1
|
Li C, Han Y, Zou X, Zhang X, Ran Q, Dong C. A systematic discussion and comparison of the construction methods of synthetic microbial community. Synth Syst Biotechnol 2024; 9:775-783. [PMID: 39021362 PMCID: PMC11253132 DOI: 10.1016/j.synbio.2024.06.006] [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: 05/08/2024] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 07/20/2024] Open
Abstract
Synthetic microbial community has widely concerned in the fields of agriculture, food and environment over the past few years. However, there is little consensus on the method to synthetic microbial community from construction to functional verification. Here, we review the concept, characteristics, history and applications of synthetic microbial community, summarizing several methods for synthetic microbial community construction, such as isolation culture, core microbiome mining, automated design, and gene editing. In addition, we also systematically summarized the design concepts, technological thresholds, and applicable scenarios of various construction methods, and highlighted their advantages and limitations. Ultimately, this review provides four efficient, detailed, easy-to-understand and -follow steps for synthetic microbial community construction, with major implications for agricultural practices, food production, and environmental governance.
Collapse
Affiliation(s)
- Chenglong Li
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Yanfeng Han
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Xiao Zou
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Xueqian Zhang
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Qingsong Ran
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Chunbo Dong
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou, China
| |
Collapse
|
2
|
Van Le V, Kang M, Ko SR, Park CY, Lee JJ, Choi IC, Oh HM, Ahn CY. Response of particle-attached and free-living bacterial communities to Microcystis blooms. Appl Microbiol Biotechnol 2024; 108:42. [PMID: 38183480 DOI: 10.1007/s00253-023-12828-2] [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: 03/24/2023] [Revised: 07/29/2023] [Accepted: 11/13/2023] [Indexed: 01/08/2024]
Abstract
The massive proliferation of Microcystis threatens freshwater ecosystems and degrades water quality globally. Understanding the mechanisms that contribute to Microcystis growth is crucial for managing Microcystis blooms. The lifestyles of bacteria can be classified generally into two groups: particle-attached (PA; > 3 µm) and free-living (FL; 0.2-3.0 µm). However, little is known about the response of PA and FL bacteria to Microcystis blooms. Using 16S rRNA gene high-throughput sequencing, we investigated the stability, assembly process, and co-occurrence patterns of PA and FL bacterial communities during distinct bloom stages. PA bacteria were phylogenetically different from their FL counterparts. Microcystis blooms substantially influenced bacterial communities. The time decay relationship model revealed that Microcystis blooms might increase the stability of both PA and FL bacterial communities. A contrasting community assembly mechanism was observed between the PA and FL bacterial communities. Throughout Microcystis blooms, homogeneous selection was the major assembly process that impacted the PA bacterial community, whereas drift explained much of the turnover of the FL bacterial community. Both PA and FL bacterial communities could be separated into modules related to different phases of Microcystis blooms. Microcystis blooms altered the assembly process of PA and FL bacterial communities. PA bacterial community appeared to be more responsive to Microcystis blooms than FL bacteria. Decomposition of Microcystis blooms may enhance cooperation among bacteria. Our findings highlight the importance of studying bacterial lifestyles to understand their functions in regulating Microcystis blooms. KEY POINTS: • Microcystis blooms alter the assembly process of PA and FL bacterial communities • Microcystis blooms increase the stability of both PA and FL bacterial communities • PA bacteria seem to be more responsive to Microcystis blooms than FL bacteria.
Collapse
Affiliation(s)
- Ve Van Le
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Mingyeong Kang
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - So-Ra Ko
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
| | - Chan-Yeong Park
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Jay Jung Lee
- Geum River Environment Research Center, National Institute of Environmental Research, Chungbuk, 29027, Republic of Korea
| | - In-Chan Choi
- Geum River Environment Research Center, National Institute of Environmental Research, Chungbuk, 29027, Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Chi-Yong Ahn
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea.
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea.
| |
Collapse
|
3
|
Chen H, Lei L, Li Z, Zhou H, Cheng H, Chen Z, Wang Y, Wang Y. Redundancy and resilience of microbial community under aniline stress during wastewater treatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175822. [PMID: 39197768 DOI: 10.1016/j.scitotenv.2024.175822] [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: 04/21/2024] [Revised: 08/15/2024] [Accepted: 08/25/2024] [Indexed: 09/01/2024]
Abstract
Aniline is one of the most toxic and widespread organic pollutants. Although biological treatment is cost-effective and generates minimal secondary pollution, microbial communities are significantly affected by high aniline concentrations, which result in low degradation efficiency. However, a comprehensive understanding of the microbial community response to aniline stress is lacking. Here, we performed a cyclic experiment with aniline concentrations (200, 600, 1200, 600, and 200 mg/L) to investigate the ability of microbial communities to recover their performance after exposure to high aniline concentrations. At aniline concentrations up to 600 mg/L, the bioreactor exhibited high aniline removal efficiency (almost 100 %). Comamonas, Zoogloea, and Delftia played crucial roles in removing aniline and microbial beta diversity changed. Additionally, alpha diversity and network complexity decreased with increasing aniline concentration, but these metrics recovered to their original levels when the aniline concentration was returned to 200 mg/L. Homogeneous and heterogeneous selection dominated microbial community assembly. Therefore, according to the observed variations in community structure and the recovery of keystones after aniline stress, microbial community redundancy and resilience are pivotal for ensuring system stability. Overall, this study provides valuable insights into the redundancy and resilience of microbial communities under aniline stress and establishes a scientific basis for managing and evaluating wastewater treatment plants.
Collapse
Affiliation(s)
- Hui Chen
- Institute of Zhejiang University - Quzhou, Quzhou 32400, China; Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Lecheng Lei
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Zhongjian Li
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Zhu Chen
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Yangyang Wang
- National Demonstration Center for Environmental and Planning, College of Geography and Environmental Science, Henan University, Kaifeng 475004, China
| | - Yuguang Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China.
| |
Collapse
|
4
|
Liu C, Ruan F, Chen Z, Han J, Ding X, Han C, Ye L, Yang C, Yu Y, Zuo Z, He C. Phenanthrene-induced hyperuricemia with intestinal barrier damage and the protective role of theabrownin: Modulation by gut microbiota-mediated bile acid metabolism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174923. [PMID: 39047823 DOI: 10.1016/j.scitotenv.2024.174923] [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: 05/01/2024] [Revised: 06/24/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
Hyperuricemia is prevalent globally and potentially linked to environmental pollution. As a typical persistent organic pollutant, phenanthrene (Phe) poses threats to human health through biomagnification. Although studies have reported Phe-induced toxicities to multiple organs, its impact on uric acid (UA) metabolism remains unclear. In this study, data mining on NHANES 2001-2016 indicated a positive correlation between Phe exposure and the occurrence of hyperuricemia in population. Subsequently, adolescent Balb/c male mice were orally exposed to Phe at a dosage of 10 mg/kg bw every second day for 7 weeks, resulting in dysfunction of intestinal UA excretion and disruption of the intestinal barrier. Utilizing intestinal organoids, 16S rRNA sequencing of gut microbiota, and targeted metabolomic analysis, we further revealed that an imbalance in bile acid metabolism derived from gut microbiota might mediate the intestinal barrier damage. Additionally, the tea extract theabrownin (TB) effectively improved Phe-induced hyperuricemia and intestinal dysfunction at a dose of 320 mg/kg bw per day. In conclusion, this study demonstrates that Phe exposure is positively associated with hyperuricemia and intestinal damage, which provides new insights into the toxic effects induced by Phe. Furthermore, the present study proposes that supplementation with TB would be a healthy and effective improvement strategy for patients with hyperuricemia and intestinal injury caused by environmental factors.
