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Hidalgo-Martinez K, Giachini AJ, Schneider M, Soriano A, Baessa MP, Martins LF, de Oliveira VM. Shifts in structure and dynamics of the soil microbiome in biofuel/fuel blend-affected areas triggered by different bioremediation treatments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:33663-33684. [PMID: 38687451 DOI: 10.1007/s11356-024-33304-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
The use of biofuels has grown in the last decades as a consequence of the direct environmental impacts of fossil fuel use. Elucidating structure, diversity, species interactions, and assembly mechanisms of microbiomes is crucial for understanding the influence of environmental disturbances. However, little is known about how contamination with biofuel/petrofuel blends alters the soil microbiome. Here, we studied the dynamics in the soil microbiome structure and composition of four field areas under long-term contamination with biofuel/fossil fuel blends (ethanol 10% and gasoline 90%-E10; ethanol 25% and gasoline 75%-E25; soybean biodiesel 20% and diesel 80%-B20) submitted to different bioremediation treatments along a temporal gradient. Soil microbiomes from biodiesel-polluted areas exhibited higher richness and diversity index values and more complex microbial communities than ethanol-polluted areas. Additionally, monitored natural attenuation B20-polluted areas were less affected by perturbations caused by bioremediation treatments. As a consequence, once biostimulation was applied, the degradation was slower compared with areas previously actively treated. In soils with low diversity and richness, the impact of bioremediation treatments on the microbiomes was greater, and as a result, the hydrocarbon degradation extent was higher. The network analysis showed that all abundant keystone taxa corresponded to well-known degraders, suggesting that the abundant species are core targets for biostimulation in soil remediation processes. Altogether, these findings showed that the knowledge gained through the study of microbiomes in contaminated areas may help design and conduct optimized bioremediation approaches, paving the way for future rationalized and efficient pollutant mitigation strategies.
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Affiliation(s)
- Kelly Hidalgo-Martinez
- Divisão de Recursos Microbianos, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas E Agrícolas (CPQBA), Universidade Estadual de Campinas (UNICAMP), Paulínia, SP, CEP 13148-218, Brazil.
- Programa de Pós-Graduação de Genética E Biologia Molecular, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, CEP 13083-970, Brazil.
| | - Admir José Giachini
- Núcleo Ressacada de Pesquisas Em Meio Ambiente (REMA)-Department of Microbiology, Federal University of Santa Catarina (UFSC), Campus Universitário Sul da Ilha-Rua José Olímpio da Silva, 1326-Bairro Tapera, Florianópolis, SC, 88049-500, Brazil
| | - Marcio Schneider
- Núcleo Ressacada de Pesquisas Em Meio Ambiente (REMA)-Department of Microbiology, Federal University of Santa Catarina (UFSC), Campus Universitário Sul da Ilha-Rua José Olímpio da Silva, 1326-Bairro Tapera, Florianópolis, SC, 88049-500, Brazil
| | - Adriana Soriano
- PETROBRAS/R&D Center (CENPES), Cidade Universitária, Av. Horácio Macedo, Ilha Do Fundão, Rio de Janeiro, 950, ZIP 21941-915, Brazil
| | - Marcus Paulus Baessa
- PETROBRAS/R&D Center (CENPES), Cidade Universitária, Av. Horácio Macedo, Ilha Do Fundão, Rio de Janeiro, 950, ZIP 21941-915, Brazil
| | - Luiz Fernando Martins
- PETROBRAS/R&D Center (CENPES), Cidade Universitária, Av. Horácio Macedo, Ilha Do Fundão, Rio de Janeiro, 950, ZIP 21941-915, Brazil
| | - Valéria Maia de Oliveira
- Divisão de Recursos Microbianos, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas E Agrícolas (CPQBA), Universidade Estadual de Campinas (UNICAMP), Paulínia, SP, CEP 13148-218, Brazil
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Pan Z, Chen Y, Zhou M, McAllister TA, Mcneilly TN, Guan LL. Linking active rectal mucosa-attached microbiota to host immunity reveals its role in host-pathogenic STEC O157 interactions. THE ISME JOURNAL 2024; 18:wrae127. [PMID: 38984791 PMCID: PMC11304501 DOI: 10.1093/ismejo/wrae127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/30/2024] [Accepted: 07/08/2024] [Indexed: 07/11/2024]
Abstract
