1
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Wang A, Li X, Luo X, He G, Huang D, Huang Q, Zhang XX, Chen W. Dissolved organic matter characteristics linked to bacterial community succession and nitrogen removal performance in woodchip bioreactors. J Environ Sci (China) 2025; 148:625-636. [PMID: 39095195 DOI: 10.1016/j.jes.2024.01.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 08/04/2024]
Abstract
Woodchip bioreactors are an eco-friendly technology for removing nitrogen (N) pollution. However, there needs to be more clarity regarding the dissolved organic matter (DOM) characteristics and bacterial community succession mechanisms and their association with the N removal performance of bioreactors. The laboratory woodchip bioreactors were continuously operated for 360 days under three influent N level treatments, and the results showed that the average removal rate of TN was 45.80 g N/(m3·day) when the influent N level was 100 mg N/L, which was better than 10 mg N/L and 50 mg N/L. Dynamic succession of bacterial communities in response to influent N levels and DOM characteristics was an important driver of TN removal rates. Medium to high N levels enriched a copiotroph bacterial module (Module 1) detected by network analysis, including Phenylobacterium, Xanthobacteraceae, Burkholderiaceae, Pseudomonas, and Magnetospirillaceae, carrying N-cycle related genes for denitrification and ammonia assimilation by the rapid consumption of DOM. Such a process can increase carbon limitation to stimulate local organic carbon decomposition to enrich oligotrophs with fewer N-cycle potentials (Module 2). Together, this study reveals that the compositional change of DOM and bacterial community succession are closely related to N removal performance, providing an ecological basis for developing techniques for N-rich effluent treatment.
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Affiliation(s)
- Achen Wang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiang Li
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuesong Luo
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangwen He
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Daqing Huang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xue-Xian Zhang
- School of Natural Sciences, Massey University at Albany, Auckland 0745, New Zealand
| | - Wenli Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
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2
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Liu Z, Guo Z, Zhou J, Guo X, Chen Y. Biotic interactions and environmental modifications determine symbiotic microbial diversity and stability. Comput Struct Biotechnol J 2024; 23:2717-2726. [PMID: 39040687 PMCID: PMC11260581 DOI: 10.1016/j.csbj.2024.05.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 05/09/2024] [Accepted: 05/28/2024] [Indexed: 07/24/2024] Open
Abstract
Taking amphibians as island models, we examined the effects of interspecific interaction on the diversity and stability of microbial ecological. As skin area increased, the diversity and stability of skin microbes decreased, but the strength of negative interactions increased significantly. In contrast, as gut area increased, the diversity and stability of gut microbes increased, but the strength of interactions remained constant. These results indicate that microbial interactions are affected by habitat properties. When living in fluctuating environments without strong filtering, microorganisms can enhance their negative interactions with other taxa by changing the pH of their surroundings. In contrast, the pH of the gut is relatively stable, and colonized microorganisms cannot alter the gut pH and inhibit other colonizers. This study demonstrates that in the field of microbiology, diversity and stability are predominantly influenced by the intensity of interspecies interactions. The findings in this study deepen our understanding of microbial diversity and stability and provide a mechanistic link between species interactions, biodiversity, and stability in microbial ecosystems.
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Affiliation(s)
- Zhidong Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zeguang Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuecheng Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Youhua Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
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3
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Jiao G, Huang Y, Tang H, Chen Y, Zhou D, Yu D, Ma Z, Ni S. Unveiling the hidden impact: How human disturbances threaten aquatic microorganisms in cities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175305. [PMID: 39117200 DOI: 10.1016/j.scitotenv.2024.175305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 07/23/2024] [Accepted: 08/03/2024] [Indexed: 08/10/2024]
Abstract
Urban activity emissions have important ecological significance to bacterial communities' spatial and temporal distribution and the mechanism of bacterial community construction. The mechanism of bacterial community construction is the key to community structure and lifestyle, and the influence of this aspect has not been thoroughly studied. This study analyzed the response of bacteria in water and sediment in different seasons to urban activities in Jinsha River. The results showed that the influence of urban activities on bacterial community structure in sediment was greater than that in water. The input of pollution in different regions changed the diversity and abundance of water and sediments bacteria and promoted bacterial community reconstruction to a certain extent. Co-network analysis found that many metal-mediated species are core species within the same module and can be used to mitigate pollution caused by metal or organic pollutants due to interspecific solid interactions. Different potential pollution sources around urban rivers affect the metabolic function of bacteria in aquatic ecosystems and promote the detoxification function of bacteria in different media. The results of this study supplement our understanding of the characteristics of microbial communities in urban river systems and provide clues for understanding the maintenance mechanism of microbial diversity in multi-pollution environments.
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Affiliation(s)
- Ganghui Jiao
- College of Geosciences, Chengdu University of Technology, Sichuan 610059, China; Yunnan Earthquake Agency, Yunnan 650000, China; Observation Station for Field Scientific Research of Crustal Tectonic Activity in Northwest Yunnan, Dali 671000, China
| | - Yi Huang
- College of Geosciences, Chengdu University of Technology, Sichuan 610059, China; State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, College of Ecology and Environment, Chengdu University of Technology, Sichuan 610059, China.
| | - Hua Tang
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, College of Ecology and Environment, Chengdu University of Technology, Sichuan 610059, China
| | - Ying Chen
- College of Geosciences, Chengdu University of Technology, Sichuan 610059, China
| | - Dan Zhou
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, College of Ecology and Environment, Chengdu University of Technology, Sichuan 610059, China
| | - Daming Yu
- Pangang Group Company Limited, Sichuan 617050, China
| | - Zhongjian Ma
- Pangang Group Company Limited, Sichuan 617050, China
| | - Shijun Ni
- College of Geosciences, Chengdu University of Technology, Sichuan 610059, China
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4
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Cui S, Zhou L, Fang Q, Xiao H, Jin D, Liu Y. Growth period and variety together drive the succession of phyllosphere microbial communities of grapevine. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175334. [PMID: 39117232 DOI: 10.1016/j.scitotenv.2024.175334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/29/2024] [Accepted: 08/04/2024] [Indexed: 08/10/2024]
Abstract
Phyllosphere microbes play a crucial role in plant health and productivity. However, the influence of abiotic and biotic factors on these communities is poorly understood. Here, we used amplicon sequencing to investigate the microbiome variations across eight grape cultivars and three distinct leaf ages. The diversity and richness of phyllosphere microbiomes were significantly affected by cultivars and leaf age. Young leaves of most grape cultivars had a higher diversity. Beta-diversity analyses revealed notable differences in microbial communities across leaf ages, with bacterial communities varying substantially between cultivars. The main bacterial genera included Staphylococcus, Exiguobacterium, Acinetobacter, Enterococcus, and Erwinia; the principal fungal genera were Cladosporium, Moesziomyces, Alternaria, Didymella, and Coprinellus across all samples. LEfSe analysis revealed significant differences in bacterial and fungal biomarkers at different leaf ages, with no biomarkers identified among different cultivars. Fungal biomarkers were more abundant than bacterial at three leaf ages, and older leaves had more fungal biomarkers. Notably, beneficial microbial taxa with biocontrol potential were present on the phyllosphere at 45 d, whereas certain fungal groups associated with increased disease risk were first detected at 100 d. The bacterial network was more complex than the fungal network, and young leaves had a more complex network in most cultivars. Our study elucidated the dynamics of early grape phyllosphere microbes, providing valuable insights for early detection and prediction of grape diseases and a foundation for leveraging the grape leaf microbiome for agricultural purposes.
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Affiliation(s)
- Shaowei Cui
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; School of Grassland Science, Beijing Forestry University, Beijing 100083, China
| | - Lianzhu Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qiandong Fang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Haijun Xiao
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China
| | - Decai Jin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Yongqiang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Shu D, Banerjee S, Mao X, Zhang J, Cui W, Zhang W, Zhang B, Chen S, Jiao S, Wei G. Conversion of monocropping to intercropping promotes rhizosphere microbiome functionality and soil nitrogen cycling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174953. [PMID: 39069174 DOI: 10.1016/j.scitotenv.2024.174953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/07/2024] [Accepted: 07/20/2024] [Indexed: 07/30/2024]
Abstract
Intercropping can increase soil nutrient availability and provide greater crop yields for intensive agroecosystems. Despite its multiple benefits, how intercropping influences rhizosphere microbiome assemblages, functionality, and complex soil nitrogen cycling is not fully understood. Here, a three-year field experiment was carried out on different cropping system with five fertilization treatments at the main soybean production regions. We found that soybean yields in intercropped systems were on average 17 % greater than in monocropping system, regardless of fertilization treatments. We also found that intercropping systems significant increased network modularity (by 46 %) and functional diversity (by 11 %) than monocropping systems. Metagenomics analyses further indicated intercropping promotes microbiome functional adaptation, particularly enriching core functions related to nitrogen metabolism. Cropping patterns had a stronger influence on the functional genes associated with soil nitrogen cycling (R2 = 0.499). Monocropping systems increased the abundance of functional genes related to organic nitrogen ammonification, nitrogen fixation, and denitrification, while functional guilds of nitrate assimilation (by 28 %), nitrification (by 31 %), and dissimilatory nitrate reduction (by 10.1 %) genes were enriched in intercropping systems. Furthermore, we found that abiotic factors (i.e. AP, pH, and Moisture) are important drivers in shaping soil microbial community assemblage and nitrogen cycling. The functional genes include hzsB, and nrfA, and nxrA that affected by these biotic and abiotic variables were strongly related to crop yield (R2 = 0.076 ~ R2 = 0.249), suggesting a key role for maintaining crop production. We demonstrated that land use conversion from maize monocropping to maize-soybean intercropping diversify rhizosphere microbiome and functionality signatures, and intercropping increased key gene abundance related to soil nitrogen cycling to maintain the advantage of crop yield. The results of this study significantly facilitate our understanding of the complex soil nitrogen cycling processes and lay the foundation for manipulating desired specific functional taxa for improved crop productivity under sustainable intensification.
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Affiliation(s)
- Duntao Shu
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China.
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo 58102, ND, USA
| | - Xinyi Mao
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Jiaqi Zhang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Weili Cui
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Wu Zhang
- Heihe Branch, Heilongjiang Academy of Agricultural Sciences, Heihe, Heilongjiang 150086, China
| | - Baogang Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Sanfeng Chen
- College of Biological Sciences, China Agricultural University, Beijing 100091, China
| | - Shuo Jiao
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Gehong Wei
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China.
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6
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Wang X, Deng W, Hu H, Jia X, Chen J, Fang P, Cheng C, Zhang S, Jiang X, Ding D, Ma B. Seasonal variations in soil microbial community co-occurrence network complexity respond differently to field-simulated warming experiments in a northern subtropical forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174692. [PMID: 39002597 DOI: 10.1016/j.scitotenv.2024.174692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024]
Abstract
Global warming may reshape seasonal changes in microbial community diversity and co-occurrence network patterns, with significant implications for terrestrial ecosystem function. We conducted a 2-year in situ field simulation of the effects of warming on the seasonal dynamics of soil microbial communities in a northern subtropical Quercus acutissima forest. Our study revealed that warming had no significant effect on the richness or diversity of soil bacteria or fungi in the growing season, whereas different warming gradients had different effects on their diversity in the nongrowing season. Warming also changed the microbial community structure, increasing the abundance of some thermophilic microbial species and decreasing the abundance of some symbiotrophic microorganisms. The co-occurrence network analysis of the microbial community showed that warming decreased the complexity of the intradomain network in the soil bacterial community in the growing and nongrowing seasons but increased it in the fungal community. Moreover, increasing warming temperatures increased the complexity of the interdomain network between bacteria and fungi in the growing season but decreased it in the nongrowing season, and the keystone species in the interdomain network changed with warming. Warming also reduced the proportion of positive microbial community interactions, indicating that warming reduced the mutualism, commensalism, and neutralism of microorganisms as they adapted to soil environmental stress. The factors affecting the fungal community varied considerably across warming gradients, with the bacterial community being significantly affected by soil temperature, MBC, NO3--N and NH4+-N, moreover, SOC and TN significantly affected fungal communities in the 4 °C warming treatment. These results suggest that warming increases seasonal differences in the diversity and complexity of soil microbial communities in the northern subtropical region, significantly influencing soil dynamic processes regulating forest ecosystems under global warming.
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Affiliation(s)
- Xia Wang
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Soil and Water Conservation and Ecological Restoration in Jiangsu Province, Nanjing 210037, China
| | - Wenbin Deng
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Soil and Water Conservation and Ecological Restoration in Jiangsu Province, Nanjing 210037, China
| | - Haibo Hu
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Soil and Water Conservation and Ecological Restoration in Jiangsu Province, Nanjing 210037, China.
| | - Xichuan Jia
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Soil and Water Conservation and Ecological Restoration in Jiangsu Province, Nanjing 210037, China
| | - Jianyu Chen
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Soil and Water Conservation and Ecological Restoration in Jiangsu Province, Nanjing 210037, China
| | - Pei Fang
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Soil and Water Conservation and Ecological Restoration in Jiangsu Province, Nanjing 210037, China
| | - Can Cheng
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Soil and Water Conservation and Ecological Restoration in Jiangsu Province, Nanjing 210037, China
| | - Shuai Zhang
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Soil and Water Conservation and Ecological Restoration in Jiangsu Province, Nanjing 210037, China
| | - Xuyi Jiang
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Soil and Water Conservation and Ecological Restoration in Jiangsu Province, Nanjing 210037, China
| | - Dongxia Ding
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Soil and Water Conservation and Ecological Restoration in Jiangsu Province, Nanjing 210037, China
| | - Bing Ma
- Geological Environment Exploration Institute of Jiangsu Province, Nanjing 211102, China
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7
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Wang N, Ding D, Zhang H, Ding X, Zhang D, Yao C, Fan X, Ding R, Wang H, Jiang T. Anthropogenic activity shapes the assemble and co-occurrence pattern of microbial communities in fishing harbors around the Bohai economic circle. ENVIRONMENTAL RESEARCH 2024; 259:119563. [PMID: 38971358 DOI: 10.1016/j.envres.2024.119563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/25/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
This study aimed to elucidate the effects of coastal environmental stress on the composition of sediment bacterial communities and their cooccurrence patterns in fishing harbors around the Bohai Economic Circle, China. Compared with the natural sea area, fishing harbors contained higher levels of organic pollution (organic pollution index = 0.12 ± 0.026) and considerably reduced bacterial richness and evenness. The distributions of sediment microbial communities clustered along the pollutant concentration gradients across fishing harbors. Betaproteobacteria dominated (76%) organically polluted fishing harbors, which were mostly disturbed by anthropogenic activities. However, the harbors also revealed the absence of numerous pathogenic (Coxiella and Legionella) and photosynthetic (Synechococcus and Leptolyngbya) bacteria. Abundant genera, including Thiobacillus and Arenimonas, exhibited a positive correlation with total phosphorus and a negative correlation with total nitrogen in sediments. Meanwhile, Sulfurovum, Psychrobacter, and Woeseia showed the opposite trend. Pollutant accumulation and anthropogenic activities caused the decrease in the sediment microbial diversity and dispersal ability and promoted convergent evolution. Severely polluted harbors with simplified cooccurrence networks revealed the presence of destabilized microbial communities. In addition, the modularity of bacterial networks decreased with organic pollution. Our results provide important insights into the adjustment mechanism of microbial communities to community organization and functions under environmental pollution stress. Overall, this study enhanced our understanding of how microbial communities in coastal sediments adapted and survived amidst anthropogenic activities like oily effluent discharges from large ships, wash water, domestic sewage, garbage, and fisheries wastes. It also examined their resilience to future contamination.