Collapse
Affiliation(s)
- Changqian Liu
- State Key Laboratory of Cellular Stress Biology, Department of Thoracic Surgery, Xiang'an Hospital of Xiamen University, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Fengkai Ruan
- State Key Laboratory of Cellular Stress Biology, Department of Thoracic Surgery, Xiang'an Hospital of Xiamen University, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Zhiyuan Chen
- State Key Laboratory of Cellular Stress Biology, Department of Thoracic Surgery, Xiang'an Hospital of Xiamen University, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Jianrong Han
- State Key Laboratory of Cellular Stress Biology, Department of Thoracic Surgery, Xiang'an Hospital of Xiamen University, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Xiaoyan Ding
- State Key Laboratory of Cellular Stress Biology, Department of Thoracic Surgery, Xiang'an Hospital of Xiamen University, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Changshun Han
- State Key Laboratory of Cellular Stress Biology, Department of Thoracic Surgery, Xiang'an Hospital of Xiamen University, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Lingxiao Ye
- State Key Laboratory of Cellular Stress Biology, Department of Thoracic Surgery, Xiang'an Hospital of Xiamen University, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Chunyan Yang
- State Key Laboratory of Cellular Stress Biology, Department of Thoracic Surgery, Xiang'an Hospital of Xiamen University, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Yi Yu
- Department of Nephrology, Fujian Clinical Research Center for Chronic Glomerular Disease, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian 361005, China
| | - Zhenghong Zuo
- State Key Laboratory of Cellular Stress Biology, Department of Thoracic Surgery, Xiang'an Hospital of Xiamen University, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; Department of Endocrinology, Xiang'an Hospital of Xiamen University, School of Medicine, State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China
| | - Chengyong He
- State Key Laboratory of Cellular Stress Biology, Department of Thoracic Surgery, Xiang'an Hospital of Xiamen University, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; Department of Endocrinology, Xiang'an Hospital of Xiamen University, School of Medicine, State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China.
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Cuartero J, Querejeta JI, Prieto I, Frey B, Alguacil MM. Warming and rainfall reduction alter soil microbial diversity and co-occurrence networks and enhance pathogenic fungi in dryland soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175006. [PMID: 39069184 DOI: 10.1016/j.scitotenv.2024.175006] [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: 06/03/2024] [Revised: 07/10/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024]
Abstract
In this 9-year manipulative field experiment, we examined the impacts of experimental warming (2 °C, W), rainfall reduction (30 % decrease in annual rainfall, RR), and their combination (W + RR) on soil microbial communities and native vegetation in a semi-arid shrubland in south-eastern Spain. Warming had strong negative effects on plant performance across five coexisting native shrub species, consistently reducing their aboveground biomass growth and long-term survival. The impacts of rainfall reduction on plant growth and survival were species-specific and more variable. Warming strongly altered the soil microbial community alpha-diversity and changed the co-occurrence network structure. The relative abundance of symbiotic arbuscular mycorrhizal fungi (AMF) increased under W and W + RR, which could help buffer the direct negative impacts of climate change on their host plants nutrition and enhance their resistance to heat and drought stress. Indicator microbial taxa analyses evidenced that the marked sequence abundance of many plant pathogenic fungi, such as Phaeoacremonium, Cyberlindnera, Acremonium, Occultifur, Neodevriesia and Stagonosporopsis, increased significantly in the W and W + RR treatments. Moreover, the relative abundance of fungal animal pathogens and mycoparasites in soil also increased significantly under climate warming. Our findings indicate that warmer and drier conditions sustained over several years can alter the soil microbial community structure, composition, and network topology. The projected warmer and drier climate favours pathogenic fungi, which could offset the benefits of increased AMF abundance under warming and further aggravate the severe detrimental impacts of increased abiotic stress on native vegetation performance and ecosystem services in drylands.
Collapse
Affiliation(s)
- J Cuartero
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland.
| | - J I Querejeta
- Departamento de Conservación de Suelos y Agua, Centro de Edafología y Biología Aplicada del Segura - Consejo Superior de Investigaciones Científicas, Murcia, Spain
| | - I Prieto
- Departamento de Conservación de Suelos y Agua, Centro de Edafología y Biología Aplicada del Segura - Consejo Superior de Investigaciones Científicas, Murcia, Spain; Area de Ecología, Facultad de Ciencias Biológicas y Ambientales, Departamento de Biodiversidad y Gestión Ambiental, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - B Frey
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - M M Alguacil
- Departamento de Conservación de Suelos y Agua, Centro de Edafología y Biología Aplicada del Segura - Consejo Superior de Investigaciones Científicas, Murcia, Spain
| |
Collapse
|
7
|
Mu X, Shi S, Hu X, Gan X, Han Q, Yu Q, Qu J, Li H. Gut microbiome and antibiotic resistance genes in plateau model animal (Ochotona curzoniae) exhibit a relative stability under cold stress. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135472. [PMID: 39137548 DOI: 10.1016/j.jhazmat.2024.135472] [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: 04/19/2024] [Revised: 07/07/2024] [Accepted: 08/08/2024] [Indexed: 08/15/2024]
Abstract
Antibiotic resistance genes (ARGs) carried by gut pathogens may pose a threat to the host and ecological environment. However, few studies focus on the effects of cold stress on intestinal bacteria and ARGs in plateau animals. Here, we used 16S rRNA gene sequencing and gene chip technique to explore the difference of gut microbes and ARGs in plateau pika under 4 °C and 25 °C. The results showed that tetracycline and aminoglycoside resistance genes were the dominant ARGs in pika intestine. Seven kinds of high-risk ARGs (aadA-01, aadA-02, ermB, floR, mphA-01, mphA-02, tetM-02) existed in pika's intestine, and cold had no significant effect on the composition and structure of pika's intestinal ARGs. The dominant phyla in pika intestine were Bacteroidetes and Firmicutes. Cold influenced 0.47 % of pika intestinal bacteria in OTU level, while most other bacteria had no significant change. The diversity and community assembly of intestinal bacteria in pika remained relatively stable under cold conditions, while low temperature decreased gut microbial network complexity. In addition, low temperature led to the enrichment of glycine biosynthesis and metabolism-related pathways. Moreover, the correlation analysis showed that eight opportunistic pathogens (such as Clostridium, Staphylococcus, Streptococcus, etc.) detected in pika intestine might be potential hosts of ARGs.
Collapse
Affiliation(s)
- Xianxian Mu
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Shunqin Shi
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xueqian Hu
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xueying Gan
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qian Han
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qiaoling Yu
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China
| | - Jiapeng Qu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China.
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou 730000, China; Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China; State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China.
| |
Collapse
|
8
|
Zhu Y, Ma S, Wen Y, Zhao W, Jiang Y, Li M, Zou K. Deciphering assembly processes, network complexity and stability of potential pathogenic communities in two anthropogenic coastal regions of a highly urbanized estuary. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 358:124444. [PMID: 38936795 DOI: 10.1016/j.envpol.2024.124444] [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: 04/02/2024] [Revised: 06/01/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
The existence of potential pathogens may lead to severe water pollution, disease transmission, and the risk of infectious diseases, posing threats to the stability of aquatic ecosystems and human health. In-depth research on the dynamic of potential pathogenic communities is of significant importance, it can provide crucial support for assessing the health status of aquatic ecosystems, maintaining ecological balance, promoting sustainable economic development, and safeguarding human health. Nevertheless, the current understanding of the distribution and geographic patterns of potential pathogens in coastal ecosystems remains rather limited. Here, we investigated the diversity, assembly, and co-occurrence network of potential pathogenic communities in two anthropogenic coastal regions, i.e., the eight mouths (EPR) and nearshore region (NSE), of the Pearl River Estuary (PRE) and a total of 11 potential pathogenic types were detected. The composition and diversity of potential pathogenic communities exhibited noteworthy distinctions between the EPR and NSE, with 6 shared potential pathogenic families. Additionally, in the NSE, a significant pattern of geographic decay was observed, whereas in the EPR, the pattern of geographic decay was not significant. Based on the Stegen null model, it was noted that undominant processes (53.36%/69.24%) and heterogeneous selection (27.35%/25.19%) dominated the assembly of potential pathogenic communities in EPR and NSE. Co-occurrence network analysis showed higher number of nodes, a lower average path length and graph diameter, as well as higher level of negative co-occurrences and modularity in EPR than those in NSE, indicating more complex and stable correlations between potential pathogens in EPR. These findings lay the groundwork for the effective management of potential pathogens, offering essential information for ecosystem conservation and public health considerations in the anthropogenic coastal regions.