The rectal-anal junction (RAJ) is the major colonization site of Shiga toxin-producing Escherichia coli (STEC) O157 in beef cattle, leading to transmission of this foodborne pathogen from farms to food chains. To date, there is limited understanding regarding whether the mucosa-attached microbiome has a profound impact on host-STEC interactions. In this study, the active RAJ mucosa-attached microbiota and its potential role in host immunity-STEC commensal interactions were investigated using RAJ mucosal biopsies collected from calves orally challenged with two STEC O157 strains with or without functional stx2a (stx2a+ or stx2a-). The results revealed that shifts of microbial diversity, topology, and assembly patterns were subjected to stx2a production post-challenge and Paeniclostridium and Gallibacterium were the keystone taxa for both microbial interactions and assembly. Additional mucosal transcriptome profiling showed stx2a-dependent host immune responses (i.e. B- and T-cell signaling and antigen processing and presentation) post-challenge. Further integrated analysis revealed that mucosa-attached beneficial microbes (i.e. Provotella, Faecalibacterium, and Dorea) interacted with host immune genes pre-challenge to maintain host homeostasis; however, opportunistic pathogenic microbes (i.e. Paeniclostridium) could interact with host immune genes after the STEC O157 colonization and interactions were stx2a-dependent. Furthermore, predicted bacterial functions involved in pathogen (O157 and Paeniclostridium) colonization and metabolism were related to host immunity. These findings suggest that during pathogen colonization, host-microbe interactions could shift from beneficial to opportunistic pathogenic bacteria driven and be dependent on the production of particular virulence factors, highlighting the potential regulatory role of mucosa-attached microbiota in affecting pathogen-commensal host interactions in calves with STEC O157 infection.
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Affiliation(s)
- Zhe Pan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Yanhong Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Mi Zhou
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Tim A McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB T1J 4B1, Canada
| | - Tom N Mcneilly
- Moredun Research Institute, Penicuik EH26 0PZ, United Kingdom
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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Pan Z, Ma T, Steele M, Guan LL. Varied microbial community assembly and specialization patterns driven by early life microbiome perturbation and modulation in young ruminants. ISME COMMUNICATIONS 2024; 4:ycae044. [PMID: 38650709 PMCID: PMC11033733 DOI: 10.1093/ismeco/ycae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/25/2024]
Abstract
Perturbations and modulations during early life are vital to affect gut microbiome assembly and establishment. In this study, we assessed how microbial communities shifted during calf diarrhea and with probiotic yeast supplementation (Saccharomyces cerevisiae var. boulardii, SCB) and determined the key bacterial taxa contributing to the microbial assembly shifts using a total of 393 fecal samples collected from 84 preweaned calves during an 8-week trial. Our results revealed that the microbial assembly patterns differed between healthy and diarrheic calves at 6- and 8-week of the trial, with healthy calves being stochastic-driven and diarrheic calves being deterministic-driven. The two-state Markov model revealed that SCB supplementation had a higher possibility to shift microbial assembly from deterministic- to stochastic-driven in diarrheic calves. Furthermore, a total of 23 and 21 genera were specific ecotypes to assembly patterns in SCB-responsive (SCB-fed calves did not exhibit diarrhea) and nonresponsive (SCB-fed calves occurred diarrhea) calves, respectively. Among these ecotypes, the area under a receiver operating characteristic curve revealed that Blautia and Ruminococcaceae UCG 014, two unidentified genera from the Ruminococcaceae family, had the highest predictiveness for microbial assembly patterns in SCB-responsive calves, while Prevotellaceae, Blautia, and Escherichia-Shigella were the most predictive bacterial taxa for microbial assembly patterns in SCB-nonresponsive calves. Our study suggests that microbiome perturbations and probiotic yeast supplementation serving as deterministic factors influenced assembly patterns during early life with critical genera being predictive for assembly patterns, which sheds light on mechanisms of microbial community establishment in the gut of neonatal calves during early life.