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Affiliation(s)
- Nan Wang
- School of Ocean, Yantai University, Yantai, 264005, China
| | - Dongsheng Ding
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Huihui Zhang
- School of Ocean, Yantai University, Yantai, 264005, China
| | - Xiaokun Ding
- School of Ocean, Yantai University, Yantai, 264005, China
| | - Di Zhang
- School of Ocean, Yantai University, Yantai, 264005, China
| | - Chenghao Yao
- Shandong Hongxin Environmental Protection Technology Co., Ltd, China
| | - Xiao Fan
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - RenYe Ding
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Hualong Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, And Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, 266003, China.
| | - Tao Jiang
- School of Ocean, Yantai University, Yantai, 264005, China.
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Guan X, Jia D, Liu X, Ding C, Guo J, Yao M, Zhang Z, Zhou M, Sun J. Combined influence of the nanoplastics and polycyclic aromatic hydrocarbons exposure on microbial community in seawater environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 945:173772. [PMID: 38871313 DOI: 10.1016/j.scitotenv.2024.173772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/21/2024] [Accepted: 06/02/2024] [Indexed: 06/15/2024]
Abstract
Nanoplastics (NPs) and polycyclic aromatic hydrocarbons (PAHs) are recognized as persistent organic pollutant (POPs) with demonstrated physiological toxicity. When present in aquatic environments, the two pollutants could combine with each other, resulting in cumulative toxicity to organisms. However, the combined impact of NPs and PAHs on microorganisms in seawater is not well understood. In this study, we conducted an exposure experiment to investigate the individual and synergistic effects of NPs and PAHs on the composition, biodiversity, co-occurrence networks of microbial communities in seawater. Exposure of individuals to PAHs led to a reduction in microbial community richness, but an increase in the relative abundance of species linked to PAHs degradation. These PAHs-degradation bacteria acting as keystone species, maintained a microbial network complexity similar to that of the control treatment. Exposure to individual NPs resulted in a reduction in the complexity of microbial networks. Furthermore, when PAHs and NPs were simultaneously present, the toxic effect of NPs hindered the presence of keystone species involved in PAHs degradation, subsequently limiting the degradation of PAHs by marine microorganisms, resulting in a decrease in community diversity and symbiotic network complexity. This situation potentially poses a heightened threat to the ecological stability of marine ecosystems. Our work strengthened the understanding of the combined impact of NPs and PAHs on microorganisms in seawater.
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Affiliation(s)
- Xin Guan
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China
| | - Dai Jia
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China.
| | - Xinyu Liu
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China
| | - Changling Ding
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China; Institute for Advanced Marine Research, China University of Geosciences (Wuhan), Guangzhou, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, China
| | - Jinfei Guo
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China
| | - Min Yao
- Jiangsu Hydrology and Water Resources Survey Bureau, Nanjing, China
| | - Zhan Zhang
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China
| | - Mengxi Zhou
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China
| | - Jun Sun
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China; Institute for Advanced Marine Research, China University of Geosciences (Wuhan), Guangzhou, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, China.
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9
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Nef C, Pierella Karlusich JJ, Bowler C. From nets to networks: tools for deciphering phytoplankton metabolic interactions within communities and their global significance. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230172. [PMID: 39034691 PMCID: PMC11293860 DOI: 10.1098/rstb.2023.0172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/26/2024] [Accepted: 03/21/2024] [Indexed: 07/23/2024] Open
Abstract
Our oceans are populated with a wide diversity of planktonic organisms that form complex dynamic communities at the base of marine trophic networks. Within such communities are phytoplankton, unicellular photosynthetic taxa that provide an estimated half of global primary production and support biogeochemical cycles, along with other essential ecosystem services. One of the major challenges for microbial ecologists has been to try to make sense of this complexity. While phytoplankton distributions can be well explained by abiotic factors such as temperature and nutrient availability, there is increasing evidence that their ecological roles are tightly linked to their metabolic interactions with other plankton members through complex mechanisms (e.g. competition and symbiosis). Therefore, unravelling phytoplankton metabolic interactions is the key for inferring their dependency on, or antagonism with, other taxa and better integrating them into the context of carbon and nutrient fluxes in marine trophic networks. In this review, we attempt to summarize the current knowledge brought by ecophysiology, organismal imaging, in silico predictions and co-occurrence networks using 'omics data, highlighting successful combinations of approaches that may be helpful for future investigations of phytoplankton metabolic interactions within their complex communities.This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.
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Affiliation(s)
- Charlotte Nef
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris75005, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris75016, France
| | | | - Chris Bowler
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris75005, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris75016, France
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10
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Qiu J, Bai J, Wang Y, Zhai Y, Zhang X, Xu Y, Wang Y. Cadmium contamination decreased bacterial network complexity and stability in coastal reclamation areas. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:134896. [PMID: 38909464 DOI: 10.1016/j.jhazmat.2024.134896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 06/02/2024] [Accepted: 06/11/2024] [Indexed: 06/25/2024]
Abstract
Cadmium(Cd) contamination can exert significantly adverse effects on soil microbiota in reclaimed areas, however, its effects on bacterial network structure are still limitedly understood. Here we collected soil samples from typical reclaimed wetlands (RW) and ditch wetlands (DW) in coastal reclamation areas and examined the effects of Cd contamination on the bacterial network complexity and stability. The results showed that the bacterial networks were destabilized by the Cd contamination, while bacteria in DW soils showed robust invulnerability characterized by higher node constancy and compositional stability compared with RW soils. Soil bacteria resisted Cd stress by forming a network with intensive connections in the module but sparser connections among the modules. Especially, network modularity was higher in DW soils than in RW soils, but made it more vulnerable to nodes removal. In addition, Cd contamination promoted bacterial positive cohesion but decreased negative cohesion in RW soils. Flavobacteriaceae, Xanthomonadaceae, and Alcaligenaceae were identified as core phylotypes, which played pivotal roles in regulating interspecies interactions due to higher contributions to cohesion and significant correlations with soil nutrients. The findings of this work indicate the changes of bacterial network structure and the indispensable role of core phylotypes in regulating interactions and maintaining network sustainability under Cd contamination.
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Affiliation(s)
- Jichen Qiu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China.
| | - Yimeng Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Yujia Zhai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Xuehui Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Yuhao Xu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Yaqi Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
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11
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Wang Y, Gu W, Xu Z, Lv L, Wang D, Jin Y, Wang X. Comprehensive multi-omics investigation of sub-chronic toxicity induced by Cadmium and Triazophos Co-exposure in hook snout carps (Opsariichthys bidens). JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135104. [PMID: 38970972 DOI: 10.1016/j.jhazmat.2024.135104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/18/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
The coexistence of heavy metals and pesticides poses a critical challenge in agricultural ecosystems. Traditional toxicity assessments often focus only on the individual impacts of either pesticides or heavy metals. Here, the untargeted metabolomics and 16 S rRNA sequencing were used to assess the individual and combined effects of cadmium (Cd) and triazophos (TRI) on hook snout carps (Opsariichthys bidens). Cd caused much more serious impacts on hepatic metabolism and gut microbiota than those in TRI. Combined Cd and TRI exposure synergistically affected hepatic metabolism, causing mitochondrial dysfunction and even oxidative damage. Simultaneously, 16 S rRNA sequencing highlighted significant variations in the composition and abundance of gut microbiota. A noteworthy connection emerged between these distinct microbiota profiles and disruptions in energy metabolism, ultimately leading to disorders in metabolites. These findings enhanced the understanding of risks posed by heavy metals and pesticides, providing insights for better environmental risk assessments of aquatic organisms.
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Affiliation(s)
- Yanhua Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, PR China
| | - Weijie Gu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, Zhejiang, PR China
| | - Zhenlan Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, PR China
| | - Lu Lv
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, PR China
| | - Dou Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, PR China
| | - Yuanxiang Jin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, Zhejiang, PR China.
| | - Xinquan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, PR China.
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12
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Zhong S, Feng JC, Chen X, Huang YJ, Wu XN, Zhang S. Exploring optimal incubation conditions and characteristics of methane oxidizing organisms in deep-sea environments. BIORESOURCE TECHNOLOGY 2024; 407:131084. [PMID: 39025372 DOI: 10.1016/j.biortech.2024.131084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/20/2024]
Abstract
Anaerobic methanotrophic archaea (ANME) play key roles in buffering the methane budget in the deep-sea environment. This study aimed to explore the optimal environmental conditions for ANME enrichment. The result showed that the sample at 10.5 MPa contained the largest copy numbers of methyl-coenzyme M reductase alpha subunit (mcrA) gene (1.1 × 106 copies/g) compared to any other pressures and the sample at 4 °C contained higher mcrA gene (1.6 × 106 copies/g) than other temperatures. The optimal enrichment pressure for ANME-2c is 10.5 MPa at 4 °C, with an optimal subsequent incubation for ANME-2c less than 211days. Moreover, the beta nearest taxon index was significantly correlated with the incubation time (P<0.05). Total inorganic carbon and sulfate ion were key environmental factors driving community construction. This study offers insights into how ANME-2c was enriched and how species coexist in shared habitats during enrichment.
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Affiliation(s)
- Song Zhong
- School of Ecology, Environmental, and Resources, Guangdong University of Technology, Guangzhou 510006, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
| | - Jing-Chun Feng
- School of Ecology, Environmental, and Resources, Guangdong University of Technology, Guangzhou 510006, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Guangdong Basic Research Center of Excellence for Ecological Security and Green Development, Guangzhou 511458, China.
| | - Xiao Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
| | - Yong-Ji Huang
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Xiao-Nan Wu
- School of Ecology, Environmental, and Resources, Guangdong University of Technology, Guangzhou 510006, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
| | - Si Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
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13
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Yang Z, Liu T, Fan J, Chen Y, Wu S, Li J, Liu Z, Yang Z, Li L, Liu S, Yang H, Yin H, Meng D, Tang Q. Biocontrol agents modulate phyllosphere microbiota interactions against pathogen Pseudomonas syringae. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 21:100431. [PMID: 38883559 PMCID: PMC11177076 DOI: 10.1016/j.ese.2024.100431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 06/18/2024]
Abstract
The pathogen Pseudomonas syringae, responsible for a variety of diseases, poses a considerable threat to global crop yields. Emerging biocontrol strategies employ antagonistic microorganisms, utilizing phyllosphere microecology and systemic resistance to combat this disease. However, the interactions between phyllosphere microbial dynamics and the activation of the plant defense system remain poorly understood. Here we show significant alterations in phyllosphere microbiota structure and plant gene expression following the application of biocontrol agents. We reveal enhanced collaboration and integration of Sphingomonas and Methylobacterium within the microbial co-occurrence network. Notably, Sphingomonas inhibits P. syringae by disrupting pathogen chemotaxis and virulence. Additionally, both Sphingomonas and Methylobacterium activate plant defenses by upregulating pathogenesis-related gene expression through abscisic acid, ethylene, jasmonate acid, and salicylic acid signaling pathways. Our results highlighted that biocontrol agents promote plant health, from reconstructing beneficial microbial consortia to enhancing plant immunity. The findings enrich our comprehension of the synergistic interplays between phyllosphere microbiota and plant immunity, offering potential enhancements in biocontrol efficacy for crop protection.
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Affiliation(s)
- Zhaoyue Yang
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, Hunan, China
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China
| | - Tianbo Liu
- Hunan Tobacco Research Institute, Changsha, 410004, Hunan, China
| | - Jianqiang Fan
- Technology Center, Fujian Tobacco Industrial Co.,Ltd., Xiamen, 361000, Fujian, China
| | - Yiqiang Chen
- Technology Center, Fujian Tobacco Industrial Co.,Ltd., Xiamen, 361000, Fujian, China
| | - Shaolong Wu
- Hunan Tobacco Research Institute, Changsha, 410004, Hunan, China
| | - Jingjing Li
- Technology Center, Fujian Tobacco Industrial Co.,Ltd., Xiamen, 361000, Fujian, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China
| | - Zhendong Yang
- School of Architecture and Civil Engineering, Chengdu University, Chengdu, 610106, Sichuan, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China
| | - Suoni Liu
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Hongwu Yang
- Yongzhou Tobacco Corporation, Yongzhou, 425000, Hunan, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China
| | - Qianjun Tang
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, Hunan, China
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14
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Fang K, Kou YP, Tang N, Liu J, Zhang XY, He HL, Xia RX, Zhao WQ, Li DD, Liu Q. Differential responses of soil bacteria, fungi and protists to root exudates and temperature. Microbiol Res 2024; 286:127829. [PMID: 39018940 DOI: 10.1016/j.micres.2024.127829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 06/30/2024] [Indexed: 07/19/2024]
Abstract
The impact of climate warming on soil microbes has been well documented, with studies revealing its effects on diversity, community structure and network dynamics. However, the consistency of soil microbial community assembly, particularly in response to diverse plant root exudates under varying temperature conditions, remains an unresolved issue. To address this issue, we employed a growth chamber to integrate temperature and root exudates in a controlled experiment to examine the response of soil bacteria, fungi, and protists. Our findings revealed that temperature independently regulated microbial diversity, with distinct patterns observed among bacteria, fungi, and protists. Both root exudates and temperature significantly influenced microbial community composition, yet interpretations of these factors varied among prokaryotes and eukaryotes. In addition to phototrophic bacteria and protists, as well as protistan consumers, root exudates determined to varying degrees the enrichment of other microbial functional guilds at specific temperatures. The effects of temperature and root exudates on microbial co-occurrence patterns were interdependent; root exudates primarily simplified the network at low and high temperatures, while responses to temperature varied between single and mixed exudate treatments. Moreover, temperature altered the composition of keystone species within the microbial network, while root exudates led to a decrease in their number. These results emphasize the substantial impact of plant root exudates on soil microbial community responses to temperature, underscoring the necessity for future climate change research to incorporate additional environmental variables.