Collapse
Affiliation(s)
- Yiyi Zhu
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Shanshan Ma
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Yongjing Wen
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Wencheng Zhao
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Yun Jiang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Min Li
- Key Laboratory for Sustainable Utilization of Open-sea Fishery, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Keshu Zou
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China.
| |
Collapse
|
9
|
Yüksel E, Voragen AGJ, Kort R. The pectin metabolizing capacity of the human gut microbiota. Crit Rev Food Sci Nutr 2024:1-23. [PMID: 39264366 DOI: 10.1080/10408398.2024.2400235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
The human gastrointestinal microbiota, densely populated with a diverse array of microorganisms primarily from the bacterial phyla Bacteroidota, Bacillota, and Actinomycetota, is crucial for maintaining health and physiological functions. Dietary fibers, particularly pectin, significantly influence the composition and metabolic activity of the gut microbiome. Pectin is fermented by gut bacteria using carbohydrate-active enzymes (CAZymes), resulting in the production of short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate, which provide various health benefits. The gastrointestinal microbiota has evolved to produce CAZymes that target different pectin components, facilitating cross-feeding within the microbial community. This review explores the fermentation of pectin by various gut bacteria, focusing on the involved transport systems, CAZyme families, SCFA synthesis capacity, and effects on microbial ecology in the gut. It addresses the complexities of the gut microbiome's response to pectin and highlights the importance of microbial cross-feeding in maintaining a balanced and diverse gut ecosystem. Through a systematic analysis of pectinolytic CAZyme production, this review provides insights into the enzymatic mechanisms underlying pectin degradation and their broader implications for human health, paving the way for more targeted and personalized dietary strategies.
Collapse
Affiliation(s)
- Ecem Yüksel
- Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Alphons G J Voragen
- Keep Food Simple, Driebergen, The Netherlands
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, The Netherlands
| | - Remco Kort
- Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- ARTIS-Micropia, Amsterdam, The Netherlands
| |
Collapse
|
10
|
Zhang B, Ma Y, Duan W, Fan Q, Sun J. Pinewood nematode induced changes in the assembly process of gallery microbiomes benefit its vector beetle's development. Microbiol Spectr 2024:e0141224. [PMID: 39258937 DOI: 10.1128/spectrum.01412-24] [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: 06/10/2024] [Accepted: 08/03/2024] [Indexed: 09/12/2024] Open
Abstract
Microbiomes play crucial roles in insect adaptation, especially under stress such as pathogen invasion. Yet, how beneficial microbiomes assemble remains unclear. The wood-boring beetle Monochamus alternatus, a major pest and vector of the pine wilt disease (PWD) nematode, offers a unique model. We conducted controlled experiments using amplicon sequencing (16S rRNA and ITS) within galleries where beetles and microbes interact. PWD significantly altered bacterial and fungal communities, suggesting distinct assembly processes. Deterministic factors like priority effects, host selection, and microbial interactions shaped microbiome composition, distinguishing healthy from PWN-infected galleries. Actinobacteria, Firmicutes, and Ophiostomataceae emerged as potentially beneficial, aiding beetle's development and pathogen resistance. This study unveils how nematode-induced changes in gallery microbiomes influence beetle's development, shedding light on microbiome assembly amid insect-pathogen interactions. Insights gleaned enhance understanding of PWD spread and suggest novel management strategies via microbiome manipulation.IMPORTANCEThis study explores the assembly process of gallery microbiomes associated with a wood-boring beetles, Monochamus alternatus, a vector of the pine wilt disease (PWD). By conducting controlled comparison experiments and employing amplicon approaches, the study reveals significant changes in taxonomic composition and functional adaptation of bacterial and fungal communities induced by PWD. It identifies deterministic processes, including priority effects, host selection, and microbial interactions, as major drivers in microbiome assembly. Additionally, the study highlights the presence of potentially beneficial microbes such as Actinobacteria, Firmicutes, and Ophiostomataceae, which could enhance beetle development and resistance to pathogens. These findings shed light on the intricate interplay among insects, microbiomes, and pathogens, contributing to a deeper understanding of PWD prevalence and suggesting innovative management strategies through microbiome manipulation.
Collapse
Affiliation(s)
- Bin Zhang
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Yafei Ma
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Wenzhao Duan
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Qi Fan
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Jianghua Sun
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
11
|
Cheng S, Gong X, Xue W, Kardol P, Delgado-Baquerizo M, Ling N, Chen X, Liu M. Evolutionarily conserved core microbiota as an extended trait in nitrogen acquisition strategy of herbaceous species. THE NEW PHYTOLOGIST 2024. [PMID: 39253787 DOI: 10.1111/nph.20118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 08/27/2024] [Indexed: 09/11/2024]
Abstract
Microbiota have co-evolved with plants over millions of years and are intimately linked to plants, ranging from symbiosis to pathogenesis. However, our understanding of the existence of a shared core microbiota across phylogenetically diverse plants remains limited. A common garden field experiment was conducted to investigate the rhizosphere microbial communities of phylogenetically contrasting herbaceous families. Through a combination of metagenomic sequencing, analysis of plant economic traits, and soil biochemical properties, we aimed to elucidate the eco-evolutionary role of the core rhizosphere microbiota in light of plant economic strategies. We identified a conserved core microbiota consisting of 278 taxa that was closely associated with the phylogeny of the plants studied. This core microbiota actively participated in multiple nitrogen metabolic processes and showed a strong correlation with the functional potential of rhizosphere nitrogen cycling, thereby serving as an extended trait in the plant nitrogen acquisition. Furthermore, our examination of simulated species loss revealed the crucial role of the core microbiota in maintaining the rhizosphere community's network stability. Our study highlighted that the core microbiota, which exhibited a phylogenetically conserved association with plants, potentially represented an extension of the plant phenotype and played an important role in nitrogen acquisition. These findings held implications for the utilization of microbiota-mediated plant functions.
Collapse
Affiliation(s)
- Saisai Cheng
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xin Gong
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenfeng Xue
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Paul Kardol
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Science, 75651, Uppsala, Sweden
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, 90751, Umeå, Sweden
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, 41012, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Ning Ling
- Centre for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Xiaoyun Chen
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Manqiang Liu
- Centre for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| |
Collapse
|
12
|
Chen J, Zhuang J, Dai T, Zhang R, Zeng Y, Jiang B, Guo H, Guo X, Yang Y. Enhancing soil petrochemical contaminant remediation through nutrient addition and exogenous bacterial introduction. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135078. [PMID: 38964043 DOI: 10.1016/j.jhazmat.2024.135078] [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: 05/04/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/06/2024]
Abstract
Biostimulation (providing favorable environmental conditions for microbial growth) and bioaugmentation (introducing exogenous microorganisms) are effective approaches in the bioremediation of petroleum-contaminated soil. However, uncertainty remains in the effectiveness of these two approaches in practical application. In this study, we constructed mesocosms using petroleum hydrocarbon-contaminated soil. We compared the effects of adding nutrients, introducing exogenous bacterial degraders, and their combination on remediating petroleum contamination in the soil. Adding nutrients more effectively accelerated total petroleum hydrocarbon (TPH) degradation than other treatments in the initial 60 days' incubation. Despite both approaches stimulating bacterial richness, the community turnover caused by nutrient addition was gentler than bacterial degrader introduction. As TPH concentrations decreased, we observed a succession in microbial communities characterized by a decline in copiotrophic, fast-growing bacterial r-strategists with high rRNA operon (rrn) copy numbers. Ecological network analysis indicated that both nutrient addition and bacterial degrader introduction enhanced the complexity and stability of bacterial networks. Compared to the other treatment, the bacterial network with nutrient addition had more keystone species and a higher proportion of negative associations, factors that may enhance microbial community stability. Our study demonstrated that nutrient addition effectively regulates community succession and ecological interaction to accelerate the soil TPH degradation.