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Affiliation(s)
- Zhe Pan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Tao Ma
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Michael Steele
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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Wang D, Chen L, Tang G, Yu J, Chen J, Li Z, Cao Y, Lei X, Deng L, Wu S, Guan LL, Yao J. Multi-omics revealed the long-term effect of ruminal keystone bacteria and the microbial metabolome on lactation performance in adult dairy goats. MICROBIOME 2023; 11:215. [PMID: 37773207 PMCID: PMC10540338 DOI: 10.1186/s40168-023-01652-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 08/23/2023] [Indexed: 10/01/2023]
Abstract
BACKGROUND The increased growth rate of young animals can lead to higher lactation performance in adult goats; however, the effects of the ruminal microbiome on the growth of young goats, and the contribution of the early-life rumen microbiome to lifelong growth and lactation performance in goats has not yet been well defined. Hence, this study assessed the rumen microbiome in young goats with different average daily gains (ADG) and evaluated its contribution to growth and lactation performance during the first lactation period. RESULTS Based on monitoring of a cohort of 99 goats from youth to first lactation, the 15 highest ADG (HADG) goats and 15 lowest ADG (LADG) goats were subjected to rumen fluid microbiome and metabolome profiling. The comparison of the rumen metagenome of HADG and LADG goats revealed that ruminal carbohydrate metabolism and amino acid metabolism function were enhanced in HADG goats, suggesting that the rumen fluid microbiome of HADG goats has higher feed fermentation ability. Co-occurrence network and correlation analysis revealed that Streptococcus, Candidatus Saccharimonans, and Succinivibrionaceae UCG-001 were significantly positively correlated with young goats' growth rates and some HADG-enriched carbohydrate and protein metabolites, such as propionate, butyrate, maltoriose, and amino acids, while several genera and species of Prevotella and Methanogens exhibited a negative relationship with young goats' growth rates and correlated with LADG-enriched metabolites, such as rumen acetate as well as methane. Additionally, some functional keystone bacterial taxa, such as Prevotella, in the rumen of young goats were significantly correlated with the same taxa in the rumen of adult lactation goats. Prevotella also enriched the rumen of LADG lactating goats and had a negative effect on rumen fermentation efficiency in lactating goats. Additional analysis using random forest machine learning showed that rumen fluid microbiota and their metabolites of young goats, such as Prevotellaceae UCG-003, acetate to propionate ratio could be potential microbial markers that can potentially classify high or low ADG goats with an accuracy of prediction of > 81.3%. Similarly, the abundance of Streptococcus in the rumen of young goats could be predictive of milk yield in adult goats with high accuracy (area under the curve 91.7%). CONCLUSIONS This study identified the keystone bacterial taxa that influence carbohydrate and amino acid metabolic functions and shape the rumen fluid microbiota in the rumen of adult animals. Keystone bacteria and their effects on rumen fluid microbiota and metabolome composition during early life can lead to higher lactation performance in adult ruminants. These findings suggest that the rumen microbiome together with their metabolites in young ruminants have long-term effect on feed efficiency and animal performance. The fundamental knowledge may allow us to develop advanced methods to manipulate the rumen microbiome and improve production efficiency of ruminants. Video Abstract.
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Affiliation(s)
- Dangdang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Luyu Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Guangfu Tang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Junjian Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jie Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Zongjun Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yangchun Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xinjian Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Lu Deng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Shengru Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 116 St. and 85 Ave, Edmonton, AB, Canada.