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Affiliation(s)
- Kai Fang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China; College of Agriculture and Biological Sciences, Dali University, Dali 671003, China
| | - Yong-Ping Kou
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China.
| | - Na Tang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Jia Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Xiao-Ying Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - He-Liang He
- College of Agriculture, Forestry and Food Engineering, Yibin University, Yibin 644007, China
| | - Rui-Xue Xia
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Wen-Qiang Zhao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Dan-Dan Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Qing Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China.
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15
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Cao F, Shu W, Liu Q, Wan J, Jiang Z, Liu M, Jiang Y. Distinct structure, assembly, and gene expression of microplankton in two Arctic estuaries with varied terrestrial inputs. ENVIRONMENTAL RESEARCH 2024; 256:119207. [PMID: 38782345 DOI: 10.1016/j.envres.2024.119207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/05/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
The Laptev Sea is a major Marginal Sea in the Western Arctic Ocean. The Arctic amplification brought by global warming influences the hydrological properties of rivers passing through the permafrost zone, which would alter the biological community structure at continental margin. In this study, the structure, assembly, and gene expression of planktonic microbial communities in two estuaries (Protoka Ularovskaya River Estuary, PURE; Lena River Estuary, LRE) of Laptev Sea were examined to investigate the environmental effects of polar rivers. PURE and LRE exhibited distinct environmental characteristics: low temperature and high salinity for PURE, and high temperature and low salinity for LRE, influenced by runoff size. Salinity more closely influenced microbial communities in LRE, with freshwater species playing a significant role in community composition. The findings revealed differences between two estuaries in community composition and diversity. Prokaryotes and microeukaryotes had shown different assembly patterns in response to habitat changes caused by terrestrial freshwater input. Furthermore, compared with the PURE, the co-occurrence and inter-domain network of the LRE, which was more affected by terrestrial input, was more complex and stable. Functional gene prediction revealed a higher gene expression of methane metabolism in LRE than in PURE, particularly those related to methane oxidation, and this conclusion could help better explore the impact of global warming on the methane cycle in the Arctic Marginal Seas. This study explored the increased freshwater runoffs under the background of global warming dramatically affect Arctic microplankton communities from community structure, assembly and gene expression aspects.
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Affiliation(s)
- Furong Cao
- MoE Key Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China; College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Wangxinze Shu
- MoE Key Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Qian Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266003, China
| | - Jiyuan Wan
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Zhiyang Jiang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Mingjian Liu
- MoE Key Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China; College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
| | - Yong Jiang
- MoE Key Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China; College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China; Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China.
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16
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Wu R, Xia H, Wu Y, Zhang S, Fang J, Wang Y, Wang H, Zhu Y, Liu L, Du S. Graphene oxide inhibits the transfer of ARGs in rice by reducing the root endophytic bacterial complexity. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 368:122241. [PMID: 39186855 DOI: 10.1016/j.jenvman.2024.122241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 08/12/2024] [Accepted: 08/16/2024] [Indexed: 08/28/2024]
Abstract
Antibiotic resistance genes (ARGs) as an emerging contaminant have attracted much attention for their transfer in agricultural ecosystems. Meanwhile, graphene oxide (GO), due to its high adsorption capacity and antibacterial properties, poses potential environmental ecological risks to the occurrence of ARGs, bacteria, and plant physiological ecology. However, the impact and mechanism of GO on the transfer of ARGs in host plants remain unclear. Therefore, this study selected rice as the research object and inoculated Bacillus subtilis carrying ARGs to investigate the influence of GO on the migration of ARGs into rice and its microbiological mechanism. The study found that GO had a certain inhibitory effect on the transfer of ARGs in rice. Although GO reduced the rhizosphere pH in rice, leading to a transition in endophytic bacteria from dominance by Burkholderia to dominance by Gordonia, this process did not directly affect the transfer of ARGs in rice. Further analysis of bacterial interactions revealed that GO could inhibit the transfer of ARGs in rice by reducing the network complexity of endophytic bacteria. Additionally, GO inhibited the formation of endophytic bacterial biofilms and mobile elements, which might affect ARGs' migration in rice. This study elucidated the key microbiological ecological processes of GO on the transfer of ARGs in rice, providing fundamental information for the ecological risk assessment of GO.
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Affiliation(s)
- Ran Wu
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China
| | - Hanche Xia
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China
| | - Yue Wu
- Zhejiang Zhongyi Testing Research Institute Co., Ltd, Ningbo, 315040, China
| | - Siyu Zhang
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China
| | - Jin Fang
- College of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Yuying Wang
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China
| | - Hua Wang
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Yaxin Zhu
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China
| | - Lijuan Liu
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China
| | - Shaoting Du
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China.
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17
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Afarin M, Naeimpoor F. Effect of microbial interactions on performance of community metabolic modeling algorithms: flux balance analysis (FBA), community FBA (cFBA) and SteadyCom. Bioprocess Biosyst Eng 2024:10.1007/s00449-024-03072-7. [PMID: 39180547 DOI: 10.1007/s00449-024-03072-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 07/30/2024] [Indexed: 08/26/2024]
Abstract
To explore the impact of microbial interactions on outcomes from three prevalent algorithms (Flux Balance Analysis (FBA), community FBA (cFBA), and SteadyCom) analyzing microbial community metabolic networks, five toy community models representing common microbial interactions were designed. These include commensalism, mutualism, competition, mutualism-competition, and commensalism-competition. Various scenarios, considering different biomass yields and substrate constraints, were examined for each type. In commensal communities, all algorithms consistently produced similar results. However, changes in biomass yields and substrate constraints led to variable abundances (0.33-0.8) and community growth rates (2-5 1/h) within a broad range. For competitive communities, all algorithms predicted growth of fastest-growing member. To comply with the natural coexistence of members, suboptimal solutions over optimal point are recommended. FBA faced challenges in modeling mutualism, consistently predicting growth of only one member. Although cFBA and SteadyCom resulted in a lower community growth rate, coexistence of both members were satisfied. In toy models with dual interactions, more realistic outcomes were achieved contrary to purely competitive model as the dependency fosters the coexistence which was missing in the competitive only scenarios. These findings emphasize the importance of algorithm choice based on specific microbial interaction types for reliable community behavior predictions..
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Affiliation(s)
- Maryam Afarin
- Biotechnology Research Laboratory, School of Chemical, Petroleum and Gas Engineering, Iran University of Science and Technology, Tehran, Iran
| | - Fereshteh Naeimpoor
- Biotechnology Research Laboratory, School of Chemical, Petroleum and Gas Engineering, Iran University of Science and Technology, Tehran, Iran.
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18
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Skičková Š, Kratou M, Svobodová K, Maitre A, Abuin-Denis L, Wu-Chuang A, Obregón D, Said MB, Majláthová V, Krejčí A, Cabezas-Cruz A. Functional redundancy and niche specialization in honeybee and Varroa microbiomes. Int Microbiol 2024:10.1007/s10123-024-00582-y. [PMID: 39172274 DOI: 10.1007/s10123-024-00582-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/07/2024] [Accepted: 08/13/2024] [Indexed: 08/23/2024]
Abstract
The honeybee (Apis mellifera) is a key pollinator critical to global agriculture, facing threats from various stressors, including the ectoparasitic Varroa mite (Varroa destructor). Previous studies have identified shared bacteria between Varroa mites and honeybees, yet it remains unclear if these bacteria assemble similarly in both species. This study builds on existing knowledge by investigating co-occurrence patterns in the microbiomes of both Varroa mites and honeybees, shedding light on potential interactions. Leveraging 16S rRNA datasets, we conducted co-occurrence network analyses, explored Core Association Networks (CAN) and assess network robustness. Comparative network analyses revealed structural differences between honeybee and mite microbiomes, along with shared core features and microbial motifs. The mite network exhibited lower robustness, suggesting less resistance to taxa extension compared to honeybees. Furthermore, analyses of predicted functional profiling and taxa contribution revealed that common central pathways in the metabolic networks have different taxa contributing to Varroa mites and honeybee microbiomes. The results show that while both microbial systems exhibit functional redundancy, in which different taxa contribute to the functional stability and resilience of the ecosystem, there is evidence for niche specialization resulting in unique contributions to specific pathways in each part of this host-parasite system. The specificity of taxa contribution to key pathways offers targeted approaches to Varroa microbiome management and preserving honeybee microbiome. Our findings provide valuable insights into microbial interactions, aiding farmers and beekeepers in maintaining healthy and resilient bee colonies amid increasing Varroa mite infestations.
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Affiliation(s)
- Štefánia Skičková
- Pavol Jozef Šafárik University in Košice, Faculty of Science, Institute of Biology and Ecology, Department of Animal Physiology, Košice, 04181, Slovakia.
| | - Myriam Kratou
- Laboratory of Microbiology, National School of Veterinary Medicine of Sidi Thabet, University of Manouba, 2010, Manouba, Tunisia
| | - Karolína Svobodová
- University of South Bohemia, Faculty of Science, České Budějovice, 37005, Czech Republic
| | - Apolline Maitre
- ANSES, INRAE, École Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France
- INRAE, UR 0045 Laboratoire de Recherches Sur Le Développement de L'Elevage (SELMET-LRDE), 20250, Corte, France
- EA 7310, Laboratoire de Virologie, Université de Corse, 20250, Corte, France
| | - Lianet Abuin-Denis
- ANSES, INRAE, École Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France
- Animal Biotechnology Department, Center for Genetic Engineering and Biotechnology, Avenue 31 Between 158 and 190, P.O. Box 6162, 10600, Havana, Cuba
| | - Alejandra Wu-Chuang
- ANSES, INRAE, École Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France
| | - Dasiel Obregón
- School of Environmental Sciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Mourad Ben Said
- Laboratory of Microbiology, National School of Veterinary Medicine of Sidi Thabet, University of Manouba, 2010, Manouba, Tunisia
- Department of Basic Sciences, Higher Institute of Biotechnology of Sidi Thabet, University of Manouba, 2010, Manouba, Tunisia
| | - Viktória Majláthová
- Pavol Jozef Šafárik University in Košice, Faculty of Science, Institute of Biology and Ecology, Department of Animal Physiology, Košice, 04181, Slovakia
| | - Alena Krejčí
- University of South Bohemia, Faculty of Science, České Budějovice, 37005, Czech Republic
- Czech Academy of Sciences, Biology Centre, Institute of Entomology, České Budějovice, 37005, Czech Republic
| | - Alejandro Cabezas-Cruz
- ANSES, INRAE, École Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France.
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19
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Chen J, Cui Y, Xiao Q, Lin K, Wang B, Zhou J, Li X. Difference in microbial community structure along a gradient of crater altitude: insights from the Nushan volcano. Appl Environ Microbiol 2024; 90:e0075324. [PMID: 39028194 PMCID: PMC11337807 DOI: 10.1128/aem.00753-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/20/2024] [Indexed: 07/20/2024] Open
Abstract
The variation in the soil microbial community along the altitude gradient has been widely documented. However, the structure and function of the microbial communities distributed along the altitude gradient in the crater still need to be determined. We gathered soil specimens from different elevations within the Nushan volcano crater to bridge this knowledge gap. We investigated the microbial communities of bacteria and fungi in the soil. It is noteworthy that the microbial alpha diversity peaks in the middle of the crater. However, network analysis shows that bacterial (nodes 760 vs 613 vs 601) and fungal (nodes 328 vs 224 vs 400) communities are most stable at the bottom and top of the crater, respectively. Furthermore, the soil microbial network exhibited a decline, followed by an increase across varying altitudes. The core microorganisms displayed the highest correlation with pH and alkaline phosphatase (AP, as determined through redundancy analysis (RDA) and Mantel tests for correlation analysis. The fungal community has a higher number of core microorganisms, while the bacterial core microorganisms demonstrate greater susceptibility to environmental factors. In conclusion, we utilized Illumina sequencing techniques to assess the disparities in the structure and function of bacteria and fungi in the soil.IMPORTANCEThese findings serve as a foundation for future investigations on microbial communities present in volcanic soil.