Collapse
Affiliation(s)
- Jiayu Chen
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Jugui Zhuang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Tianjiao Dai
- School of Environment, Tsinghua University, Beijing 100084, China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China.
| | - Ruihuan Zhang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Yufei Zeng
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Bo Jiang
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Huaming Guo
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China
| | - Xue Guo
- School of Environment, Tsinghua University, Beijing 100084, China; Research Center for Eco-Environmental Sciences, Chinese Academy of Science, Beijing 100085, China
| | - Yunfeng Yang
- School of Environment, Tsinghua University, Beijing 100084, China; Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| |
Collapse
|
13
|
Meng L, Liang L, Shi Y, Yin H, Li L, Xiao J, Huang N, Zhao A, Xia Y, Hou J. Biofilms in plastisphere from freshwater wetlands: Biofilm formation, bacterial community assembly, and biogeochemical cycles. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:134930. [PMID: 38901258 DOI: 10.1016/j.jhazmat.2024.134930] [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: 03/04/2024] [Revised: 05/10/2024] [Accepted: 06/13/2024] [Indexed: 06/22/2024]
Abstract
Microorganisms can colonize to the surface of microplastics (MPs) to form biofilms, termed "plastisphere", which could significantly change their physiochemical properties and ecological roles. However, the biofilm characteristics and the deep mechanisms (interaction, assembly, and biogeochemical cycles) underlying plastisphere in wetlands currently lack a comprehensive perspective. In this study, in situ biofilm formation experiments were performed in a park with different types of wetlands to examine the plastisphere by extrinsic addition of PVC MPs in summer and winter, respectively. Results from the spectroscopic and microscopic analyses revealed that biofilms attached to the MPs in constructed forest wetlands contained the most abundant biomass and extracellular polymeric substances. Meanwhile, data from the high-throughput sequencing showed lower diversity in plastisphere compared with soil bacterial communities. Network analysis suggested a simple and unstable co-occurrence pattern in plastisphere, and the null model indicated increased deterministic process of heterogeneous selection for its community assembly. Based on the quantification of biogeochemical cycling genes by high-throughput qPCR, the relative abundances of genes involving in carbon degradation, carbon fixation, and denitrification were significantly higher in plastisphere than those of soil communities. This study greatly enhanced our understanding of biofilm formation and ecological effects of MPs in freshwater wetlands.
Collapse
Affiliation(s)
- Liang Meng
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China; Key Laboratory of Environment Remediation and Ecological Health, Zhejiang University, Ministry of Education, Hangzhou 310058, China; Yangtze River Delta Urban Wetland Ecosystem National Field Scientific Observation and Research Station, Shanghai 201722, China
| | - Longrui Liang
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yansong Shi
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Haitao Yin
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Li Li
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jiamu Xiao
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Nannan Huang
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Angang Zhao
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yangrongchang Xia
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jingwen Hou
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai 200240, China.
| |
Collapse
|
14
|
Sun S, Qiao Z, Sun K, Huo D. Assembly process and co-occurrence network of microbial community in response to free ammonia gradient distribution. Microbiol Spectr 2024; 12:e0105124. [PMID: 39058029 PMCID: PMC11370247 DOI: 10.1128/spectrum.01051-24] [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: 04/25/2024] [Accepted: 06/29/2024] [Indexed: 07/28/2024] Open
Abstract
Microorganisms are crucial components of the aquatic ecosystem due to their immense diversity and abundance. They are vital in sustaining ecological services, especially in maintaining essential biogeochemical cycles. Recent years have seen a substantial increase in surplus nitrogenous pollutants in aquatic ecosystems due to the heightened occurrence of anthropogenic activities. Elevated levels of free ammonia (FA, NH3), stemming from the discharge of excess nitrogenous pollutants, have caused notable fluctuations in aquatic ecosystems, leading to water eutrophication and various ecological challenges. The impact of these oscillations on microbial communities in aquatic ecosystems has not been extensively studied. This study employed 16S rRNA gene amplicon sequencing to systematically investigate the dynamics, co-occurrence networks, and assembly processes of microbial communities and their subcommunities (abundant, moderate, and rare) in the Luanhe River Diversion Project in China. Our findings indicate that NH3 concentration significantly influences the dynamics of microbial communities, with a notable decrease in community Richness and Phylogenetic Distance alongside increased community dissimilarity under higher NH3 conditions. The analysis revealed that certain microbial groups, particularly Actinobacteriaota, were notably more prevalent in environments with elevated NH3 levels, suggesting their potential resilience or adaptive responses to NH3 stress. Additionally, through co-occurrence network analysis, we observed dynamic changes in network topology and increased connectedness under NH3 stress. Key nodes, identified as connectors and module hubs, played crucial roles in maintaining network structure, particularly Cyanobacteria and Actinobacteriaota. Furthermore, stochastic processes, particularly drift and dispersal limitation, predominantly shaped the microbial communities. Within the three subcommunities, the impact of drift became more pronounced as the effect of dispersal limitation diminished. Overall, elucidating the dynamics of microbial communities in aquatic ecosystems exposed to NH3 can enhance our comprehension of the ecological mechanisms of microbial communities and provide new insights into the conservation of microbial community diversity and ecological functions. IMPORTANCE The research presented in this paper explores how varying concentrations of free ammonia impact microbial communities in aquatic ecosystems. By employing advanced gene sequencing techniques, the study reveals significant changes in microbial diversity and network structures in response to increased ammonia levels. Key findings indicate that high ammonia concentrations lead to a decrease in microbial richness and diversity while increasing community dissimilarity. Notably, certain microbial groups, like Actinobacteria, show resilience to ammonia stress. This research enhances our understanding of how pollution affects microbial ecosystems and underscores the importance of maintaining balanced ammonia levels to preserve microbial diversity and ecosystem health.
Collapse
Affiliation(s)
- Shengjie Sun
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Zhiyi Qiao
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Kexin Sun
- Frasergen Bioinformatics Co., Ltd, Wuhan, China
| | - Da Huo
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| |
Collapse
|
15
|
Manus MB, Lucore J, Kuthyar S, Moy M, Savo Sardaro ML, Amato KR. Technical note: A biological anthropologist's guide for applying microbiome science to studies of human and non-human primates. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024:e25020. [PMID: 39222382 DOI: 10.1002/ajpa.25020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/28/2024] [Accepted: 08/18/2024] [Indexed: 09/04/2024]
Abstract
A central goal of biological anthropology is connecting environmental variation to differences in host physiology, biology, health, and evolution. The microbiome represents a valuable pathway for studying how variation in host environments impacts health outcomes. While there are many resources for learning about methods related to microbiome sample collection, laboratory analyses, and genetic sequencing, there are fewer dedicated to helping researchers navigate the dense portfolio of bioinformatics and statistical approaches for analyzing microbiome data. Those that do exist are rarely related to questions in biological anthropology and instead are often focused on human biomedicine. To address this gap, we expand on existing tutorials and provide a "road map" to aid biological anthropologists in understanding, selecting, and deploying the data analysis and visualization methods that are most appropriate for their specific research questions. Leveraging an existing dataset of fecal samples and survey data collected from wild geladas living in Simien Mountains National Park in Ethiopia (Baniel et al., 2021), this paper guides researchers toward answering three questions related to variation in the gut microbiome across host and environmental factors. By providing explanations, examples, and a reproducible workflow for different analytic methods, we move beyond the theoretical benefits of considering the microbiome within anthropological research and instead present researchers with a guide for applying microbiome science to their work. This paper makes microbiome science more accessible to biological anthropologists and paves the way for continued research into the microbiome's role in the ecology, evolution, and health of human and non-human primates.
