Effects of integrated multi-trophic aquaculture on microbial communities, antibiotic resistance genes, and cultured species: A case study of four mariculture systems

Zhang, Mingqing; Yang, Jinlin; Lai, Xingxing; Li, Wen; Zhan, Manjun; Zhang, Cuiping; Jiang, Jing‐Zhe; Shu, Hu

doi:10.1016/j.aquaculture.2022.738322

Cited by 14 publications

(5 citation statements)

References 83 publications

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“…The dominant families were Rhodobacteraceae, Cyanobiaceae, Flavobacteriaceae, Microbacteriaceae, norank_o__Chloroplast, and Cryomorphaceae in water, which are Proteobacteria, Cyanobacteria, Bacteroidetes, Firmicutes, and Actinobacteria, respectively. This was consistent with a previously reported IMTA system mainly composed of Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteriota (Bao, et al 2021;Califano, et al 2020;Ying, et al 2018;Zhang, et al 2022). Most of the major families belonged to Proteobacteria and Bacteroidetes, which are important microorganisms in the nitrogen cycle (Rurangwa and Verdegem 2014) and contain ammonia-oxidising bacteria with a highly stable deamination capacity (Zhao, et al 2013).…”

Section: Bacterial Community and Diversity Of Watersupporting

confidence: 93%

Cultivation of Ulva lactuca changes bacterial community structure and abundances of nitrogen cycling functional genes in an IMTA system

Kong

Chen

Zhao

et al. 2023

Preprint

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To study nitrogen removal by Ulva lactuca and its effects on the structure of the bacterial community and abundance of nitrogen cycle functional genes in the ‘sea cucumber–shrimp–crab–fish’ integrated multi-trophic aquaculture (IMTA) system, we analysed bacterial community composition by Illumina MiSeq high-throughput sequencing and nitrogen cycling functional gene levels by real-time quantitative PCR in water and sediment with (Y) and without the presence of U. lactuca (N). Diversity and abundance indices, including Sobs, Shannon, Ace, and Chao1, were higher in Group Y water and sediment. In the water, the predominant phyla were Proteobacteria in Group Y and Cyanobacteria in Group N in September. Flavobacteriaceae and Rhodobacteraceae were the dominant families in Group Y and Group N in October and November, respectively. In the sediment, Bacillaceae was the dominant family in Group Y throughout the experimental period, whereas Desulfocapsaceae was the dominant family in Group N in October and November. Regarding nitrogen cycle functional genes, millions of Amx, nosZ, nxrB, and nrfA genes were detected in both water and sediment. The abundances of nifH, amoA, nxrB, norB, and nrfA genes were higher in Group Y than those in Group N, which can improve ammonia removal without nitrogen loss. In this study, a potential novel approach was proposed to enhance the development of sustainable aquaculture, promote the nitrogen cycle, and remediate and optimise the water environment by cultivating bacteria and algae, according to the effects of U. lactuca on water quality, bacterial communities, and abundance of functional nitrogen cycling genes in IMTA systems.

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Section: Bacterial Community and Diversity Of Watersupporting

confidence: 93%

Cultivation of Ulva lactuca changes bacterial community structure and abundances of nitrogen cycling functional genes in an IMTA system

Kong

Chen

Zhao

et al. 2023

Preprint

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“…In general, Proteobacteria, Bacteroidota, Firmicutes, and Actinobacteriota are the dominant bacterial phyla in water in IMTA systems [48][49][50][51]. In addition, some IMTA systems with diferent species showed diferent bacterial abundances; for instance, Actinobacteriota was the predominant phylum in a system containing shrimps, crabs, and bivalves, and Firmicutes was the predominant phylum in a system containing shrimps and crabs.…”

Section: Discussionmentioning

confidence: 97%

Bivalves Improved Water Quality by Changing Bacterial Composition in Sediment and Water in an IMTA System