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Affiliation(s)
- Jin Chen
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Stress Resistance and High-Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Ye Cui
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Stress Resistance and High-Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Qingchen Xiao
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Stress Resistance and High-Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Keqin Lin
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Stress Resistance and High-Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Boyan Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Stress Resistance and High-Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Jing Zhou
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Stress Resistance and High-Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Xiaoyu Li
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Stress Resistance and High-Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
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Liu J, Qian Y, Yang W, Yang M, Zhang Y, Duan B, Yang Y, Tao A, Xia C. Elucidating the interaction of rhizosphere microorganisms and environmental factors influencing the quality of Polygonatum kingianum Coll. et Hemsl. Sci Rep 2024; 14:19092. [PMID: 39154075 PMCID: PMC11330475 DOI: 10.1038/s41598-024-69673-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 08/07/2024] [Indexed: 08/19/2024] Open
Abstract
Polygonatum kingianum Collett & Hemsl., is one of the most important traditional Chinese medicines in China. The purpose of this study is to investigate the relationship between herb quality and microbial-soil variables, while also examining the composition and structure of the rhizosphere microbial community in Polygonatum kingianum, the ultimate goal is to provide a scientific approach to enhancing the quality of P. kingianum. Illumina NovaSeq technology unlocks comprehensive genetic variation and biological functionality through high-throughput sequencing. And in this study it was used to analyze the rhizosphere microbial communities in the soils of five P. kingianum planting areas. Conventional techniques were used to measure the organic elements, pH, and organic matter content. The active ingredient content of P. kingianum was identified by High Performance Liquid Chromatography (HPLC) and Colorimetry. A total of 12,715 bacterial and 5487 fungal Operational Taxonomic Units (OTU) were obtained and taxonomically categorized into 81 and 7 different phyla. Proteobacteria, Bacteroidetes, and Acidobacteriae were the dominant bacterial phyla Ascomycota and Basidiomycota were the dominat fungal phyla. The key predictors for bacterial community structure included hydrolysable nitrogen and available potassium, while for altering fungal community structure, soil organic carbon content (OCC), total nitrogen content (TNC), and total potassium content (TPOC) were the main influencing factors. Bryobacter and Candidatus Solibacter may indirectly increase the polysaccharide content of P. kingianum, and can be developed as potential Plant Growth Promoting Rhizobacteria (PGPR). This study has confirmed the differences in the soil and microorganisms of different origins of P. kingianum, and their close association with its active ingredients. And it also broadens the idea of studying the link between plants and microorganisms.
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Affiliation(s)
- Jiahao Liu
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
- Western Yunnan Traditional Chinese Medicine and Ethnic Drug Engineering Center, Dali, 671000, China
| | - Yan Qian
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
- Western Yunnan Traditional Chinese Medicine and Ethnic Drug Engineering Center, Dali, 671000, China
| | - Wanqing Yang
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
- Western Yunnan Traditional Chinese Medicine and Ethnic Drug Engineering Center, Dali, 671000, China
| | - Meihua Yang
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
- Western Yunnan Traditional Chinese Medicine and Ethnic Drug Engineering Center, Dali, 671000, China
| | - Yue Zhang
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
- Western Yunnan Traditional Chinese Medicine and Ethnic Drug Engineering Center, Dali, 671000, China
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
- Western Yunnan Traditional Chinese Medicine and Ethnic Drug Engineering Center, Dali, 671000, China
| | - Yongcheng Yang
- College of Pharmaceutical Science, Dali University, Dali, 671000, China.
- Western Yunnan Traditional Chinese Medicine and Ethnic Drug Engineering Center, Dali, 671000, China.
| | - Aien Tao
- College of Medicine, Lijiang Culture and Tourism College, Lijiang, 674100, China.
| | - Conglong Xia
- College of Pharmaceutical Science, Dali University, Dali, 671000, China.
- Western Yunnan Traditional Chinese Medicine and Ethnic Drug Engineering Center, Dali, 671000, China.
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Ouyang H, Chen J, Lin L, Zheng H, Xie C, Wang C, Wang Z. Metabarcoding and co-occurrence network reveal significant effects of mariculture on benthic eukaryotic microalgal community: A case study in Daya Bay of the South China Sea. MARINE POLLUTION BULLETIN 2024; 207:116832. [PMID: 39128232 DOI: 10.1016/j.marpolbul.2024.116832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/19/2024] [Accepted: 08/06/2024] [Indexed: 08/13/2024]
Abstract
Benthic eukaryotic microalgae were analyzed by metabarcoding the partial 18S rRNA gene in Daya Bay bi-monthly in 2021. Altogether 941 eukaryotic microalgal OTUs were detected, belonging to 27 classes of 8 phyla. Dinophyta and Chlorophyta were the dominant phyla. Microalgal community in the mariculture zone differed significantly from those in non-mariculture zone, reflected by low alpha diversity indexes and increasing abundance and richness of chlorophytes and correspondingly decreasing of dinoflagellates. The abundant occurrences of the pico- and nano-sized taxa such as the chlorophyte Picochlorum in the mariculture zone suggested that nutrient enrichment might result in the miniaturization of the benthic eukaryotic microalgae. The co-occurrence network suggested more negative interactions between taxa in the mariculture zone. A total of 41 algal bloom and/or harmful algal bloom (HAB) species were detected in this study, suggesting a high potential risk of HABs in Daya Bay, especially for the recurrent bloom species Scrippsiella acuminata.
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Affiliation(s)
- Hong Ouyang
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jiazhuo Chen
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lanping Lin
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hu Zheng
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Changliang Xie
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Chaofan Wang
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhaohui Wang
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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22
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Xin Y, Gao Q, Chen X, Sun S, Liu J, Gao H, Zhou J, Xia X. High biological N fixation potential dominated by heterotrophic diazotrophs in alpine permafrost rivers on the Qinghai‒Tibet Plateau. WATER RESEARCH 2024; 264:122239. [PMID: 39137482 DOI: 10.1016/j.watres.2024.122239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 07/02/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024]
Abstract
Biological nitrogen (N) fixation is a pivotal N source in N-deficient ecosystems. The Qinghai‒Tibet Plateau (QTP) region, which is assumed to be N limited and suboxic, is an ideal habitat for diazotrophs. However, the diazotrophic communities and associated N fixation rates in these high-altitude alpine permafrost QTP rivers remain largely unknown. Herein, we examined diazotrophic communities in the sediment and biofilm of QTP rivers via the nitrogenase (nifH) gene sequencing and assessed their N fixing activities via a 15N isotope incubation assay. Strikingly, anaerobic heterotrophic diazotrophs, such as sulfate- and iron-reducing bacteria, had emerged as dominant N fixers. Remarkably, the nifH gene abundance and N fixation rates increased with altitude, and the average nifH gene abundance (2.57 ± 2.60 × 108 copies g-1) and N fixation rate (2.29 ± 3.36 nmol N g-1d-1) surpassed that documented in most aquatic environments (nifH gene abundance: 1.31 × 105 ∼ 2.57 × 108 copies g-1, nitrogen fixation rates: 2.34 × 10-4 ∼ 4.11 nmol N g-1d-1). Such distinctive heterotrophic diazotrophic communities and high N fixation potential in QTP rivers were associated with low-nitrogen, abundant organic carbon and unique C:N:P stoichiometries. Additionally, the significant presence of psychrophilic bacteria within the diazotrophic communities, along with the enhanced stability and complexity of the diazotrophic networks at higher altitudes, clearly demonstrate the adaptability of diazotrophic communities to extreme cold and high-altitude conditions in QTP rivers. We further determined that altitude, coupled with organic carbon and phosphorus, was the predominant driver shaping diazotrophic communities and their N-fixing activities. Overall, our study reveals high N fixation potential in N-deficient QTP rivers, which provides novel insights into nitrogen dynamics in alpine permafrost rivers.
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Affiliation(s)
- Yuan Xin
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Qun Gao
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China.
| | - Xin Chen
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Siyue Sun
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Jiao Liu
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Hui Gao
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA; School of Biological Sciences, University of Oklahoma, Norman, OK 73019, USA; School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA; School of Computer Science, University of Oklahoma, Norman, OK, USA; Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Xinghui Xia
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China.
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23
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Crocker K, Lee KK, Chakraverti-Wuerthwein M, Li Z, Tikhonov M, Mani M, Gowda K, Kuehn S. Environmentally dependent interactions shape patterns in gene content across natural microbiomes. Nat Microbiol 2024; 9:2022-2037. [PMID: 38977908 DOI: 10.1038/s41564-024-01752-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 06/03/2024] [Indexed: 07/10/2024]
Abstract
Sequencing surveys of microbial communities in hosts, oceans and soils have revealed ubiquitous patterns linking community composition to environmental conditions. While metabolic capabilities restrict the environments suitable for growth, the influence of ecological interactions on patterns observed in natural microbiomes remains uncertain. Here we use denitrification as a model system to demonstrate how metagenomic patterns in soil microbiomes can emerge from pH-dependent interactions. In an analysis of a global soil sequencing survey, we find that the abundances of two genotypes trade off with pH; nar gene abundances increase while nap abundances decrease with declining pH. We then show that in acidic conditions strains possessing nar fail to grow in isolation but are enriched in the community due to an ecological interaction with nap genotypes. Our study provides a road map for dissecting how associations between environmental variables and gene abundances arise from environmentally modulated community interactions.
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Affiliation(s)
- Kyle Crocker
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL, USA
- Center for Living Systems, The University of Chicago, Chicago, IL, USA
| | - Kiseok Keith Lee
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL, USA
- Center for Living Systems, The University of Chicago, Chicago, IL, USA
| | - Milena Chakraverti-Wuerthwein
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL, USA
- Center for Living Systems, The University of Chicago, Chicago, IL, USA
- Biophysical Sciences Graduate Program, The University of Chicago, Chicago, IL, USA
| | - Zeqian Li
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL, USA
- Department of Physics, The University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mikhail Tikhonov
- Department of Physics, Washington University in St. Louis, St. Louis, MO, USA
| | - Madhav Mani
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, USA
- National Institute for Theory and Mathematics in Biology, Northwestern University and The University of Chicago, Chicago, IL, USA
| | - Karna Gowda
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, USA.
| | - Seppe Kuehn
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA.
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL, USA.
- Center for Living Systems, The University of Chicago, Chicago, IL, USA.
- National Institute for Theory and Mathematics in Biology, Northwestern University and The University of Chicago, Chicago, IL, USA.
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24
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Chen CZ, Yin MH, Niu LJ, Wang JX, Liu L, Sun YJ, Ju WM, Li P, Li ZH. Exploring seasonal variations, assembly dynamics, and relationships of bacterial communities in different habitats of marine ranching. MARINE POLLUTION BULLETIN 2024; 205:116658. [PMID: 38964192 DOI: 10.1016/j.marpolbul.2024.116658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024]
Abstract
Offshore coastal marine ranching ecosystems provide habitat for diverse and active bacterial communities. In this study, 16S rRNA gene sequencing and multiple bioinformatics methods were applied to investigate assembly dynamics and relationships in different habitats. The higher number of edges in the water network, more balanced ratio of positive and negative links, and more keystone species included in the co-occurrence network of water. Stochastic processes dominated in shaping gut and sediment community assembly (R2 < 0.5), while water bacterial community assembly were dominated by deterministic processes (R2 > 0.5). Dissimilarity-overlap curve model indicated that the communities in different habitats have general dynamics and interspecific interaction (P < 0.001). Bacterial source-tracking analysis revealed that the gut was more similar to the sediment than the water bacterial communities. In summary, this study provides basic data for the ecological study of marine ranching through the study of bacterial community dynamics.
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Affiliation(s)
| | - Ming-Hao Yin
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Lin-Jing Niu
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Jin-Xin Wang
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Ling Liu
- Marine College, Shandong University, Weihai, Shandong 264209, China.
| | - Yong-Jun Sun
- Homey Group Co. Ltd, Rongcheng, Shandong 264306, China
| | - Wen-Ming Ju
- Homey Group Co. Ltd, Rongcheng, Shandong 264306, China
| | - Ping Li
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Zhi-Hua Li
- Marine College, Shandong University, Weihai, Shandong 264209, China.
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25
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Zhang C, Ndungu CN, Feng L, Huang J, Ba S, Liu W, Cai M. Plant diversity is more important than soil microbial diversity in explaining soil multifunctionality in Qinghai-Tibetan plateau wetlands. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 365:121509. [PMID: 38897088 DOI: 10.1016/j.jenvman.2024.121509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 06/11/2024] [Accepted: 06/16/2024] [Indexed: 06/21/2024]
Abstract
The Qinghai-Tibetan Plateau harbors rich and diverse wetlands that provide multiple ecological functions simultaneously. Although the relationships between biodiversity and wetland functioning have been well studied in recent decades, the links between the multiple features of plant and microbial communities and soil multifunctionality (SMF) remain unknown in the high-altitude wetlands that are extremely sensitive to human disturbance. Here, using the single function, averaging, weighted, and multiple-threshold methods, we calculated the SMF of Qinghai-Tibetan wetlands based on 15 variables associated with soil nutrient status, nutrient cycle, and greenhouse gas emission. We then related SMF to multidimensional (species, phylogenetic, and functional) diversity of plants and soil microorganisms and microbial network modules. The results showed that plant diversity explained more variance in SMF than soil microbial diversity, and plant species richness and phylogenetic distance were positive predictors of SMF. Bacterial network modules were more positively related to SMF than fungal network modules, and the alpha diversity of bacterial network modules contributed more to SMF than the diversity of the whole bacterial community. Pediococcus, Hirsutella, and Rhodotorula were biomarkers for SMF and had significant relationships with nitrogen mineralization and greenhouse gas emissions. Together, these results highlight the importance of plant diversity and bacterial network modules in determining the SMF, which are crucial to predicting the response of ecosystem functioning to biodiversity loss under intensifying anthropogenic activities.
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Affiliation(s)
- Caifang Zhang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Caroline Njambi Ndungu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lian Feng
- School of Ecology and Environment, Tibet University, Lhasa 850000, China
| | - Jieya Huang
- School of Ecology and Environment, Tibet University, Lhasa 850000, China
| | - Sang Ba
- School of Ecology and Environment, Tibet University, Lhasa 850000, China; Center for Carbon Neutrality in the Earth's Third Pole, Tibet University, Lhasa 850000, China
| | - Wenzhi Liu
- Center for Carbon Neutrality in the Earth's Third Pole, Tibet University, Lhasa 850000, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan, 430074, China.
| | - Miaomiao Cai
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan, 430074, China.