Collapse
Affiliation(s)
- Melissa B Manus
- Department of Anthropology, University of Texas at San Antonio, San Antonio, Texas, USA
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Jordan Lucore
- Department of Anthropology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sahana Kuthyar
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Madelyn Moy
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Maria Luisa Savo Sardaro
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
- Department of Human Science and Promotion of the Quality of Life, University of San Raffaele, Rome, Italy
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| |
Collapse
|
16
|
Hou X, Hu X, Li Y, Zhang H, Niu L, Huang R, Xu J. From disruption to adaptation: Response of phytoplankton communities in representative impounded lakes to China's South-to-North Water Diversion Project. WATER RESEARCH 2024; 261:122001. [PMID: 38964215 DOI: 10.1016/j.watres.2024.122001] [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: 04/28/2024] [Revised: 06/08/2024] [Accepted: 06/24/2024] [Indexed: 07/06/2024]
Abstract
Impounded lakes are often interconnected in large-scale water diversion projects to form a coordinated system for water allocation and regulation. The alternating runoff and transferred water can significantly impact local ecosystems, which are initially reflected in the sensitive phytoplankton. Nonetheless, limited information is available on the temporal dynamics and assembly patterns of phytoplankton community in impounded lakes responding to continuous and periodic water diversion. Herein, a long-term monitoring from 2013 to 2020 were conducted to systematically investigate the response of phytoplankton community, including its characteristics, stability, and the ecological processes governing community assembly, in representative impounded lakes to the South-to-North Water Diversion Project (SNWDP) in China. In the initial stage of the SNWDP, the phytoplankton diversity indices experienced a decrease during both non-water diversion periods (8.5 %∼21.2 %) and water diversion periods (5.6 %∼12.2 %), implying a disruption in the aquatic ecosystem. But the regular delivery of high-quality water from the Yangtze River gradually increased phytoplankton diversity and mediated ecological assembly processes shifting from stochastic to deterministic. Meanwhile, reduced nutrients restricted the growth of phytoplankton, pushing species to interact more closely to maintain the functionality and stability of the co-occurrence network. The partial least squares path model revealed that ecological process (path coefficient = 0.525, p < 0.01) and interspecies interactions in networks (path coefficient = -0.806, p < 0.01) jointly influenced the keystone and dominant species, ultimately resulting in an improvement in stability (path coefficient = 0.878, p < 0.01). Overall, the phytoplankton communities experienced an evolutionary process from short-term disruption to long-term adaptation, demonstrating resilience and adaptability in response to the challenges posed by the SNWDP. This study revealed the response and adaptation mechanism of phytoplankton communities in impounded lakes to water diversion projects, which is helpful for maintaining the lake ecological health and formulating rational water management strategies.
Collapse
Affiliation(s)
- Xing Hou
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China; Institute of Water Science and Technology, Hohai University, Nanjing, 210098, PR China
| | - Xiaodong Hu
- Jiangsu Hydraulic Research Institute, Nanjing, 210017, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Rui Huang
- Jiangsu Hydraulic Research Institute, Nanjing, 210017, PR China
| | - Jixiong Xu
- Jiangsu Hydraulic Research Institute, Nanjing, 210017, PR China
| |
Collapse
|
17
|
Kern WV. [Multi-resistant bacteria - epidemiological trends and new treatment options]. Dtsch Med Wochenschr 2024; 149:1133-1142. [PMID: 39250951 DOI: 10.1055/a-2258-1412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Multi-resistant bacteria such as Escherichia coli and Klebsiella pneumoniae are a growing threat worldwide. The spread of Carbapenemase-producing strains is particularly worrying. New antibiotics and combination therapies offer treatment options, but the development of resistant pathogens remains a major challenge.
Collapse
|
18
|
Ping X, Khan RAA, Chen S, Jiao Y, Zhuang X, Jiang L, Song L, Yang Y, Zhao J, Li Y, Mao Z, Xie B, Ling J. Deciphering the role of rhizosphere microbiota in modulating disease resistance in cabbage varieties. MICROBIOME 2024; 12:160. [PMID: 39215347 PMCID: PMC11363401 DOI: 10.1186/s40168-024-01883-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 07/27/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND Cabbage Fusarium wilt (CFW) is a devastating disease caused by the soil-borne fungus Fusarium oxysporum f. sp. conglutinans (Foc). One of the optimal measures for managing CFW is the employment of tolerant/resistant cabbage varieties. However, the interplay between plant genotypes and the pathogen Foc in shaping the rhizosphere microbial community, and the consequent influence of these microbial assemblages on biological resistance, remains inadequately understood. RESULTS Based on amplicon metabarcoding data, we observed distinct differences in the fungal alpha diversity index (Shannon index) and beta diversity index (unweighted Bray-Curtis dissimilarity) within the rhizosphere of the YR (resistant to Foc) and ZG (susceptible to Foc) cabbage varieties, irrespective of Foc inoculation. Notably, the Shannon diversity shifts in the resistant YR variety were more pronounced following Foc inoculation. Disease-resistant plant variety demonstrate a higher propensity for harboring beneficial microorganisms, such as Pseudomonas, and exhibit superior capabilities in evading harmful microorganisms, in contrast to their disease-susceptible counterparts. Furthermore, the network analysis was performed on rhizosphere-associated microorganisms, including both bacteria and fungi. The networks of association recovered from YR exhibited greater complexity, robustness, and density, regardless of Foc inoculation. Following Foc infection in the YR rhizosphere, there was a notable increase in the dominant bacterium NA13, which is also a hub taxon in the microbial network. Reintroducing NA13 into the soil significantly improved disease resistance in the susceptible ZG variety, by directly inhibiting Foc and triggering defense mechanisms in the roots. CONCLUSIONS The rhizosphere microbial communities of these two cabbage varieties are markedly distinct, with the introduction of the pathogen eliciting significant alterations in their microbial networks which is correlated with susceptibility or resistance to soil-borne pathogens. Furthermore, we identified a rhizobacteria species that significantly boosts disease resistance in susceptible cabbages. Our results indicated that the induction of resistance genes leading to varied responses in microbial communities to pathogens may partly explain the differing susceptibilities of the cabbage varieties tested to CFW. Video Abstract.
Collapse
Affiliation(s)
- Xingxing Ping
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Raja Asad Ali Khan
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, YaZhou, 572024, China
| | - Shumin Chen
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yang Jiao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xia Zhuang
- School of Life Sciences, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, China
| | - Lijun Jiang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Liqun Song
- Microbial Research Institute of Liaoning Province, Liaoning Academy of Agricultural Sciences, Chaoyang, China
| | - Yuhong Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jianlong Zhao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yan Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhenchuan Mao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Bingyan Xie
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Jian Ling
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
19
|
Fu X, Ma Y, Yang T, He S, Wang D, Jin L, Zhan L, Guo Z, Fan K, Li J, Chu H. Bacterial community composition of wheat aboveground compartments correlates with yield during the reproductive phase. Appl Environ Microbiol 2024:e0107824. [PMID: 39212378 DOI: 10.1128/aem.01078-24] [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: 05/31/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024] Open
Abstract
Plant-associated microbial communities play important roles in agricultural productivity, and their composition has been shown to vary across plant compartments and developmental stages. However, the response of microbial communities within different plant compartments and at different developmental stages to diverse long-term fertilization treatments, as well as their linkages with crop yields, remains underexplored. This study analyzed wheat-associated bacterial communities within various soil and plant compartments under three fertilization treatments throughout the vegetative and reproductive phases. The variance in bacterial community was primarily attributed to compartments, followed by fertilization treatments and developmental stages. The composition of belowground bacterial communities (bulk soil, rhizosphere soil, and root) exhibited stronger responses to fertilization treatments than aboveground compartments (stem and leaf). The composition of belowground bacterial communities responded to fertilization treatments at all developmental stages, and it was significantly correlated with crop yields during the vegetative phase, whereas the aboveground community composition only showed a response to fertilization during the reproductive phase, at which point it was significantly correlated with crop yields. Moreover, during this reproductive phase, the co-occurrence network of aboveground bacterial communities exhibited enhanced complexity, and it contained an increased number of keystone species associated with crop yields, such as Sphingomonas spp., Massilia spp., and Frigoribacterium spp. Structural equation modeling indicated that augmenting total phosphorus levels in aboveground compartments could enhance crop yields by increasing the relative abundance of these keystone species during the reproductive phase. These findings highlight the pivotal role of aboveground bacterial communities in wheat production during the reproductive phase. IMPORTANCE The developmental stage significantly influences crop-associated bacterial communities, but the relative importance of bacterial communities in different compartments to crop yields across various stages is still not well understood. This study reveals that belowground bacterial communities during the vegetative phase are significantly correlated with crop yields. Notably, during the reproductive phase, the composition of aboveground bacterial communities was significantly correlated with crop yields. During this phase, the complexity and enriched keystone species within the aboveground co-occurrence network underscore their role in boosting crop production. These results provide a foundation for developing microbiome-based products that are phase-specific and promote sustainable agricultural practices.