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Raimi AR, Ezeokoli OT, Adeleke RA. Soil nutrient management influences diversity, community association and functional structure of rhizosphere bacteriome under vegetable crop production. Front Microbiol 2023; 14:1229873. [PMID: 37840710 PMCID: PMC10568080 DOI: 10.3389/fmicb.2023.1229873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 09/01/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction Rhizosphere bacterial communities play a crucial role in promoting plant and soil ecosystem health and productivity. They also have great potential as key indicators of soil health in agroecosystems. Various environmental factors affect soil parameters, which have been demonstrated to influence soil microbial growth and activities. Thus, this study investigated how rhizosphere bacterial community structure and functions are affected by agronomic practices such as organic and conventional fertiliser application and plant species types. Methods Rhizosphere soil of vegetable crops cultivated under organic and conventional fertilisers in different farms was analysed using high-throughput sequencing of the 16S rRNA gene and co-occurrence network pattern among bacterial species. The functional structure was analysed with PICRUSt2 pipeline. Results Overall, rhizosphere bacterial communities varied in response to fertiliser type, with soil physicochemical parameters, including NH4, PO4, pH and moisture content largely driving the variations across the farms. Organic farms had a higher diversity richness and more unique amplicon sequence variants than conventional farms. Bacterial community structure in multivariate space was highly differentiated across the farms and between organic and conventional farms. Co-occurrence network patterns showed community segmentation for both farms, with keystone taxa more prevalent in organic than conventional farms. Discussion Module hub composition and identity varied, signifying differences in keystone taxa across the farms and positive correlations between changes in microbial composition and ecosystem functions. The organic farms comprised functionally versatile communities characterised by plant growth-promoting keystone genera, such as Agromyces, Bacillus and Nocardioides. The results revealed that organic fertilisers support high functional diversity and stronger interactions within the rhizosphere bacterial community. This study provided useful information about the overall changes in soil microbial dynamics and how the changes influence ecosystem functioning under different soil nutrient management and agronomic practices.
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Lu Y, Yang J, Zhang L, Chen F, Han P, Fu Y. Characteristics of bacterial community and ARG profiles in the surface and air environments in a spacecraft assembly cleanroom. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 329:121613. [PMID: 37087089 DOI: 10.1016/j.envpol.2023.121613] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/13/2023] [Accepted: 04/09/2023] [Indexed: 05/03/2023]
Abstract
Understanding the microbial communities and antibiotic resistance genes (ARGs) in spacecraft assembly cleanrooms is crucial for spacecraft microbial control and astronaut safety. However, there have been few reports of ARG profiles and their relationship with microbiomes in such environments. In the present study, we assessed the bacterial community and ARGs in the air dust and surface environments of a typical spacecraft assembly cleanroom. Our results show a significant difference in bacterial composition between surfaces and air dust, as they belong to two distinct ecostates. Bacillus and Acinetobacter were significantly enriched in the air samples. Bacterial community network analysis revealed lower topological parameters and robustness of bacterial networks in the air samples. We also observed different distribution patterns of some typical ARGs between surface and air dust samples. Notably, the ermB gene exhibited a relatively high copy number and was enriched in the surface environment, compared to that in the air. Overall, our study provides insight into the complex microbial community and the distribution and transfer of ARGs in spacecraft assembly cleanrooms, and offers important input for developing control strategies against ARGs.
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Affiliation(s)
- Yueying Lu
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing, 100083, China.
| | - Jianlou Yang
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing, 100083, China.
| | - Lantao Zhang
- Institute of Manned Space System and Engineering, China Academy of Space Technology, Beijing, 100094, China.
| | - Fangqi Chen
- Shen Yuan Honors College, Beihang University, Beijing, 100191, China.
| | - Pei Han
- Laboratory of Space Utilization, Technology and Engineering Center for Space Utilization, Chinese Academy of Sciences, Beijing, 100094, China.
| | - Yuming Fu
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China; State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing, 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing, 100083, China.