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26
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Jiang MZ, Liu C, Xu C, Jiang H, Wang Y, Liu SJ. Gut microbial interactions based on network construction and bacterial pairwise cultivation. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1751-1762. [PMID: 38600293 DOI: 10.1007/s11427-023-2537-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 01/27/2024] [Indexed: 04/12/2024]
Abstract
Association networks are widely applied for the prediction of bacterial interactions in studies of human gut microbiomes. However, the experimental validation of the predicted interactions is challenging due to the complexity of gut microbiomes and the limited number of cultivated bacteria. In this study, we addressed this challenge by integrating in vitro time series network (TSN) associations and co-cultivation of TSN taxon pairs. Fecal samples were collected and used for cultivation and enrichment of gut microbiome on YCFA agar plates for 13 days. Enriched cells were harvested for DNA extraction and metagenomic sequencing. A total of 198 metagenome-assembled genomes (MAGs) were recovered. Temporal dynamics of bacteria growing on the YCFA agar were used to infer microbial association networks. To experimentally validate the interactions of taxon pairs in networks, we selected 24 and 19 bacterial strains from this study and from the previously established human gut microbial biobank, respectively, for pairwise co-cultures. The co-culture experiments revealed that most of the interactions between taxa in networks were identified as neutralism (51.67%), followed by commensalism (21.67%), amensalism (18.33%), competition (5%) and exploitation (3.33%). Genome-centric analysis further revealed that the commensal gut bacteria (helpers and beneficiaries) might interact with each other via the exchanges of amino acids with high biosynthetic costs, short-chain fatty acids, and/or vitamins. We also validated 12 beneficiaries by adding 16 additives into the basic YCFA medium and found that the growth of 66.7% of these strains was significantly promoted. This approach provides new insights into the gut microbiome complexity and microbial interactions in association networks. Our work highlights that the positive relationships in gut microbial communities tend to be overestimated, and that amino acids, short-chain fatty acids, and vitamins are contributed to the positive relationships.
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Affiliation(s)
- Min-Zhi Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China
| | - Chang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China
| | - Chang Xu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China
| | - He Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China
| | - Yulin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China.
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China.
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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27
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Wei J, Chen W, Wen D. Rare biosphere drives deterministic community assembly, co-occurrence network stability, and system performance in industrial wastewater treatment system. ENVIRONMENT INTERNATIONAL 2024; 190:108887. [PMID: 39024826 DOI: 10.1016/j.envint.2024.108887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 07/08/2024] [Accepted: 07/13/2024] [Indexed: 07/20/2024]
Abstract
Bacterial community is strongly associated with activated sludge performance, but there still remains a knowledge gap regarding the rare bacterial community assembly and their influence on the system performance in industrial wastewater treatment plants (IWWTPs). Here, we investigated bacterial communities in 11 full-scale IWWTPs with similar process designs, aiming to uncover ecological processes and functional traits regulating abundant and rare communities. Our findings indicated that abundant bacterial community assembly was governed by stochastic processes; thereby, abundant taxa are generally present in wastewater treatment compartments across different industrial types. On the contrary, rare bacterial taxa were primarily driven by deterministic processes (homogeneous selection 61.9%-79.7%), thus they only exited in specific IWWTPs compartments and wastewater types. The co-occurrence networks analysis showed that the majority of keystone taxa were rare bacterial taxa, with rare taxa contributing more to network stability. Furthermore, rare bacteria rather than abundant bacteria in the oxic compartment contributed more to the degradation of xenobiotics compounds, and they were main potential drivers of pollutant removal. This study demonstrated the irreplaceable roles of rare bacterial taxa in maintaining system performance of IWWTPs, and called for environmental engineers and microbial ecologists to increase their attention on rare biosphere.
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Affiliation(s)
- Jie Wei
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Weidong Chen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China.
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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28
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Lin L, Tao M, He WM, Wu QH, Huang HK, Murero AK, Shao XL, Wang LM, Qian GL. Identification of non-canonical antagonistic bacteria via interspecies contact-dependent killing. PEST MANAGEMENT SCIENCE 2024; 80:3997-4005. [PMID: 38527976 DOI: 10.1002/ps.8103] [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: 10/31/2023] [Revised: 01/18/2024] [Accepted: 03/26/2024] [Indexed: 03/27/2024]
Abstract
BACKGROUND Canonical biocontrol bacteria were considered to inhibit pathogenic bacteria mainly by secreting antibiotic metabolites or enzymes. Recent studies revealed that some biocontrol bacteria can inhibit pathogenic bacteria through contact-dependent killing (CDK) mediated by contact-dependent secretion systems. The CDK was independent of antibiotic metabolites and often ignored in normal biocontrol activity assay. RESULTS In this study, we aimed to use a pathogen enrichment strategy to isolate non-canonical bacteria with CDK ability. Rhizosphere soil samples from Chinese cabbage showing soft rot symptom were collected and Pectobacterium carotovorum subsp. carotovorum (Pcc), the pathogen of cabbage soft rot, were added into these samples to enrich bacteria which attached on Pcc cells. By co-culture with Pcc, four bacteria strains (named as PcE1, PcE8, PcE12 and PcE13) showing antibacterial activity were isolated from Chinese cabbage rhizosphere. These four bacteria strains showed CDK abilities to different pathogenic bacteria of horticultural plants. Among them, PcE1 was identified as Chryseobacterium cucumeris. Genome sequencing showed that PcE1 genome encoded a type VI secretion system (T6SS) gene cluster. By heterologous expression, four predicted T6SS effectors of PcE1 showed antibacterial activity to Escherichia coli. CONCLUSION Overall, this study isolated four bacteria strains with CDK activity to various horticultural plant pathogens, and revealed possible involvement of T6SS of Chryseobacterium cucumeris in antibacterial activity. These results provide valuable insight for potential application of CDK activity in biocontrol bacteria. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Long Lin
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Min Tao
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Wei-Mei He
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Qian-Hua Wu
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Hao-Kai Huang
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Aprodisia Kavutu Murero
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Xiao-Long Shao
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Li-Min Wang
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Guo-Liang Qian
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
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Gallardo-Navarro O, Aguilar-Salinas B, Rocha J, Olmedo-Álvarez G. Higher-order interactions and emergent properties of microbial communities: The power of synthetic ecology. Heliyon 2024; 10:e33896. [PMID: 39130413 PMCID: PMC11315108 DOI: 10.1016/j.heliyon.2024.e33896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Accepted: 06/28/2024] [Indexed: 08/13/2024] Open
Abstract
Humans have long relied on microbial communities to create products, produce energy, and treat waste. The microbiota residing within our bodies directly impacts our health, while the soil and rhizosphere microbiomes influence the productivity of our crops. However, the complexity and diversity of microbial communities make them challenging to study and difficult to develop into applications, as they often exhibit the emergence of unpredictable higher-order phenomena. Synthetic ecology aims at simplifying complexity by constituting synthetic or semi-natural microbial communities with reduced diversity that become easier to study and analyze. This strategy combines methodologies that simplify existing complex systems (top-down approach) or build the system from its constituent components (bottom-up approach). Simplified communities are studied to understand how interactions among populations shape the behavior of the community and to model and predict their response to external stimuli. By harnessing the potential of synthetic microbial communities through a multidisciplinary approach, we can advance knowledge of ecological concepts and address critical public health, agricultural, and environmental issues more effectively.
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Affiliation(s)
- Oscar Gallardo-Navarro
- Centro de Investigación y de Estudios Avanzado del Instituto Politécnico Nacional, Unidad Irapuato, Mexico
| | - Bernardo Aguilar-Salinas
- Centro de Investigación y de Estudios Avanzado del Instituto Politécnico Nacional, Unidad Irapuato, Mexico
| | - Jorge Rocha
- Centro de Investigaciones Biológicas del Noroeste, S. C., La Paz, Mexico
| | - Gabriela Olmedo-Álvarez
- Centro de Investigación y de Estudios Avanzado del Instituto Politécnico Nacional, Unidad Irapuato, Mexico
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Miao W, Wang S, Lin T, Yan Y, Bao Z, Zhang D, Jiang Z, Zhang H. Interaction patterns and assembly mechanisms of dinoflagellates and diatoms in a coastal bay suffering from long-term eutrophication. mSphere 2024; 9:e0036624. [PMID: 38940511 PMCID: PMC11288026 DOI: 10.1128/msphere.00366-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/11/2024] [Indexed: 06/29/2024] Open
Abstract
Dinoflagellates and diatoms are highly prevalent and ecologically important phytoplankton in coastal waters, greatly contributing to primary productivity in marine ecosystems. Although their composition and diversity have been extensively elucidated in the open ocean, their interaction patterns and community assembly in long-term eutrophic coastal waters remain poorly understood. This investigation aimed to elucidate the seasonal successional patterns of dinoflagellates and diatoms by 18S rRNA gene amplicon sequencing in a semi-enclosed bay. The results revealed that dinoflagellate and diatom communities have pronounced seasonal succession patterns, which are primarily associated with temperature. Furthermore, the most prevalent species throughout the year were Heterocapsa rotundata and Skeletonema costatum. Moreover, the assembly of dinoflagellate and diatom communities was mainly dominated by stochastic processes, with drift being the major factor. The co-occurrence of dinoflagellates and diatoms showed seasonal patterns, with the highest interactions observed in autumn. In addition, interactions of Syndiniales with dinoflagellates and diatoms highlighted the roles of parasites in eutrophic conditions. Flavobacteriaceae and Rhodobacteraceae are the bacterial taxa that most frequently interacted with dinoflagellates and diatoms, with interactions between dinoflagellates and bacteria being more complex than those between diatoms and bacteria. Overall, this study provides results that deepen our understanding of the phytoplankton dynamics in coastal eutrophic waters.IMPORTANCEDinoflagellates and diatoms are major phytoplankton groups in coastal waters. The composition and diversity of dinoflagellates and diatoms in the open ocean have been well documented; however, it remains uncertain to what extent their adaptation to long-term eutrophic conditions influences their response to environmental disturbances. Here, we investigated the interactions and assembly processes of dinoflagellates and diatoms in a eutrophic bay throughout the whole year. Our findings revealed that interactions between dinoflagellates and diatoms are primarily shaped by seasonal transitions, while prolonged eutrophic conditions tend to amplify stochastic processes in community assembly. These findings provide novel perspectives on the influence of long-term eutrophication on phytoplankton dynamics within eutrophic waters.
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Affiliation(s)
- Wenfei Miao
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Shuqi Wang
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Tenghui Lin
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Yi Yan
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Zhen Bao
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Demin Zhang
- School of Marine Sciences, Ningbo University, Ningbo, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Zhibing Jiang
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Huajun Zhang
- School of Marine Sciences, Ningbo University, Ningbo, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
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Kudjordjie EN, Santos SS, Topalović O, Vestergård M. Distinct changes in tomato-associated multi-kingdom microbiomes during Meloidogyne incognita parasitism. ENVIRONMENTAL MICROBIOME 2024; 19:53. [PMID: 39068487 DOI: 10.1186/s40793-024-00597-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/17/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND The interplay between root-knot nematode (RKN) parasitism and the complex web of host-associated microbiota has been recognized as pivotal for effective management of the pest. However, studies assessing this relationship have focussed on the bacterial and fungal communities, neglecting the unicellular eukaryotic members. Here, we employed amplicon sequencing analysis of the bacterial 16S rRNA, fungal ITS and eukaryotic 18S rRNA genes, and comprehensively examined how the microbiome composition, diversity and networking developed with time in the rhizospheres and roots of RKN-inoculated and non-inoculated tomato plants. RESULTS As expected, infection with the RKN Meloidogyne incognita decreased plant growth. At individual timepoints, we found distinct bacterial, fungal and eukaryote community structures in the RKN-inoculated and non-inoculated rhizospheres and roots, and RKN inoculation affected several taxa in the root-associated microbiome differentially. Correlation analysis revealed several bacterial and fungal and few protist taxa that correlated negatively or positively with M. incognita. Moreover, network analysis using bacterial, fungal and eukaryotic data revealed more dynamic networks with higher robustness to disturbances in the RKN-inoculated than in the non-inoculated rhizospheres/roots. Hub taxa displayed a noticeable successional pattern that coincided with different phases of M. incognita parasitism. We found that fungal hubs had strong negative correlations with bacteria and eukaryotes, while positive correlations characterized hub members within individual kingdoms. CONCLUSION Our results reveal dynamic tomato-associated microbiomes that develop along different trajectories in plants suffering M. incognita infestation and non-infested plants. Overall, the results identify stronger associations between RKN and bacterial and fungal taxa than between eukaryotic taxa and RKN, suggesting that fungal and bacterial communities could play a larger role in the regulation of RKN. The study identifies several putative RKN-antagonistic bacterial and fungal taxa and confirms the antagonistic potential previously identified in other taxa.
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Affiliation(s)
- Enoch Narh Kudjordjie
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, 4200, Denmark
| | - Susana S Santos
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, 4200, Denmark
| | - Olivera Topalović
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, 4200, Denmark
- Department of Biology, Section of Terrestrial Ecology, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Mette Vestergård
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, 4200, Denmark.
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Cai X, Chen C, Singh AK, Zhu X, Liu W. Anthropogenic restoration exhibits more complex and stable microbial co-occurrence patterns than natural restoration in rubber plantations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174935. [PMID: 39053530 DOI: 10.1016/j.scitotenv.2024.174935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/05/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
Forest restoration is an effective method for restoring degraded soil ecosystems (e.g., converting primary tropical forests into rubber monoculture plantations; RM). The effects of forest restoration on microbial community diversity and composition have been extensively studied. However, how rubber plantation-based forest restoration reshapes soil microbial communities, networks, and inner assembly mechanisms remains unclear. Here, we explored the effects of jungle rubber mixed (JRM; secondary succession and natural restoration of RM) plantation and introduction of rainforest species (AR; anthropogenic restoration established by mimicking the understory and overstory tree species of native rainforests) to RM stands on soil physico-chemical properties and microbial communities. We found that converting tropical rainforest (RF) to RM decreased soil fertility and simplified microbial composition and co-occurrence patterns, whereas the conversion of RM to JRM and AR exhibited opposite results. These changes were significantly correlated with pH, soil moisture content (SMC), and soil nutrients, suggesting that vegetation restoration can provide a favorable soil microenvironment that promotes the development of soil microorganisms. The complexity and stability of the bacterial-fungal cross-kingdom, bacterial, and fungal networks increased with JRM and AR. Bacterial community assembly was primarily governed by stochastic (78.79 %) and deterministic (59.09 %) processes in JRM and AR, respectively, whereas stochastic processes (limited dispersion) predominantly shaped fungal assembly across all forest stands. AR has more significant benefits than JRM, such as a relatively slower and natural vegetation succession with more nutritive soil conditions, microbial diversity, and complex and stable microbial networks. These results highlight the importance of sustainable forest management to restore soil biodiversity and ecosystem functions after extensive soil degradation and suggest that anthropogenic restoration can more effectively improve soil quality and microbial communities than natural restoration in degraded rubber plantations.