Collapse
Affiliation(s)
- Xiao Fu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuying Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shuobing He
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Daozhong Wang
- Key Laboratory of Nutrient Cycling and Resources Environment of Anhui Province, Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Lin Jin
- Key Laboratory of Nutrient Cycling and Resources Environment of Anhui Province, Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Linchuan Zhan
- Key Laboratory of Nutrient Cycling and Resources Environment of Anhui Province, Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Zhibin Guo
- Key Laboratory of Nutrient Cycling and Resources Environment of Anhui Province, Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Kunkun Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jiasui Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
20
|
Mortzfeld BM, Bhattarai SK, Bucci V. Expanding the toolbox: Novel class IIb microcins show activity against Gram-negative ESKAPE and plant pathogens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.05.570296. [PMID: 39253482 PMCID: PMC11383050 DOI: 10.1101/2023.12.05.570296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Interspecies interactions involving direct competition via bacteriocin production play a vital role in shaping ecological dynamics within microbial ecosystems. For instance, the ribosomally-produced siderophore bacteriocins, known as class IIb microcins, affect the colonization of host-associated pathogenic Enterobacteriaceae species. Notably, to date, only five of these antimicrobials have been identified, all derived from specific Escherichia coli and Klebsiella pneumoniae strains. We hypothesized that class IIb microcin production extends beyond these specific compounds and organisms. With a customized informatics-driven approach, screening bacterial genomes in public databases with BLAST and manual curation, we have discovered twelve previously unknown class IIb microcins in seven additional Enterobacteriaceae species, encompassing phytopathogens and environmental isolates. We introduce three novel clades of microcins (MccW, MccX, and MccZ), while also identifying eight new variants of the five known class IIb microcins. To validate their antimicrobial potential, we heterologously expressed these microcins in E. coli and demonstrated efficacy against a variety of bacterial isolates, including plant pathogens from the genera Brenneria, Gibbsiella, and Rahnella . Two newly discovered microcins exhibit activity against Gram-negative ESKAPE pathogens, i.e. Acinetobacter baumannii or Pseudomonas aeruginosa , providing the first evidence that class IIb microcins can target bacteria outside of the Enterobacteriaceae family. This study underscores that class IIb microcin genes are more prevalent in the microbial world than previously recognized and that synthetic hybrid microcins can be a viable tool to target clinically relevant drug-resistant pathogens. Our findings hold significant promise for the development of innovative engineered live biotherapeutic products tailored to combat these resilient bacteria.
Collapse
|
21
|
Shen Y, Wang Y, Wang J, Xie P, Xie C, Chen Y, Banaei N, Ren K, Cai Z. High-resolution 3D spatial distribution of complex microbial colonies revealed by mass spectrometry imaging. J Adv Res 2024:S2090-1232(24)00375-8. [PMID: 39214416 DOI: 10.1016/j.jare.2024.08.031] [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: 03/26/2024] [Revised: 06/21/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024] Open
Abstract
INTRODUCTION Bacterial living states and the distribution of microbial colony signaling molecules are widely studied using mass spectrometry imaging (MSI). However, current approaches often treat 3D colonies as flat 2D disks, inadvertently omitting valuable details. The challenge of achieving 3D MSI in biofilms persists due to the unique properties of microbial samples. OBJECTIVES The study aimed to develop a new biofilm sample preparation method that can realize high-resolution 3D MSI of bacterial colonies to reveal the spatial organization of bacterial colonies. METHODS This article introduces the moisture-assisted cryo-section (MACS) method, enabling embedding-free sectioning parallel to the growth plane. The MACS method secures intact sections by controlling ambient humidity and slice thickness, preventing molecular delocalization. RESULTS Combined with matrix-assisted laser desorption ionization mass spectrometry (MALDI)-MSI, the MACS method provides high-resolution insights into endogenic and exogenous molecule distributions in Pseudomonas aeruginosa (P. aeruginosa) biofilms, including isomeric pairs. Moreover, analyzed colonies are revived into 3D models, vividly depicting molecular distribution from inner to outer layers. Additionally, we investigated metabolite spatiotemporal dynamics in multiple colonies, observing changes over time and distinct patterns in single versus merged colonies. These findings shed light on the repel-merge process for multi-colony formation. Furthermore, our study monitored chemical responses inside biofilms after antibiotic treatment, showing increased antibiotic levels in the outer biofilm layer over time while maintaining low levels in the inner region. Moreover, the MACS method demonstrated its universality and applicability to other bacterial strains. CONCLUSION These results unveil complex cell activities within biofilm colonies, offering insights into microbe communities. The MACS method is universally applicable to loosely packed microorganism colonies, overcoming the limitations of previously reported MSI methods. It has great potential for studying bacterial-infected cancer tissues and artificial organs, making it a valuable tool in microbiological research.
Collapse
Affiliation(s)
- Yuting Shen
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, PR China
| | - Yisu Wang
- Department of Chemistry, Hong Kong Baptist University, Hong Kong 999077, PR China
| | - Jianing Wang
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, PR China
| | - Peisi Xie
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, PR China
| | - Chengyi Xie
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, PR China
| | - Yanyan Chen
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, PR China
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94304, USA; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94304, USA; Clinical Microbiology Laboratory, Stanford Health Care, Stanford, CA 94304, USA
| | - Kangning Ren
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, PR China; Department of Chemistry, Hong Kong Baptist University, Hong Kong 999077, PR China.
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, PR China.
| |
Collapse
|
22
|
Wyatt M, Choudhury A, Von Dohlen G, Heileson JL, Forsse JS, Rajakaruna S, Zec M, Tfaily MM, Greathouse L. Randomized control trial of moderate dose vitamin D alters microbiota stability and metabolite networks in healthy adults. Microbiol Spectr 2024:e0008324. [PMID: 39189761 DOI: 10.1128/spectrum.00083-24] [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: 01/10/2024] [Accepted: 07/10/2024] [Indexed: 08/28/2024] Open
Abstract
Evidence indicates that both vitamin D and the gut microbiome are involved in the process of colon carcinogenesis. However, it is unclear what effects supplemental vitamin D3 has on the gut microbiome and its metabolites in healthy adults. We conducted a double-blind, randomized, placebo-controlled trial to identify the acute and long-term microbiota structural and metabolite changes that occur in response to a moderate dose (4,000 IU) of vitamin D3 for 12 weeks in healthy adults. Our results demonstrated a significant increase in serum 25-hydroxy-vitamin D (25(OH)D) in the treatment group compared to placebo (P < 0.0001). Vitamin D3 significantly increased compositional similarity (P < 0.0001) in the treatment group, and enriched members of the Bifidobacteriaceae family. We also identified a significant inverse relationship between the percent change in serum 25(OH)D and microbial stability in the treatment group (R = -0.52, P < 0.019). Furthermore, vitamin D3 supplementation resulted in notable metabolic shifts, in addition to resulting in a drastic rewiring of key gut microbial-metabolic associations. In conclusion, we show that a moderate dose of vitamin D3 among healthy adults has unique acute and persistent effects on the fecal microbiota, and suggest novel mechanisms by which vitamin D may affect the host-microbiota relationship. IMPORTANCE Preventative measures to reduce the rise in early-onset colorectal cancer are of critical need. Both vitamin D, dietary and serum levels, and the gut microbiome are implicated in the etiology of colorectal cancer. By understanding the intimate relationship between vitamin D, the gut microbiome, and its metabolites, we may be able to identify key mechanisms that can be targeted for intervention, including inflammation and metabolic dysfunction. Furthermore, the similarity of vitamin D to cholesterol, which is metabolized by the gut microbiome, gives precedence to its ability to produce metabolites that can be further studied and leveraged for controlling colorectal cancer incidence and mortality.