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Gao P, Qi K, Han Y, Ma L, Zhang B, Zhang Y, Guan X, Qi J. Effect of Trichoderma viride on rhizosphere microbial communities and biocontrol of soybean root rot. Front Microbiol 2023; 14:1204688. [PMID: 37333630 PMCID: PMC10272447 DOI: 10.3389/fmicb.2023.1204688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/15/2023] [Indexed: 06/20/2023] Open
Abstract
Biological seed dressing is a cost-effective means to protect plant roots from pathogens. Trichoderma is generally considered as one of the most common biological seed dressings. However, there is still a dearth of information on the effects of Trichoderma on microbial community of rhizosphere soil. High-throughput sequencing was used to analyze the effects of Trichoderma viride and a chemical fungicide on microbial community of soybean rhizosphere soil. The results showed that both T. viride and chemical fungicide could significantly reduce the disease index of soybean (15.11% for Trichoderma and 17.33% for Chemical), while no significant difference was observed between them. Both T. viride and chemical fungicide could affect the structure of rhizosphere microbial community, they increased the β-diversity of microbial community and significantly reduce the relative abundance of Saprotroph-Symbiotroph. Chemical fungicide could reduce the complexity and stability of co-occurrence network. However, T. viride is beneficial for maintaining network stability and increasing network complexity. There were 31 bacterial genera and 21 fungal genera significantly correlated with the disease index. Furthermore, several potential plant pathogenic microorganisms were also positively correlated with disease index, such as Fusarium, Aspergillus, Conocybe, Naganishia, and Monocillium. From this work, T. viride may be used as a substitute for chemical fungicide to control soybean root rot and be more friendly to soil microecology.
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Affiliation(s)
- Peixin Gao
- Shandong Key Laboratory of Plant Virology, Institution of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Kai Qi
- Shandong Key Laboratory of Plant Virology, Institution of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yujuan Han
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Liguo Ma
- Shandong Key Laboratory of Plant Virology, Institution of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Bo Zhang
- Shandong Key Laboratory of Plant Virology, Institution of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yueli Zhang
- Shandong Key Laboratory of Plant Virology, Institution of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xiumin Guan
- Shandong Agricultural Technology Extension Center, Jinan, China
| | - Junshan Qi
- Shandong Key Laboratory of Plant Virology, Institution of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
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Yuan D, Wang L, Wang H, Miao R, Wang Y, Jin H, Tan L, Wei C, Hu Q, Gong Y. Application of microalgae Scenedesmus acuminatus enhances water quality in rice-crayfish culture. Front Bioeng Biotechnol 2023; 11:1143622. [PMID: 37214297 PMCID: PMC10192885 DOI: 10.3389/fbioe.2023.1143622] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Improper management of aquatic environments substantially restricts the development of the aquaculture industry. The industrialisation of the crayfish Procambarus clarkii, for example, is currently being limited by poor water quality. Research suggests that microalgal biotechnology has a great potential for water quality regulation. However, the ecological effects of microalgal applications on aquatic communities in aquaculture systems remain largely unknown. In the present study, 5 L Scenedesmus acuminatus GT-2 culture (biomass 120 g L-1) was added to an approximately 1,000 m2 rice-crayfish culture to examine the response of aquatic ecosystems to microalgal application. The total nitrogen content decreased significantly as a result of microalgal addition. Moreover, the microalgal addition changed the bacterial community structure directionally and produced more nitrate reducing and aerobic bacteria. The effect of microalgal addition on plankton community structure was not obvious, except for a significant difference in Spirogyra growth which was inhibited by 81.0% under microalgal addition. Furthermore, the network of microorganisms in culture systems with the added microalga had higher interconnectivity and was more complex, which indicating microalgal application enhance the stability of aquaculture systems. The application of microalgae was found to have the greatest effect on the 6th day of the experiment, as supported by both environmental and biological evidence. These findings can provide valuable guidance for the practical application of microalgae in aquaculture systems.