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Affiliation(s)
- Xiaoyi Cai
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunfeng Chen
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China.
| | - Ashutosh Kumar Singh
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - Xiai Zhu
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China.
| | - Wenjie Liu
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China.
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Kang H, Xue Y, Cui Y, Moorhead DL, Lambers H, Wang D. Nutrient limitation mediates soil microbial community structure and stability in forest restoration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 935:173266. [PMID: 38759924 DOI: 10.1016/j.scitotenv.2024.173266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/19/2024]
Abstract
Soil microorganisms are often limited by nutrients, representing an important control of heterotrophic metabolic processes. However, how nutrient limitations relate to microbial community structure and stability remains unclear, which creates a knowledge gap to understanding microbial biogeography and community changes during forest restoration. Here, we combined an eco-enzymatic stoichiometry model and high-throughput DNA sequencing to assess the potential roles of nutrient limitation on microbial community structure, assembly, and stability along a forest restoration sequence in the Qinling Mountains, China. Results showed that nutrient limitations tended to decrease during the oak forest restoration. Carbon and phosphorus limitations enhanced community dissimilarity and significantly increased bacterial alpha diversity, but not fungal diversity. Stochastic assembly processes primarily structured both bacterial (average contribution of 74.73 % and 74.17 % in bulk and rhizosheath soils, respectively) and fungal (average contribution of 77.23 % and 72.04 % in bulk and rhizosheath soils, respectively) communities during forest restoration, with nutrient limitation also contributing to the importance of stochastic processes in the bacterial communities. The migration rate (m) for bacteria was 0.19 and 0.23, respectively in both bulk soil and rhizosheath soil, and was greater than that for the fungi (m was 1.19 and 1.41, respectively), indicating a stronger dispersal limitation for fungal communities. Finally, nutrient limitations significantly affected bacterial and fungal co-occurrence with more interconnections occurring among weakly nutrient-limited microbial taxa and nutrient limitations reducing community stability when nutrient availability changed during forest restoration. Our findings highlight the fundamental effects of nutrient limitations on microbial communities and their self-regulation under changing environmental resources.
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Affiliation(s)
- Haibin Kang
- College of Forestry, Northwest Agriculture & Forestry University, Yangling 712100, China; School of Biological Sciences, The University of Western Australia, Perth 6009, Australia
| | - Yue Xue
- School of Geography and Oceanography, Nanjing University, Nanjing 210023, China
| | - Yongxing Cui
- Institute of Biology, Freie Universität Berlin, Berlin 14195, Germany
| | - Daryl L Moorhead
- Department of Environmental Sciences, University of Toledo, Toledo 43606, USA
| | - Hans Lambers
- School of Biological Sciences, The University of Western Australia, Perth 6009, Australia
| | - Dexiang Wang
- College of Forestry, Northwest Agriculture & Forestry University, Yangling 712100, China.
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He L, Sun X, Li S, Zhou W, Yu J, Zhao G. Biogeographic and co-occurrence network differentiation of fungal communities in warm-temperate montane soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174911. [PMID: 39038676 DOI: 10.1016/j.scitotenv.2024.174911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 07/16/2024] [Accepted: 07/18/2024] [Indexed: 07/24/2024]
Abstract
Studying the biogeographic patterns of fungal communities across altitudinal and soil depth gradients is essential for understanding how environmental variations shape the diversity and functionality of these complex ecological assemblages. Here, we evaluated the response and assembly patterns of fungal communities to altitude and soil depth, and the co-occurrence patterns influencing soil fungal metabolic preferences on Dongling Mountain. We observed significant variations in fungal β-diversity, driven by elevation and soil depth, with climatic parameters (MAT and MAP) and nutrient concentrations (TOC, TP, and TN) serving as prominent influencers. Additionally, we found that the multiple substrate-induced respiration rate of fungi degrading various carbon substrates was diminished in high-altitude and subsurface soils compared to low-altitude and surface soils. Stochastic processes play a more important role in controlling fungal community assembly than deterministic processes, with dispersal limitation emerging as the main driver of community assembly. While greater network complexity was evident in the topsoil compared to the subsoil, both layers harbored altitude-sensitive OTUs (asOTUs) that belonging to distinct modules. Moreover, fungal groups sensitive to the same altitude exhibited similar metabolic preferences. The asOTUs designated for lower altitude areas favored unstable carbon substrates (glucose and sucrose), while those designated as higher altitude areas exhibited a preference for recalcitrant carbon (xylan and lignin). This evidence suggests that soil fungal communities respond to environmental changes by trading off their life strategies and metabolic characteristics.
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Affiliation(s)
- Libing He
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Xiangyang Sun
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China.
| | - Suyan Li
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Wenzhi Zhou
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Jiantao Yu
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Guanyu Zhao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
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Shi Y, Li W, Guo X. Exploring environment-specific regulation: Characterizing bacterioplankton community dynamics in a typical lake of Inner Mongolia, China. ENVIRONMENTAL RESEARCH 2024; 253:119154. [PMID: 38754616 DOI: 10.1016/j.envres.2024.119154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/12/2024] [Accepted: 05/14/2024] [Indexed: 05/18/2024]
Abstract
Lakes serve as heterogeneous ecosystems with rich microbiota. Although previous studies on bacterioplankton have advanced our understanding, there are gaps in our knowledge concerning variations in the taxonomic composition and community assembly processes of bacterioplankton across different environment conditions. This study explored the spatial dynamics, assembly processes, and co-occurrence relationships among bacterioplankton communities in 35 surface water samples collected from Hulun Lake (a grassland-type lake), Wuliangsuhai Lake (an irrigated agricultural recession type lake), and Daihai Lake (an inland lake with mixed farming and grazing) in the Inner Mongolia Plateau, China. The results indicated a significant geographical distance decay pattern, with biomarkers (Proteobacteria and Bacteroidota) exhibiting differences in the contributions of different bacteria branches to the lakes. The relative abundance of Proteobacteria (42.23%) were high in Hulun Lake and Wuliangsuhai Lake. Despite Actinobacteriota was most dominant, Firmicutes accounted for approximately 17.07% in Daihai Lake, suggested the potential detection of anthropogenic impacts on bacteria within the agro-pastoral inland lake. Lake heterogeneity caused bacterioplankton responses to phosphorus, chlorophyll a, and salinity in Hulun Lake, Wuliangsuhai Lake, and Daihai Lake. Although bacterioplankton community assembly processes in irrigated agricultural recession type lake were more affected by dispersal limitation than those in grassland-type lake and inland lake with mixed farming and grazing (approximately 52.7% in Hulun Lake), dispersal limitation and undominated processes were key modes of bacterioplankton community assembly in three lakes. This suggested stochastic processes exerted a greater impact on bacterioplankton community assembly in a typical Inner Mongolia Lake than deterministic processes. Overall, the bacterioplankton communities displayed the potential for collaboration, with lowest connectivity observed in irrigated agricultural recession type lake, which reflected the complex dynamic patterns of aquatic bacteria in typical Inner Mongolia Plateau lakes. These findings enhanced our understanding of the interspecific relationships and assembly processes among microorganisms in lakes with distinct habitats.
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Affiliation(s)
- Yujiao Shi
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Wenbao Li
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, 010018, China; Inner Mongolia Key Laboratory of Protection and Utilization of Water Resources, Hohhot, 010018, China.
| | - Xin Guo
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, 010018, China
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Zhong L, Sun HJ, Pang JW, Ding J, Zhao L, Xu W, Yuan F, Zhang LY, Ren NQ, Yang SS. Ciprofloxacin affects nutrient removal in manganese ore-based constructed wetlands: Adaptive responses of macrophytes and microbes. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134579. [PMID: 38761761 DOI: 10.1016/j.jhazmat.2024.134579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/28/2024] [Accepted: 05/08/2024] [Indexed: 05/20/2024]
Abstract
Ciprofloxacin (CIP) has received considerable attention in recent decades due to its high ecological risk. However, little is known about the potential response of macrophytes and microbes to varying levels of CIP exposure in constructed wetlands. Therefore, lab-scale manganese ore-based tidal flow constructed wetlands (MO-TFCWs) were operated to evaluate the responses of macrophytes and microbes to CIP over the long term. The results indicated that total nitrogen removal improved from 79.93% to 87.06% as CIP rose from 0 to 4 mg L-1. The chlorophyll content and antioxidant enzyme activities in macrophytes were enhanced under CIP exposure, but plant growth was not inhibited. Importantly, CIP exposure caused a marked evolution of the substrate microbial community, with increased microbial diversity, expanded niche breadth and enhanced cooperation among the top 50 genera, compared to the control (no CIP). Co-occurrence network also indicated that microorganisms may be more inclined to co-operate than compete. The abundance of the keystone bacterium (involved in nitrogen transformation) norank_f__A0839 increased from 0.746% to 3.405%. The null model revealed drift processes (83.33%) dominated the community assembly with no CIP and 4 mg L-1 CIP. Functional predictions indicated that microbial carbon metabolism, electron transfer and ATP metabolism activities were enhanced under prolonged CIP exposure, which may contribute to nitrogen removal. This study provides valuable insights that will help achieve stable nitrogen removal from wastewater containing antibiotic in MO-TFCWs.
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Affiliation(s)
- Le Zhong
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Han-Jun Sun
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Ji-Wei Pang
- China Energy Conservation and Environmental Protection Group, CECEP Digital Technology Co., Ltd., Beijing 100096, China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Lei Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Wei Xu
- General Water of China Co., Ltd., Beijing 100022, China
| | - Fang Yuan
- General Water of China Co., Ltd., Beijing 100022, China
| | - Lu-Yan Zhang
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Shan-Shan Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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Chao J, Li J, Gao J, Bai C, Tang X, Shao K. Comparing Sediment Bacterial Communities of Volcanic Lakes and Surrounding Rivers in Inner Mongolia Autonomous Region, Northeastern China. Microorganisms 2024; 12:1435. [PMID: 39065203 PMCID: PMC11278812 DOI: 10.3390/microorganisms12071435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Volcanic lakes originate from a volcanic crater or caldera, and were a crucial component of aquatic ecosystems. Sediment bacteria play an important role in the nutrient cycling of aquatic ecosystems; however, their patterns distribution in volcanic lakes and the surrounding river habitats are unknown. In this study, we compare the sediment bacterial communities and their co-occurrence networks between these two habitats in the Inner Mongolia Autonomous Region, Northeastern China (the Arxan UNESCO Global Geopark), using 16S rRNA gene amplicon sequencing. The results revealed that there were significant variations in the physicochemical parameters of the sediment between these two habitats. The bacterial α-diversity, β-diversity, and community composition of the sediment also significantly differed between these two habitats. Network analysis showed that the co-occurrence patterns and keystone taxa in the sediment differed between these two habitats. The sediment bacterial communities in the river habitats were more stable than those in the lake habitats in the face of environmental change. Canonical correspondence analysis demonstrated that both physical (pH and MC) and nutrition-related factors (TN, TP, LOI, and TOC) were the most important environmental factors shaping the variations of bacterial community composition (BCC) in the sediment between these two habitats. This work could greatly improve our understanding of the sediment BCC of the sediment from aquatic ecosystems in the UNESCO Global Geopark.
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Affiliation(s)
- Jianying Chao
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China; (J.C.); (J.L.); (J.G.)
| | - Jian Li
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China; (J.C.); (J.L.); (J.G.)
| | - Jing Gao
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China; (J.C.); (J.L.); (J.G.)
| | - Chengrong Bai
- Shandong Key Laboratory of Eco-Environmental Science for Yellow River Delta, Shandong University of Aeronautics, Binzhou 256600, China;
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China;
| | - Keqiang Shao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China;
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Varghese S, Jisha M, Rajeshkumar K, Gajbhiye V, Alrefaei AF, Jeewon R. Endophytic fungi: A future prospect for breast cancer therapeutics and drug development. Heliyon 2024; 10:e33995. [PMID: 39091955 PMCID: PMC11292557 DOI: 10.1016/j.heliyon.2024.e33995] [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: 02/09/2024] [Revised: 06/26/2024] [Accepted: 07/02/2024] [Indexed: 08/04/2024] Open
Abstract
Globally, breast cancer is a primary contributor to cancer-related fatalities and illnesses among women. Consequently, there is a pressing need for safe and effective treatments for breast cancer. Bioactive compounds from endophytic fungi that live in symbiosis with medicinal plants have garnered significant interest in pharmaceutical research due to their extensive chemical composition and prospective medicinal attributes. This review underscores the potentiality of fungal endophytes as a promising resource for the development of innovative anticancer agents specifically tailored for breast cancer therapy. The diversity of endophytic fungi residing in medicinal plants, success stories of key endophytic bioactive metabolites tested against breast cancer and the current progress with regards to in vivo studies and clinical trials on endophytic fungal metabolites in breast cancer research forms the underlying theme of this article. A thorough compilation of putative anticancer compounds sourced from endophytic fungi that have demonstrated therapeutic potential against breast cancer, spanning the period from 1990 to 2022, has been presented. This review article also outlines the latest trends in endophyte-based drug discovery, including the use of artificial intelligence, machine learning, multi-omics approaches, and high-throughput strategies. The challenges and future prospects associated with fungal endophytes as substitutive sources for developing anticancer drugs targeting breast cancer are also being highlighted.