Kong

Chen

Ghonimy

et al. 2023

Aquaculture Research

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Integrated multitrophic aquaculture (IMTA) maximises the nitrogen cycle between system components, including bacteria. In order to maximise the bacterial role in nitrogen elimination in an IMTA system, we investigated the effect of bivalve culture on water quality and bacterial community structure in overlying water and sediment in the “shrimp-crab-bivalve-fish” IMTA system. The bacterial composition in overlying water and sediment was measured by Illumina -MiSeq high-throughput sequencing technology. The results show that dissolved oxygen was higher in the bivalve culture area. Ammonia and nitrite in the bivalve culture area were lower than those in the nonbivalve culture area; however, the nitrate and phosphate in the bivalve culture area were higher than those in the nonbivalve culture area. The Chao1, Shannon, and Ace indexes were higher in the bivalve area. More bacteria with nitrification and denitrification functions were detected in bivalve culture areas, such as Ruegeria (1.05%–4.79%), Thalassobius (0.11%–0.69%), Limibaculum (0.07%–0.69%), HIMB11 (0.13%–0.21%), and Rubellimicrobium (0.01%–0.16%). More Cyanobacteria were detected in bivalve culture areas with higher phosphate concentrations. To sum up, bivalves can release phosphorus through bioturbation, increasing the abundance of Cyanobacteria, which release dissolved oxygen into overlying water through photosynthesis, enhance nitrification (mainly ammonia oxidation), and improve the ammonia nitrogen removal capacity of the system. Meanwhile, bivalves can increase bacterial diversity and abundance by regulating dissolved oxygen. This study provided insight into bivalve interaction with bacterial activity in the IMTA system.

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“…For example, salinity and pH could reflect geological conditions but had weak effects on microbial diversity and carbon utilization. A likely explanation is that the diversity and adaptability of microorganisms allowed them to survive under different environmental conditions (Li, Li, et al, 2022; Nazina et al, 2017; Zhang, Yang, et al, 2022). For example, Thiobacillus can grow in acidic environments (Golyshina & Timmis, 2005; Monachon et al, 2019; Paknikar, 1993) but Clostridium and Desulfovibrio require neutral or alkaline environments (Kumar et al, 2020; Shi, Ma, et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

Temperature‐mediated microbial carbon utilization in China's lakes

Guo

et al. 2023

Global Change Biology

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Microbes play an important role in aquatic carbon cycling but we have a limited understanding of their functional responses to changes in temperature across large geographic areas. Here, we explored how microbial communities utilized different carbon substrates and the underlying ecological mechanisms along a space-for-time substitution temperature gradient of future climate change. The gradient included 47 lakes from five major lake regions in China spanning a difference of nearly 15°C in mean annual temperatures (MAT). Our results indicated that lakes from warmer regions generally had lower values of variables related to carbon concentrations and greater carbon utilization than those from colder regions. The greater utilization of carbon substrates under higher temperatures could be attributed to changes in bacterial community composition, with a greater abundance of Cyanobacteria and Actinobacteriota and less Proteobacteria in warmer lake regions. We also found that the core species in microbial networks changed with increasing temperature, from Hydrogenophaga and Rhodobacteraceae, which inhibited the utilization of amino acids and carbohydrates, to the CL500-29-marine-group, which promoted the utilization of all almost carbon substrates. Overall, our findings suggest that temperature can mediate aquatic carbon utilization by changing the interactions between bacteria and individual carbon substrates, and the discovery of core species that affect carbon utilization provides insight into potential carbon sequestration within inland water bodies under future climate warming.

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Effects of integrated multi-trophic aquaculture on microbial communities, antibiotic resistance genes, and cultured species: A case study of four mariculture systems

Cited by 14 publications

References 83 publications

Cultivation of Ulva lactuca changes bacterial community structure and abundances of nitrogen cycling functional genes in an IMTA system

Cultivation of Ulva lactuca changes bacterial community structure and abundances of nitrogen cycling functional genes in an IMTA system

Bivalves Improved Water Quality by Changing Bacterial Composition in Sediment and Water in an IMTA System

Temperature‐mediated microbial carbon utilization in China's lakes

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