Collapse
Affiliation(s)
- Madhur Wyatt
- Human Health Performance and Recreation, Robbins College of Health and Human Sciences, Baylor University, Waco, Texas, USA
| | - Ankan Choudhury
- Human Science and Design, Robbins College of Health and Human Sciences, Baylor University, Waco, Texas, USA
| | - Gabriella Von Dohlen
- Human Science and Design, Robbins College of Health and Human Sciences, Baylor University, Waco, Texas, USA
| | - Jeffery L Heileson
- Human Health Performance and Recreation, Robbins College of Health and Human Sciences, Baylor University, Waco, Texas, USA
- Nutrition Services Division, Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Jeffrey S Forsse
- Human Health Performance and Recreation, Robbins College of Health and Human Sciences, Baylor University, Waco, Texas, USA
- Department of Biology, Baylor University, Waco, Texas, USA
| | - Sumudu Rajakaruna
- Department of Environmental Science, University of Arizona, Tucson, Arizona, USA
- BIO5 Institute, The University of Arizona, Tucson, Arizona, USA
| | - Manja Zec
- Department of Environmental Science, University of Arizona, Tucson, Arizona, USA
- Colorado Program for Musculoskeletal Research, Department of Orthopedics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Malak M Tfaily
- Department of Environmental Science, University of Arizona, Tucson, Arizona, USA
- BIO5 Institute, The University of Arizona, Tucson, Arizona, USA
| | - Leigh Greathouse
- Human Science and Design, Robbins College of Health and Human Sciences, Baylor University, Waco, Texas, USA
- Department of Biology, Baylor University, Waco, Texas, USA
| |
Collapse
|
23
|
Li Y, Xu G, Wang J, Yu Y. Freeze-thaw aging increases the toxicity of microplastics to earthworms and enriches pollutant-degrading microbial genera. JOURNAL OF HAZARDOUS MATERIALS 2024; 479:135651. [PMID: 39208630 DOI: 10.1016/j.jhazmat.2024.135651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/21/2024] [Accepted: 08/24/2024] [Indexed: 09/04/2024]
Abstract
Freeze-thaw (FT) aging can change the physicochemical characteristics of microplastics (MPs). The toxic impacts of FT-aged-MPs to soil invertebrates are poorly understood. Here the toxic mechanisms of FT-aged-MPs were investigated in earthworms after 28 d exposure. Results showed that FT 50 µm PE-MPs significantly increased reactive oxygen species (ROS) by 5.78-9.04 % compared to pristine 50 µm PE-MPs (41.80-45.05 ng/mgprot), whereas FT 500 µm PE-MPs reduced ROS by 7.52-7.87 % compared to pristine 500 µm PE-MPs (51.44-54.46 ng/mgprot). FT-PP-MPs significantly increased ROS and malondialdehyde (MDA) content in earthworms by 14.82-44.06 % and 46.75-110.21 %, respectively, compared to pristine PP-MPs (40.56-44.66 ng/mgprot, 0.41-2.53 nmol/mgprot). FT-aged PE- and PP-MPs caused more severe tissue damage to earthworms. FT-aged PE-MPs increased the alpha diversity of the gut flora of earthworms compared to pristine MPs. Earthworm guts exposed to FT-aged-MPs were enriched with differential microbial genera of contaminant degradation capacity. FT-PE-MPs affected membrane translocation by up-regulating lipids and lipid-like molecules, whereas FT-PP-MPs changed xenobiotic biodegradation and metabolism by down-regulating organoheterocyclic compounds compared to the pristine PE- and PP-MPs. This study concludes that FT-aged MPs cause greater toxicity to earthworms compared to pristine MPs.
Collapse
Affiliation(s)
- Yanjun Li
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Guanghui Xu
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Jian Wang
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Yong Yu
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| |
Collapse
|
24
|
Zhu A, Liang Z, Gao L, Xie Z. Dispersal limitation determines the ecological processes that regulate the seasonal assembly of bacterial communities in a subtropical river. Front Microbiol 2024; 15:1430073. [PMID: 39252829 PMCID: PMC11381306 DOI: 10.3389/fmicb.2024.1430073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 08/13/2024] [Indexed: 09/11/2024] Open
Abstract
Bacteria play a crucial role in pollutant degradation, biogeochemical cycling, and energy flow within river ecosystems. However, the underlying mechanisms governing bacterial community assembly and their response to environmental factors at seasonal scales in subtropical rivers remain poorly understood. In this study, we conducted 16S rRNA gene amplicon sequencing on water samples from the Liuxi River to investigate the composition, assembly processes, and co-occurrence relationships of bacterial communities during the wet season and dry season. The results demonstrated that seasonal differences in hydrochemistry significantly influenced the composition of bacterial communities. A more heterogeneous community structure and increased alpha diversity were observed during the dry season. Water temperature emerged as the primary driver for seasonal changes in bacterial communities. Dispersal limitation predominantly governed community assembly, however, during the dry season, its contribution increased due to decreased immigration rates. Co-occurrence network analysis reveals that mutualism played a prevailing role in shaping bacterial community structure. Compared to the wet season, the network of bacterial communities exhibited higher modularity, competition, and keystone species during the dry season, resulting in a more stable community structure. Although keystone species displayed distinct seasonal variations, Proteobacteria and Actinobacteria were consistently abundant keystone species maintaining network structure in both seasons. Our findings provide insights into how bacterial communities respond to seasonal environmental changes, uncovering underlying mechanisms governing community assembly in subtropical rivers, which are crucial for the effective management and conservation of riverine ecosystems.
Collapse
Affiliation(s)
- Aiping Zhu
- School of Geography and Tourism, Anhui Normal University, Wuhu, China
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Chinese Academy of Sciences, Guangzhou, China
| | - Zuobing Liang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Lei Gao
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Chinese Academy of Sciences, Guangzhou, China
| | - Zhenglan Xie
- School of Geomatics and Municipal Engineering, Zhejiang University of Water Resources and Electric Power, Hangzhou, China
| |
Collapse
|
25
|
Cherrak Y, Salazar MA, Näpflin N, Malfertheiner L, Herzog MKM, Schubert C, von Mering C, Hardt WD. Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut. Nat Microbiol 2024:10.1038/s41564-024-01775-x. [PMID: 39160293 DOI: 10.1038/s41564-024-01775-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 07/04/2024] [Indexed: 08/21/2024]
Abstract
Resource competition is a driver of gut microbiota composition. Bacteria can outcompete metabolically similar rivals through the limitation of shared growth-fuelling nutrients. The mechanisms underlying this remain unclear for bacteria with identical sets of metabolic genes. Here we analysed the lactose utilization operon in the murine commensal Escherichia coli 8178. Using in vitro and in vivo approaches, we showed that translation of the lactose utilization repressor gene lacI from its native non-canonical GTG start codon increases the basal expression of the lactose utilization cluster, enhancing adaptation to lactose consumption. Consequently, a strain carrying the wild type lacI GTG start codon outperformed the lacI ATG start codon mutant in the mouse intestine. This advantage was attenuated upon limiting host lactose intake through diet shift or altering the mutant frequency, emphasizing the context-dependent effect of a single nucleotide change on the bacterial fitness of a common member of the gut microbiota. Coupled with a genomic analysis highlighting the selection of non-ATG start codons in sugar utilization regulator genes across the Enterobacteriaceae family, our data exposed an unsuspected function of non-canonical start codons in metabolic competition.