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Affiliation(s)
- Danni Yuan
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Lan Wang
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Hongxia Wang
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Rongli Miao
- Hydrobiological Data Analysis Center, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yulu Wang
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Hu Jin
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Lu Tan
- Systems Ecology and Watershed Ecology Center for Freshwater Ecology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chaojun Wei
- Hydrobiological Data Analysis Center, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Qiang Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yingchun Gong
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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McClure R, Garcia M, Couvillion S, Farris Y, Hofmockel KS. Removal of primary nutrient degraders reduces growth of soil microbial communities with genomic redundancy. Front Microbiol 2023; 13:1046661. [PMID: 36762098 PMCID: PMC9902710 DOI: 10.3389/fmicb.2022.1046661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/21/2022] [Indexed: 01/25/2023] Open
Abstract
Introduction Understanding how microorganisms within a soil community interact to support collective respiration and growth remains challenging. Here, we used a model substrate, chitin, and a synthetic Model Soil Consortium (MSC-2) to investigate how individual members of a microbial community contribute to decomposition and community growth. While MSC-2 can grow using chitin as the sole carbon source, we do not yet know how the growth kinetics or final biomass yields of MSC-2 vary when certain chitin degraders, or other important members, are absent. Methods To characterize specific roles within this synthetic community, we carried out experiments leaving out members of MSC-2 and measuring biomass yields and CO2 production. We chose two members to iteratively leave out (referred to by genus name): Streptomyces, as it is predicted via gene expression analysis to be a major chitin degrader in the community, and Rhodococcus as it is predicted via species co-abundance analysis to interact with several other members. Results Our results showed that when MSC-2 lacked Streptomyces, growth and respiration of the community was severely reduced. Removal of either Streptomyces or Rhodococcus led to major changes in abundance for several other species, pointing to a comprehensive shifting of the microbial community when important members are removed, as well as alterations in the metabolic profile, especially when Streptomyces was lacking. These results show that when keystone, chitin degrading members are removed, other members, even those with the potential to degrade chitin, do not fill the same metabolic niche to promote community growth. In addition, highly connected members may be removed with similar or even increased levels of growth and respiration. Discussion Our findings are critical to a better understanding of soil microbiology, specifically in how communities maintain activity when biotic or abiotic factors lead to changes in biodiversity in soil systems.
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Affiliation(s)
- Ryan McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Marci Garcia
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Sneha Couvillion
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Yuliya Farris
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kirsten S. Hofmockel
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
- Department of Agronomy, Iowa State University, Ames, IA, United States
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Liu MJ, Guo HY, Gao J, Zhu KC, Guo L, Liu BS, Zhang N, Jiang SG, Zhang DC. Characteristics of microplastic pollution in golden pompano (Trachinotus ovatus) aquaculture areas and the relationship between colonized-microbiota on microplastics and intestinal microflora. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159180. [PMID: 36191704 DOI: 10.1016/j.scitotenv.2022.159180] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Microplastic (MPs) pollution is a global marine environmental problem. The effects of MPs on the gut microbiota of aquatic organisms have received considerable attention. For example, microbes colonizing MPs in pond cultures alter the structure and function of the intestinal microbes of shrimp and fish. It was hypothesized that bacteria on MPs in natural mariculture areas also interact with the intestinal flora of golden pompano (Trachinotus ovatus) because biofilms can form on the surface of MPs during long-term floating in seawater. To our knowledge, this study is the first to investigate MPs pollution in T. ovatus aquaculture. DNA sequencing and bioinformatics analysis confirmed the effect of microbial colonization of MPs on the intestinal flora of T. ovatus. The MPs detected in the gut wet weight (w.w.) of golden pompano (546 ± 52 items/g) were mainly pellets and fragments of blue or green, whereas the sediment MPs dry weight (d.w.) (4765 ± 116 items/kg) were mainly black fibers. The MPs richness in the sediment gradually increased from the open-sea aquaculture area to the estuarine aquaculture area and was positively correlated with the MPs richness in the intestinal tract of golden pompano. MPs 20-200 μm were the most common in the gut and sediment. The intake of MPs increased the abundance of Proteobacteria and decreased that of Firmicutes in the intestinal flora. The functional compositions of MP-colonizing microbes and gut microbiota were similar, suggesting that the two communities influence each other. Network analysis further confirmed this and revealed that Vibrio plays a key role in the intestinal flora and surface microorganisms of MPs. Overall, the intake of MPs by aquatic animals not only affects the intestinal flora and intestinal microbial function, but also poses potential risks to aquaculture.
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Affiliation(s)
- Ming-Jian Liu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, Guangdong Province, China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, Guangdong Province, China; College of Fisheries, Tianjin Agricultural University, 300384 Tianjin, China
| | - Hua-Yang Guo
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, Guangdong Province, China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, Guangdong Province, China
| | - Jie Gao
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, Guangdong Province, China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, Guangdong Province, China
| | - Ke-Cheng Zhu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, Guangdong Province, China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, Guangdong Province, China
| | - Liang Guo
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, Guangdong Province, China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, Guangdong Province, China
| | - Bao-Suo Liu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, Guangdong Province, China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, Guangdong Province, China
| | - Nan Zhang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, Guangdong Province, China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, Guangdong Province, China
| | - Shi-Gui Jiang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, Guangdong Province, China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, Guangdong Province, China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, Guangdong Province, China; Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, China
| | - Dian-Chang Zhang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, Guangdong Province, China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, Guangdong Province, China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, Guangdong Province, China; Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, China.