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Affiliation(s)
- Sherin Varghese
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala, 686560, India
| | - M.S. Jisha
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala, 686560, India
| | - K.C. Rajeshkumar
- National Fungal Culture Collection of India (NFCCI), Biodiversity and Palaeobiology (Fungi) Gr., Agharkar Research Institute, G.G. Agharkar Road, Pune, 411 004, Maharashtra, India
| | - Virendra Gajbhiye
- Nanobioscience Group, Agharkar Research Institute, G.G. Agharkar Road, Pune, 411 004, Maharashtra, India
| | - Abdulwahed Fahad Alrefaei
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Rajesh Jeewon
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
- Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Reduit, Mauritius
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Liu J, Zhao R, Feng J, Fu W, Cao L, Zhang J, Lei Y, Liang J, Lin L, Li X, Li B. Bacterial assembly and succession patterns in conventional and advanced drinking water systems: From source to tap. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134613. [PMID: 38788571 DOI: 10.1016/j.jhazmat.2024.134613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 05/01/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024]
Abstract
Bacteria are pivotal to drinking water treatment and public health. However, the mechanisms of bacterial assembly and their impact on species coexistence remain largely unexplored. This study explored the assembly and succession of bacterial communities in two full-scale drinking water systems over one year. We observed a decline in bacterial biomass, diversity, and co-occurrence network complexity along the treatment processes, except for the biological activated carbon filtration stage. The conventional plant showed higher bacterial diversity than the advanced plant, despite similar bacterial concentrations and better removal efficiency. The biological activated carbon filter exhibited high phylogenetic diversity, indicating enhanced bacterial metabolic functionality for organic matter removal. Chlorination inactivated most bacteria but favored some chlorination-resistant and potentially pathogenic species, such as Burkholderia, Bosea, Brevundimonas, and Acinetobacter. Moreover, the spatiotemporal dynamics of the bacterial continuum were primarily driven by stochastic processes, explaining more than 78% of the relative importance. The advanced plant's bacterial community was less influenced by dispersal limitation and more by homogeneous selection. The stochastic process regulated bacterial diversity and influenced the complexity of the species co-occurrence network. These findings deepen our understanding of microbial ecological mechanisms and species interactions, offering insights for enhancing hygienic safety in drinking water systems.
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Affiliation(s)
- Jie Liu
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China; State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Renxin Zhao
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China; School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Jie Feng
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Wenjie Fu
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Lijia Cao
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Jiayu Zhang
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Yusha Lei
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Jiajin Liang
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Lin Lin
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Xiaoyan Li
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Bing Li
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China.
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Tian Z, Xiong Y, Li G, Cao X, Li X, Du C, Zhang L. Food wastewater treatment using a hybrid biofilm reactor: nutrient removal performance and functional microorganisms on filler biofilm and suspended sludge. RSC Adv 2024; 14:22470-22479. [PMID: 39015665 PMCID: PMC11250134 DOI: 10.1039/d4ra01631a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 07/02/2024] [Indexed: 07/18/2024] Open
Abstract
In this study, a laboratory-scale hybrid biofilm reactor (HBR) was constructed to treat food wastewater (FWW) before it is discharged into the sewer. The chemical oxygen demand (COD) of 29 860 mg L-1 in FWW was degraded to 200-350 mg L-1 using the HBR under the operating parameters of COD load 1.68 kg m-3 d-1, hydraulic retention time (HRT) of 426.63 h, dissolved oxygen (DO) of 8-9 mg L-1, and temperature of 22-23 °C. The biomass of biofilm on the surface of filler was 2.64 g L-1 for column A and 0.91 g L-1 for column O. Microbial analysis revealed richer and more diverse microorganisms in filler biofilms compared to those in suspended sludge. The hybrid filler was conducive to the development of functional microbial species, including phyla Firmicutes, Actinobacteriota, and Chloroflexi, and genus level norank_f_JG30-KF-CM45, which will improve FWW treatment efficiency. Moreover, the microorganisms on the filler biofilm had more connections and relationships than those in the suspended sludge. The combination of an up-flow anaerobic sludge bed (UASB) and HBR was demonstrated to be an economical strategy for practical applications as a shorter HRT of 118.34 h could be obtained. Overall, this study provides reliable data and a theoretical basis for the application of HBR and FWW treatments.
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Affiliation(s)
- Zhenjun Tian
- College of Water Sciences, Beijing Normal University Beijing 100875 China +86-10-84918164
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences Beijing 100012 China
| | - Ying Xiong
- Beijing Water Science and Technology Institute Beijing 100048 China
| | - Guowen Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences Beijing 100012 China
| | - Xiaoxin Cao
- China Water Environment Group Co. Ltd Beijing 101101 China
| | - Xin Li
- China Water Environment Group Co. Ltd Beijing 101101 China
| | - Caili Du
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences Beijing 100012 China
| | - Lieyu Zhang
- College of Water Sciences, Beijing Normal University Beijing 100875 China +86-10-84918164
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences Beijing 100012 China
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Yan H, Wu Y, He G, Wen S, Yang L, Ji L. Fertilization regime changes rhizosphere microbial community assembly and interaction in Phoebe bournei plantations. Appl Microbiol Biotechnol 2024; 108:417. [PMID: 38995388 PMCID: PMC11245453 DOI: 10.1007/s00253-024-13106-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/28/2024] [Accepted: 03/10/2024] [Indexed: 07/13/2024]
Abstract
Fertilizer input is one of the effective forest management practices, which improves soil nutrients and microbial community compositions and promotes forest productivity. However, few studies have explored the response of rhizosphere soil microbial communities to various fertilization regimes across seasonal dynamics. Here, we collected the rhizosphere soil samples from Phoebe bournei plantations to investigate the response of community assemblages and microbial interactions of the soil microbiome to the short-term application of four typical fertilizer practices (including chemical fertilizer (CF), organic fertilizer (OF), compound microbial fertilizer (CMF), and no fertilizer control (CK)). The amendments of organic fertilizer and compound microbial fertilizer altered the composition of rhizosphere soil bacterial and fungal communities, respectively. The fertilization regime significantly affected bacterial diversity rather than fungal diversity, and rhizosphere fungi responded more sensitively than bacteria to season. Fertilization-induced fungal networks were more complex than bacterial networks. Stochastic processes governed both rhizosphere soil bacterial and fungal communities, and drift and dispersal limitation dominated soil fungal and bacterial communities, respectively. Collectively, these findings demonstrate contrasting responses to community assemblages and interactions of rhizosphere bacteria and fungi to fertilizer practices. The application of organic fertilization strengthens microbial interactions and changes the succession of key taxa in the rhizosphere habitat. KEY POINTS: • Fertilization altered the key taxa and microbial interaction • Organic fertilizer facilitated the turnover of rhizosphere microbial communities • Stochasticity governed soil fungal and bacterial community assembly.
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Affiliation(s)
- Haoyu Yan
- School of Forestry, Central South University of Forestry and Technology, 410004, Changsha, People's Republic of China
| | - Yang Wu
- School of Forestry, Central South University of Forestry and Technology, 410004, Changsha, People's Republic of China
| | - Gongxiu He
- School of Forestry, Central South University of Forestry and Technology, 410004, Changsha, People's Republic of China
| | - Shizhi Wen
- School of Forestry, Central South University of Forestry and Technology, 410004, Changsha, People's Republic of China
| | - Lili Yang
- School of Forestry, Central South University of Forestry and Technology, 410004, Changsha, People's Republic of China.
| | - Li Ji
- School of Forestry, Central South University of Forestry and Technology, 410004, Changsha, People's Republic of China.
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Liu Z, Cao F, Wan J, Chen X, Kong B, Li D, Zhang XH, Jiang Y, Shi X. Stable microbial community diversity across large-scale Antarctic water masses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174559. [PMID: 38992373 DOI: 10.1016/j.scitotenv.2024.174559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/13/2024]
Abstract
The distinctive environmental attributes of the Southern Ocean underscore the indispensability of microorganisms in this region. We analyzed 208 samples obtained from four separate layers (Surface, Deep Chlorophyll Maximum, Middle, and Bottom) in the neighboring seas of the Antarctic Peninsula and the Cosmonaut Sea to explore variations in microbial composition, interactions and community assembly processes. The results demonstrated noteworthy distinctions in alpha and beta diversity across diverse communities, with the increase in water depth, a gradual rise in community diversity was observed. In particular, the co-occurrence network analysis exposed pronounced microbial interactions within the same water mass, which are notably stronger than those observed between different water masses. Co-occurrence network complexity was higher in the surface water mass than in the bottom water mass. Yet, the surface water mass exhibited greater network stability. Moreover, in the phylogenetic-based β-nearest taxon distance analyses, deterministic processes were identified as the primary factors influencing community assembly in Antarctic microorganisms. This study contributes to exploring diversity and assembly processes under the complex hydrological conditions of Antarctica.
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Affiliation(s)
- Zhengang Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Furong Cao
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Jiyuan Wan
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Xing Chen
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Bin Kong
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Dong Li
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yong Jiang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
| | - Xiaochong Shi
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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Kumbhare SV, Pedroso I, Joshi B, Muthukumar KM, Saravanan SK, Irudayanathan C, Kochhar GS, Dulai PS, Sinha R, Almonacid DE. Longitudinal gut microbial signals are associated with weight loss: insights from a digital therapeutics program. Front Nutr 2024; 11:1363079. [PMID: 39040930 PMCID: PMC11262244 DOI: 10.3389/fnut.2024.1363079] [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: 12/29/2023] [Accepted: 06/24/2024] [Indexed: 07/24/2024] Open
Abstract
Introduction The gut microbiome's influence on weight management has gained significant interest for its potential to support better obesity therapeutics. Patient stratification leading to personalized nutritional intervention has shown benefits over one-size-fit-all diets. However, the efficacy and impact on the gut's microbiome of personalizing weight loss diets based on individual factors remains under-investigated. Methods This study assessed the impact of Digbi Health's personalized dietary and lifestyle program on weight loss and the gut microbiome end-points in 103 individuals. Participants' weight loss patterns and gut microbiome profiles were analyzed from baseline to follow-up samples. Results Specific microbial genera, functional pathways, and communities associated with BMI changes and the program's effectiveness were identified. 80% of participants achieved weight loss. Analysis of the gut microbiome identified genera and functional pathways associated with a reduction in BMI, including Akkermansia, Christensenella, Oscillospiraceae, Alistipes, and Sutterella, short-chain fatty acid production, and degradation of simple sugars like arabinose, sucrose, and melibiose. Network analysis identified a microbiome community associated with BMI, which includes multiple taxa known for associations with BMI and obesity. Discussion The personalized dietary and lifestyle program positively impacted the gut microbiome and demonstrated significant associations between gut microbial changes and weight loss. These findings support the use of the gut microbiome as an endpoint in weight loss interventions, highlighting potential microbiome biomarkers for further research.
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Affiliation(s)
| | | | | | | | | | | | - Gursimran S. Kochhar
- Division of Gastroenterology, Hepatology and Nutrition, Allegheny Health Network, Pittsburgh, PA, United States
| | - Parambir S. Dulai
- Division of Gastroenterology, Northwestern University, Chicago, IL, United States
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Jiao JY, Ma SC, Salam N, Zhou Z, Lian ZH, Fu L, Chen Y, Peng CH, OuYang YT, Fan H, Li L, Yi Y, Zhang JY, Wang JY, Liu L, Gao L, Oren A, Woyke T, Dodsworth JA, Hedlund BP, Li WJ, Cheng L. Cultivation of novel Atribacterota from oil well provides new insight into their diversity, ecology, and evolution in anoxic, carbon-rich environments. MICROBIOME 2024; 12:123. [PMID: 38971798 PMCID: PMC11227167 DOI: 10.1186/s40168-024-01836-7] [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: 11/24/2023] [Accepted: 05/13/2024] [Indexed: 07/08/2024]
Abstract
BACKGROUND The Atribacterota are widely distributed in the subsurface biosphere. Recently, the first Atribacterota isolate was described and the number of Atribacterota genome sequences retrieved from environmental samples has increased significantly; however, their diversity, physiology, ecology, and evolution remain poorly understood. RESULTS We report the isolation of the second member of Atribacterota, Thermatribacter velox gen. nov., sp. nov., within a new family Thermatribacteraceae fam. nov., and the short-term laboratory cultivation of a member of the JS1 lineage, Phoenicimicrobium oleiphilum HX-OS.bin.34TS, both from a terrestrial oil reservoir. Physiological and metatranscriptomics analyses showed that Thermatribacter velox B11T and Phoenicimicrobium oleiphilum HX-OS.bin.34TS ferment sugars and n-alkanes, respectively, producing H2, CO2, and acetate as common products. Comparative genomics showed that all members of the Atribacterota lack a complete Wood-Ljungdahl Pathway (WLP), but that the Reductive Glycine Pathway (RGP) is widespread, indicating that the RGP, rather than WLP, is a central hub in Atribacterota metabolism. Ancestral character state reconstructions and phylogenetic analyses showed that key genes encoding the RGP (fdhA, fhs, folD, glyA, gcvT, gcvPAB, pdhD) and other central functions were gained independently in the two classes, Atribacteria (OP9) and Phoenicimicrobiia (JS1), after which they were inherited vertically; these genes included fumarate-adding enzymes (faeA; Phoenicimicrobiia only), the CODH/ACS complex (acsABCDE), and diverse hydrogenases (NiFe group 3b, 4b and FeFe group A3, C). Finally, we present genome-resolved community metabolic models showing the central roles of Atribacteria (OP9) and Phoenicimicrobiia (JS1) in acetate- and hydrocarbon-rich environments. CONCLUSION Our findings expand the knowledge of the diversity, physiology, ecology, and evolution of the phylum Atribacterota. This study is a starting point for promoting more incisive studies of their syntrophic biology and may guide the rational design of strategies to cultivate them in the laboratory. Video Abstract.
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Affiliation(s)
- Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shi-Chun Ma
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
- National Agri-Food Biotechnology Institute, Sector-81 (Knowledge City), Mohali, 140306, Punjab, India
| | - Zhuo Zhou
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Zheng-Han Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Li Fu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Ying Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Cheng-Hui Peng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Yu-Ting OuYang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Hui Fan
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Ling Li
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Yue Yi
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Jing-Yi Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jing-Yuan Wang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Lei Gao
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California Merced, Life and Environmental Sciences, Merced, CA, USA
| | | | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China.
