abundance of N cycling genes in sediment.…”

Section: Discussionmentioning

confidence: 56%

“…The response of the microbiome to the coculture of S. constricta in shrimp-crab ponds and different environments involved a re-accommodation of microbial community βdiversity. The separation of the microbial community may indicate the functions of rare species and revealed the stability of the core microbial community [41,42]. In this study, the results indicate that the clear separation of SC and SCC in water samples would mainly be affected by changes in rare species.…”

Section: Discussionmentioning

confidence: 61%

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Metagenomic Insights into the Structure of Microbial Communities Involved in Nitrogen Cycling in Two Integrated Multitrophic Aquaculture (IMTA) Ponds

Liu

Shan

et al. 2022

JMSE

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The microbial structure and metabolic potential, particularly with regard to nitrogen (N) cycling, in integrated multitrophic aquaculture (IMTA) ponds with shrimp remain unclear. In this study, an analysis of microbial community taxonomic diversity and a metagenomic analysis of N-related genes were performed in a shrimp-crab pond (Penaeus japonicus-Portunus trituberculatus, SC) and a shrimp-crab-clam pond (P. japonicus-P. trituberculatus-Sinonovacula constricta, SCC) to evaluate microbial structure and N transformation capacities in these two shrimp IMTA ponds. The composition of the microbial communities was similar between SC and SCC, but the water and sediments shared few common members in either pond. The relative abundances of N cycling genes were significantly higher in sediment than in water in both SC and SCC, except for assimilatory nitrate reduction genes. The main drivers of the differences in the relative abundances of N cycling genes in SC and SCC were salinity and pH in water and the NO2- and NH4+ contents of pore water in sediment. These results indicate that the coculture of S. constricta in a shrimp-crab pond may result in decreased N cycling in sediment. The reduced N flux in the shrimp IMTA ponds primarily originates within the sediment, except for assimilatory nitrate reduction.

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Section: Discussionmentioning

confidence: 56%

Section: Discussionmentioning

confidence: 61%

Metagenomic Insights into the Structure of Microbial Communities Involved in Nitrogen Cycling in Two Integrated Multitrophic Aquaculture (IMTA) Ponds

Liu

Shan

et al. 2022

JMSE

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“…For example, temperature is one of the main factors regulating the balance of stochastic and deterministic assembly processes in hot spring sediment communities, with differences in temperature increasing the contribution of determinism [ 50 ]; the increasing levels of eutrophication likely enhance the deterministic process of bacterial community assembly [ 51 ]. In addition, a dominant role of homogeneous selection in microbial community assembly processes has been reported in the Three Gorges Reservoir sediments [ 52 ]; stochasticity regulates the assembly processes of bacterial communities in the sediment of shrimp culture ponds [ 53 ]. One potential explanation for this discrepancy in the prevalent community assembly processes could attribute to differences in the studied spatial scales [ 54 , 55 ].…”

Section: Discussionmentioning

confidence: 99%

pH Drives Differences in Bacterial Community β-Diversity in Hydrologically Connected Lake Sediments

Yuan

Qin

et al. 2023

Microorganisms

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As microorganisms are very sensitive to changes in the lake environment, a comprehensive and systematic understanding of the structure and diversity of lake sediment microbial communities can provide feedback on sediment status and lake ecosystem protection. Xiao Xingkai Lake (XXL) and Xingkai Lake (XL) are two neighboring lakes hydrologically connected by a gate and dam, with extensive agricultural practices and other human activities existing in the surrounding area. In view of this, we selected XXL and XL as the study area and divided the area into three regions (XXLR, XXLD, and XLD) according to different hydrological conditions. We investigated the physicochemical properties of surface sediments in different regions and the structure and diversity of bacterial communities using high-throughput sequencing. The results showed that various nutrients (nitrogen, phosphorus) and carbon (DOC, LOC, TC) were significantly enriched in the XXLD region. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant bacterial phyla in the sediments, accounting for more than 60% of the entire community in all regions. Non-metric multidimensional scaling analysis and analysis of similarities confirmed that β-diversity varied among different regions. In addition, the assembly of bacterial communities was dominated by a heterogeneous selection in different regions, indicating the important influence of sediment environmental factors on the community. Among these sediment properties, the partial least squares path analysis revealed that pH was the best predictor variable driving differences in bacterial communities in different regions, with higher pH reducing beta diversity among communities. Overall, our study focused on the structure and diversity of bacterial communities in lake sediments of the Xingkai Lake basin and revealed that high pH causes the β-diversity of bacterial communities in the sediment to decrease. This provides a reference for further studies on sediment microorganisms in the Xingkai Lake basin in the future.

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“…Firmicutes was abundant in aquaculture pond sediments, but generally with a proportion of less than 10% (Hou et al 2021;Nho et al 2018). In the current study, the clustering analysis result showed that the two different fish ponds had similar bacterial community structure on day 0, and Firmicutes was the dominant phyla in fish pond sediment bacterial communities on day 0, with the relative abundance of more than 60%.…”

Section: Effects Of Phenol On Sediment Bacterial Community Structurementioning

confidence: 99%

Shifts in structure and function of bacterial community in river and fish pond sediments after a phenol spill

Chen

Feng

Zheng

et al. 2021

Environ Sci Pollut Res

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Phenol is widely used in industrial processes and has microbial toxicity. However, the effects of a phenol spill on the microbial community are not clear. The present study explored the changes of bacterial communities in river and fish pond sediments after a phenol spill. The bacterial richness and diversity in river sediments were lower on day 30 (36 days after the spill) than on day 0, while they increased in fish pond sediments. The structures and functions of bacterial communities in both river and fish pond sediments were changed, and a more dramatical variation was detected in fish pond sediments. In river sediments, Proteobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Nitrospirae were the major bacterial phyla, and Chloroflexi was enriched. In fish pond sediments, genera Brevibacillus dominated bacterial communities initially, and bacterial composition showed a dramatic change on day 30. Most predicted metabolism functions, as well as genetic information processing functions of translation, replication, and repair, were enhanced in both river and fish pond sediments, while they showed an opposite change trend for xenobiotic degradation function. This work could strengthen our understanding of the effects of phenol spills on sediment bacterial communities in both lotic and lentic ecosystems.

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Stochastic processes shape the bacterial community assembly in shrimp cultural pond sediments

Cited by 29 publications

References 59 publications

Metagenomic Insights into the Structure of Microbial Communities Involved in Nitrogen Cycling in Two Integrated Multitrophic Aquaculture (IMTA) Ponds

Metagenomic Insights into the Structure of Microbial Communities Involved in Nitrogen Cycling in Two Integrated Multitrophic Aquaculture (IMTA) Ponds

pH Drives Differences in Bacterial Community β-Diversity in Hydrologically Connected Lake Sediments

Shifts in structure and function of bacterial community in river and fish pond sediments after a phenol spill

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