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Wang P, Ding L, Li F, Liao J, Wang M. Herbivore camping reshapes the taxonomy, function and network of pasture soil microbial communities. PeerJ 2022; 10:e14314. [PMID: 36389419 PMCID: PMC9653066 DOI: 10.7717/peerj.14314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/07/2022] [Indexed: 11/11/2022] Open
Abstract
Although the effects of herbivore camping on soil physicochemical properties have been studied, whether the effects alter the soil microbial communities (e.g., composition, functions, taxonomic and functional diversities, network) remain unknown, especially below the surface. Here, using paired subsoil samples from half month-camping and non-camping, we showed for the first time that camping significantly changed the relative abundance of 21 bacterial phylotypes and five fungal phylotypes. Specifically, we observed significant increases in the relative abundance of putative chitinase and terpenes vanillin-decomposition genes, nitrite reduction function (nirB, nasA), decreases in the relative abundance of putative carbon fixation genes (ackA, PGK, and Pak), starch-decomposition gene (dexB), gene coding nitrogenase (anfG), and tetracycline resistance gene (tetB) for bacterial communities, and significant decreases in the relative abundance of animal endosymbiont and increases in the relative abundance of litter saprotroph and endophyte for fungal communities. However, camping did not significantly impact the taxonomic and functional diversity. The niche restriction was the main driving force of bacterial and fungal community assembly. Compared to no camping, camping increased the stability of bacterial networks but decreased the stability of fungal networks. Camping exerted a positive effect on the network by compressing the niche width and reduced the change in the network by reducing the niche overlap. Our results suggest that camping restructures the soil microbial composition, function, and network, and provides a novel insight into the effect of animal camping on soil microbial communities in grassland.
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Affiliation(s)
- Puchang Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou, The People’s Republic of China
| | - Leilei Ding
- Guizhou Institution of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, The People’s Republic of China
| | - Fuxiang Li
- Guizhou Weining plateau Grassland Experimental Station, Weining, Guizhou, The People’s Republic of China
| | - Jiafa Liao
- Guizhou Weining plateau Grassland Experimental Station, Weining, Guizhou, The People’s Republic of China
| | - Mengya Wang
- College of Animal Science, Guizhou University, Guiyang, Guizhou, The People’s Republic of China
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Zhao X, Guo M, Chen J, Zhuang Z, Zhang T, Wang X, Li C, Hou N, Bai S. Successional dynamics of microbial communities in response to concentration perturbation in constructed wetland system. BIORESOURCE TECHNOLOGY 2022; 361:127733. [PMID: 35932946 DOI: 10.1016/j.biortech.2022.127733] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Constructed wetlands (CWs) are widely considered as resilient systems able to adapt to environmental perturbations. Little attention has been paid, however, to microbial dynamics when CWs withstand and recover from external shock. To understand the resilience of CWs, this study investigated rhizosphere microbial dynamics when CWs were subjected to influent COD perturbation (200 mg/L-1600 mg/L). Results demonstrated that CWs had strong adaptability to different influent perturbations, characterized by transitions from fluctuating to stable pollutant removal. Microbial analysis showed that rhizosphere microorganisms competed for niches in response to increased COD concentrations, and Trichococcus played key roles in resisting concentration perturbations. Structural equation modeling indicated that rhizosphere community succession and microbial energy metabolism were shaped by pH and DO. These findings provide insights into the mechanism for CW stability maintenance when facing concentration perturbations.
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Affiliation(s)
- Xinyue Zhao
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Mengran Guo
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Juntong Chen
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Zhixuan Zhuang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Tuoshi Zhang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Xiaohui Wang
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chunyan Li
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Ning Hou
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Shunwen Bai
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
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