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Liu B, Li C, Zhao X, Zhang C, He X, Qu L, Zhang N. Contrasting Patterns of Fungal and Bacterial Endophytes Inhabiting Temperate Tree Leaves in Response to Thinning. J Fungi (Basel) 2024; 10:470. [PMID: 39057355 PMCID: PMC11277613 DOI: 10.3390/jof10070470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/30/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
The phyllosphere is an important but underestimated habitat for a variety of microorganisms, with limited knowledge about leaf endophytes as a crucial component of the phyllosphere microbiome. In this study, we investigated the mechanisms of communities and co-occurrence networks of leaf endophytes in response to forest thinning in a temperate forest. As we expected, contrasting responses of fungal and bacterial endophytes were observed. Specifically, the diversity of leaf endophytic fungi and the complexity of their co-occurrence networks increased significantly with thinning intensity, whereas the complexity of endophytic bacterial co-occurrence networks decreased. In particular, microbiota inhabiting damaged leaves seem to be more intensively interacting, showing an evident fungi-bacteria trade-off under forest thinning. In damaged leaves, besides the direct effects of thinning, thinning-induced changes in neighbor tree diversity indirectly altered the diversity of leaf fungal and bacterial endophytes via modifying leaf functional traits such as leaf dry matter content and specific leaf area. These findings provide new experimental evidence for the trade-offs between leaf endophytic fungi and bacteria under the different magnitudes of deforestation, highlighting their dependence on the presence or absence of leaf damage.
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Affiliation(s)
- Beiping Liu
- State Key Laboratory of Efficient Production of Forest Resources, College of Forestry, Beijing Forestry University, Beijing 100083, China; (B.L.); (C.L.); (X.H.)
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Chunhuan Li
- State Key Laboratory of Efficient Production of Forest Resources, College of Forestry, Beijing Forestry University, Beijing 100083, China; (B.L.); (C.L.); (X.H.)
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Xiuhai Zhao
- Research Center of Forest Management Engineering of State Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China; (X.Z.); (C.Z.)
| | - Chunyu Zhang
- Research Center of Forest Management Engineering of State Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China; (X.Z.); (C.Z.)
| | - Xinyi He
- State Key Laboratory of Efficient Production of Forest Resources, College of Forestry, Beijing Forestry University, Beijing 100083, China; (B.L.); (C.L.); (X.H.)
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Laiye Qu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China;
| | - Naili Zhang
- State Key Laboratory of Efficient Production of Forest Resources, College of Forestry, Beijing Forestry University, Beijing 100083, China; (B.L.); (C.L.); (X.H.)
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan 518000, China
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46
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Luo Y, Liao H, Huang X, Zhang C, Gao L, Wang Z, Xia X. Unraveling the Metabolic Behavior and Interspecific Interaction Pattern of Lactic Acid Bacteria within Chinese Rice Wine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:14899-14911. [PMID: 38913831 DOI: 10.1021/acs.jafc.4c02461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The synthetic community of lactic acid bacteria (LAB) is commonly utilized in the food industry for manipulating product properties. However, the intermediate interactions and ecological stability resulting from metabolic differences among various LAB types remain poorly understood. We aimed to analyze the metabolic behavior of single and combined lactic acid bacteria in China rice wine based on microbial succession. Three-stage succession patterns with obligate heterofermentative LAB dominating prefermentation and homofermentative LAB prevailing in main fermentation were observed. Facultative heterofermentative LAB exhibited significant growth. Pairwise coculture interactions revealed 63.5% positive, 34.4% negative, and 2.1% neutral interactions, forming nontransitive and transitive competition modes. Nontransitive competitive combinations demonstrated stability over ∼200 generations through amino acid (mainly aspartic acid, glutamine, and serine) cross-feeding and lactic acid detoxification, which also showed potential for controlling biogenic amines and developing LAB starter cultures. Our findings offer insights into the mechanistic underpinnings of LAB interaction networks.
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Affiliation(s)
- Yi Luo
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
| | - Hui Liao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
| | - Xinlei Huang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
| | - Chenhao Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
| | - Ling Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
- Jiangsu Tanggou Liangxianghe Liquor Co., Ltd., Lianyungang, Jiangsu 222535, P. R. China
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
- College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300000, P. R. China
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47
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Jiang A, Dong Y, Asitaiken J, Zhou S, Nie T, Wu Y, Liu Z, An S, Yang K. Response of soil fungal communities and their co-occurrence patterns to grazing exclusion in different grassland types. Front Microbiol 2024; 15:1404633. [PMID: 39027108 PMCID: PMC11256198 DOI: 10.3389/fmicb.2024.1404633] [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: 03/21/2024] [Accepted: 06/03/2024] [Indexed: 07/20/2024] Open
Abstract
Overgrazing and climate change are the main causes of grassland degradation, and grazing exclusion is one of the most common measures for restoring degraded grasslands worldwide. Soil fungi can respond rapidly to environmental stresses, but the response of different grassland types to grazing control has not been uniformly determined. Three grassland types (temperate desert, temperate steppe grassland, and mountain meadow) that were closed for grazing exclusion for 9 years were used to study the effects of grazing exclusion on soil nutrients as well as fungal community structure in the three grassland types. The results showed that (1) in the 0-5 cm soil layer, grazing exclusion significantly affected the soil water content of the three grassland types (P < 0.05), and the pH, total phosphorous (TP), and nitrogen-to-phosphorous ratio (N/P) changed significantly in all three grassland types (P < 0.05). Significant changes in soil nutrients in the 5-10 cm soil layer after grazing exclusion occurred in the mountain meadow grasslands (P < 0.05), but not in the temperate desert and temperate steppe grasslands. (2) For the different grassland types, Archaeorhizomycetes was most abundant in the montane meadows, and Dothideomycetes was most abundant in the temperate desert grasslands and was significantly more abundant than in the remaining two grassland types (P < 0.05). Grazing exclusion led to insignificant changes in the dominant soil fungal phyla and α diversity, but significant changes in the β diversity of soil fungi (P < 0.05). (3) Grazing exclusion areas have higher mean clustering coefficients and modularity classes than grazing areas. In particular, the highest modularity class is found in temperate steppe grassland grazing exclusion areas. (4) We also found that pH is the main driving factor affecting soil fungal community structure, that plant coverage is a key environmental factor affecting soil community composition, and that grazing exclusion indirectly affects soil fungal communities by affecting soil nutrients. The above results suggest that grazing exclusion may regulate microbial ecological processes by changing the soil fungal β diversity in the three grassland types. Grazing exclusion is not conducive to the recovery of soil nutrients in areas with mountain grassland but improves the stability of soil fungi in temperate steppe grassland. Therefore, the type of degraded grassland should be considered when formulating suitable restoration programmes when grazing exclusion measures are implemented. The results of this study provide new insights into the response of soil fungal communities to grazing exclusion, providing a theoretical basis for the management of degraded grassland restoration.
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Affiliation(s)
- Anjing Jiang
- College of Grassland Science, Xinjiang Agricultural University, Ürümqi, China
| | - Yiqiang Dong
- College of Grassland Science, Xinjiang Agricultural University, Ürümqi, China
- Xinjiang Key Laboratory of Grassland Resources and Ecology, Ürümqi, Xinjiang, China
- Key Laboratory of Grassland Resources and Ecology of Western Arid Region, Ministry of Education, Ürümqi, China
- Postdoctoral Mobile Station of Xinjiang Agricultural University, Ürümqi, China
| | - Julihaiti Asitaiken
- College of Grassland Science, Xinjiang Agricultural University, Ürümqi, China
| | - Shijie Zhou
- College of Grassland Science, Xinjiang Agricultural University, Ürümqi, China
| | - Tingting Nie
- College of Grassland Science, Xinjiang Agricultural University, Ürümqi, China
| | - Yue Wu
- College of Grassland Science, Xinjiang Agricultural University, Ürümqi, China
| | - Zeyu Liu
- College of Grassland Science, Xinjiang Agricultural University, Ürümqi, China
| | - Shazhou An
- College of Grassland Science, Xinjiang Agricultural University, Ürümqi, China
- Xinjiang Key Laboratory of Grassland Resources and Ecology, Ürümqi, Xinjiang, China
- Key Laboratory of Grassland Resources and Ecology of Western Arid Region, Ministry of Education, Ürümqi, China
| | - Kailun Yang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
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Kawatsu K. Unraveling emergent network indeterminacy in complex ecosystems: A random matrix approach. Proc Natl Acad Sci U S A 2024; 121:e2322939121. [PMID: 38935564 PMCID: PMC11228516 DOI: 10.1073/pnas.2322939121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 05/31/2024] [Indexed: 06/29/2024] Open
Abstract
Indeterminacy of ecological networks-the unpredictability of ecosystem responses to persistent perturbations-is an emergent property of indirect effects a species has on another through interaction chains. Thus, numerous indirect pathways in large, complex ecological communities could make forecasting the long-term outcomes of environmental changes challenging. However, a comprehensive understanding of ecological structures causing indeterminacy has not yet been reached. Here, using random matrix theory (RMT), we provide mathematical criteria determining whether network indeterminacy emerges across various ecological communities. Our analytical and simulation results show that indeterminacy intricately depends on the characteristics of species interaction. Specifically, contrary to conventional wisdom, network indeterminacy is unlikely to emerge in large competitive and mutualistic communities, while it is a common feature in top-down regulated food webs. Furthermore, we found that predictable and unpredictable perturbations can coexist in the same community and that indeterminate responses to environmental changes arise more frequently in networks where predator-prey relationships predominate than competitive and mutualistic ones. These findings highlight the importance of elucidating direct species relationships and analyzing them with an RMT perspective on two fronts: It aids in 1) determining whether the network's responses to environmental changes are ultimately indeterminate and 2) identifying the types of perturbations causing less predictable outcomes in a complex ecosystem. In addition, our framework should apply to the inverse problem of network identification, i.e., determining whether observed responses to sustained perturbations can reconstruct their proximate causalities, potentially impacting other fields such as microbial and medical sciences.
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Affiliation(s)
- Kazutaka Kawatsu
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Japan
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49
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Sun J, Zhou H, Cheng H, Chen Z, Wang Y. Bacterial abundant taxa exhibit stronger environmental adaption than rare taxa in the Arctic Ocean sediments. MARINE ENVIRONMENTAL RESEARCH 2024; 199:106624. [PMID: 38943698 DOI: 10.1016/j.marenvres.2024.106624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/01/2024]
Abstract
Marine bacteria influence Earth's environmental dynamics in fundamental ways by controlling the biogeochemistry and productivity of the oceans. However, little is known about the survival strategies of their abundant and rare taxa, especially in polar marine environments. Here, bacterial environmental adaptation, community assembly processes, and co-occurrence patterns between abundant and rare taxa were compared in the Arctic Ocean sediments. Results indicated that the diversity of rare taxa is significantly higher than that of abundant taxa, whereas the distance-decay rate of rare taxa community similarity is over 1.5 times higher than that of abundant taxa. Furthermore, abundant taxa exhibited broader environmental breadth and stronger phylogenetic signals compared to rare taxa. Additionally, the community assembly processes of the abundant taxa were predominantly governed by 81% dispersal limitation, while rare taxa were primarily influenced by 48% heterogeneous selection. The co-occurrence network further revealed the abundant taxa formed a more complex network to enhance their environmental adaptability. This study revealed the differences in environmental responses and community assembly processes between bacterial abundant and rare taxa in polar ocean sediments, providing some valuable insights for understanding their environmental adaptation strategies in marine ecosystems.
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Affiliation(s)
- Jianxing Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Zhu Chen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Yuguang Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China.
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50
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Dan H, Song X, Xiang G, Song C, Dai H, Shao Y, Huang D, Luo H. The response pattern of the microbial community structure and metabolic profile of jiupei to Bacillus subtilis JP1 addition during baijiu fermentation. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:5021-5030. [PMID: 38296914 DOI: 10.1002/jsfa.13345] [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: 10/19/2023] [Revised: 12/07/2023] [Accepted: 01/19/2024] [Indexed: 02/02/2024]
Abstract
BACKGROUND Baijiu brewing is a complex and multifaceted multimicrobial co-fermentation process, in which various microorganisms interact to form an interdependent micro-ecosystem, subsequently influencing metabolic activities and compound production. Among these microorganisms, Bacillus, an important bacterial genus in the liquor brewing process, remains unclear in its role in shaping the brewing microbial community and its functional metabolism. RESULTS A baijiu fermentation system was constructed using B. subtilis JP1 isolated from native jiupei (grain mixture) combined with daqu (a saccharifying agent) and huangshui (a fermentation byproduct). Based on high-throughput amplicon sequencing analysis, it was evident that B. subtilis JP1 significantly influences bacterial microbial diversity and fungal community structure in baijiu fermentation. Of these, Aspergillus and Monascus emerge as the most markedly altered microbial genera in the jiupei community. Based on co-occurrence networks and bidirectional orthogonal partial least squares discriminant analysis models, it was demonstrated that the addition of B. subtilis JP1 intensified microbial interactions in jiupei fermentation, consequently enhancing the production of volatile flavor compounds such as heptanoic acid, butyl hexanoate and 3-methylthiopropanol in jiupei. CONCLUSION B. subtilis JP1 significantly alters the microbial community structure of jiupei, enhancing aroma formation during fermentation. These findings will contribute to a broader application in solid-state fermentation. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Hulin Dan
- College of Bioengineering, Sichuan University of Science & Engineering, Zigong, China
| | - Xuemiao Song
- College of Bioengineering, Sichuan University of Science & Engineering, Zigong, China
| | - Gangxing Xiang
- College of Bioengineering, Sichuan University of Science & Engineering, Zigong, China
| | | | | | - Yan Shao
- Luzhou Laojiao Co. Ltd, Luzhou, China
| | - Dan Huang
- College of Bioengineering, Sichuan University of Science & Engineering, Zigong, China
- Liquor Brewing Biotechnology and Application Key Laboratory of Sichuan Province, Yibin, China
| | - Huibo Luo
- College of Bioengineering, Sichuan University of Science & Engineering, Zigong, China
- Liquor Brewing Biotechnology and Application Key Laboratory of Sichuan Province, Yibin, China
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