Collapse
Affiliation(s)
- Yassine Cherrak
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland.
| | - Miguel Angel Salazar
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Nicolas Näpflin
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Mathias K-M Herzog
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Christopher Schubert
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland.
| |
Collapse
|
26
|
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.
Collapse
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.
| |
Collapse
|
27
|
Jiang H, Liu S, Chang C, Shang Y, Geng J, Chen Q. Non-invasive ventilation restores the gut microbiota in rats with acute heart failure. Heliyon 2024; 10:e35239. [PMID: 39161838 PMCID: PMC11332900 DOI: 10.1016/j.heliyon.2024.e35239] [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: 11/26/2023] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 08/21/2024] Open
Abstract
Heart failure (HF) is an increasingly prevalent disease in humans; it induces multiple symptoms and damages health. The animal gut microbiota has critical roles in host health, which might be related to HF symptoms. Currently, several options are used to treat HF, including non-invasive ventilation (NIV). However, studies on gut microbiota responses to acute HF and associated treatments effects on gut communities in patients are scarce. Here, short-term (1 week after treatments) and long-term (3 months after treatment) variations in gut microbiota variations in rats with acute HF treated were examined NIV through high-throughput sequencing of the bacterial 16S rRNA gene. Through comparison of gut microbiota alpha diversity, it was observed lower gut microbiota richness and diversity in animals with acute HF than in normal animals. Additionally, beta-diversity analysis revealed significant alterations in the gut microbiota composition induced by acute HF, as reflected by increased Firmicutes/Bacteroidetes (F/B) ratios and Proteobacteria enrichment. When network analysis results were combined with the null model, decreased stability and elevated deterministic gut microbiota assemblies were observed in animals with acute HF. Importantly, in both short- and long-term periods, NIV was found to restore gut microbiota dysbiosis to normal states in acute HF rats. Finally, it was shown that considerable gut microbiota variations existed in rats with acute HF, that underlying microbiota mechanisms regulated these changes, and confirmed that NIV is suitable for HF treatment. In future studies, these findings should be validated with different model systems or clinical samples.
Collapse
Affiliation(s)
- He Jiang
- Department of Cardiology, Clinical School of Thoracic, Tianjin Medical University, Tianjin, 300051, China
| | - Shan Liu
- Institute of Cardiology, Clinical School of Thoracic, Tianjin Medical University, Tianjin, 300222, China
| | - Chao Chang
- Department of Cardiology, Clinical School of Thoracic, Tianjin Medical University, Tianjin, 300051, China
| | - Yanwen Shang
- Department of Cardiology, Clinical School of Thoracic, Tianjin Medical University, Tianjin, 300051, China
| | - Jie Geng
- Department of Cardiology, Clinical School of Thoracic, Tianjin Medical University, Tianjin, 300051, China
- Tianjin Key Laboratory of Cardiovascular Emergency and Critical Care, Tianjin Municipal Science and Technology Bureau, Tianjin, 300051, China
| | - Qingliang Chen
- Department of Cardiology, Clinical School of Thoracic, Tianjin Medical University, Tianjin, 300051, China
- Tianjin Key Laboratory of Cardiovascular Emergency and Critical Care, Tianjin Municipal Science and Technology Bureau, Tianjin, 300051, China
| |
Collapse
|
28
|
Chen Y, Li X, Zhou D, Wei Y, Feng J, Cai B, Qi D, Zhang M, Zhao Y, Li K, Pan Z, Wang W, Xie J. Streptomyces-Secreted Fluvirucin B6 as a Potential Bio-Fungicide for Managing Banana Fusarium Wilt and Mycotoxins and Modulating the Soil Microbial Community Structure. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:17890-17902. [PMID: 39083645 DOI: 10.1021/acs.jafc.4c04077] [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: 08/02/2024]
Abstract
Banana Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc TR4) is the most destructive soil-borne fungal disease. Until now, there has been a lack of effective measures to control the disease. It is urgent to explore biocontrol agents to control Foc TR4 and the secretion of mycotoxin. In this study, fluvirucin B6 was screened from Streptomyces solisilvae using an activity-guided method. Fluvirucin B6 exhibited strong antifungal activity against Foc TR4 (0.084 mM of EC50 value) and significantly inhibited mycelial growth and spore germination. Further studies demonstrated that fluvirucin B6 could cause the functional loss of mitochondria, the disorder of metabolism of Foc TR4 cells, and the decrease of enzyme activities in the tricarboxylic acid cycle and electron transport chain, ultimately inhibiting mycotoxin metabolism. In a pot experiment, the application of fluvirucin B6 significantly decreased the incidence of banana Fusarium wilt and the amount of Foc TR4 and controlled fungal toxins in the soil. Additionally, fluvirucin B6 could positively regulate the changes in the structure of the banana rhizosphere microbial community, significantly enriching beneficial microbes associated with disease resistance. In summary, this study identifies fluvirucin B6, which plays versatile roles in managing fungal diseases and mycotoxins.
Collapse
Affiliation(s)
- Yufeng Chen
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - XiaoJuan Li
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Dengbo Zhou
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yongzan Wei
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Junting Feng
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Bingyu Cai
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Dengfeng Qi
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Miaoyi Zhang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yankun Zhao
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Kai Li
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Zhiqiang Pan
- Agricultural Research Service, Natural Products Utilization Research Unit, U.S. Department of Agriculture, University of Mississippi, University, Mississippi 38677, United States
| | - Wei Wang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Jianghui Xie
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| |
Collapse
|
29
|
Francis D, Sun F. A comparative analysis of mutual information methods for pairwise relationship detection in metagenomic data. BMC Bioinformatics 2024; 25:266. [PMID: 39143554 PMCID: PMC11323399 DOI: 10.1186/s12859-024-05883-7] [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: 08/02/2023] [Accepted: 07/29/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Construction of co-occurrence networks in metagenomic data often employs correlation to infer pairwise relationships between microbes. However, biological systems are complex and often display qualities non-linear in nature. Therefore, the reliance on correlation alone may overlook important relationships and fail to capture the full breadth of intricacies presented in underlying interaction networks. It is of interest to incorporate metrics that are not only robust in detecting linear relationships, but non-linear ones as well. RESULTS In this paper, we explore the use of various mutual information (MI) estimation approaches for quantifying pairwise relationships in biological data and compare their performances against two traditional measures-Pearson's correlation coefficient, r, and Spearman's rank correlation coefficient, ρ. Metrics are tested on both simulated data designed to mimic pairwise relationships that may be found in ecological systems and real data from a previous study on C. diff infection. The results demonstrate that, in the case of asymmetric relationships, mutual information estimators can provide better detection ability than Pearson's or Spearman's correlation coefficients. Specifically, we find that these estimators have elevated performances in the detection of exploitative relationships, demonstrating the potential benefit of including them in future metagenomic studies. CONCLUSIONS Mutual information (MI) can uncover complex pairwise relationships in biological data that may be missed by traditional measures of association. The inclusion of such relationships when constructing co-occurrence networks can result in a more comprehensive analysis than the use of correlation alone.
Collapse
Affiliation(s)
- Dallace Francis
- Quantitative and Computational Biology Department, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Fengzhu Sun
- Quantitative and Computational Biology Department, University of Southern California, Los Angeles, CA, 90089, USA
| |
Collapse
|
30
|
Nahor O, Israel Á, Barger N, Rubin-Blum M, Luzzatto-Knaan T. Epiphytic microbiome associated with intertidal seaweeds in the Mediterranean Sea: comparative analysis of bacterial communities across seaweed phyla. Sci Rep 2024; 14:18631. [PMID: 39128929 PMCID: PMC11317491 DOI: 10.1038/s41598-024-69362-y] [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: 05/08/2024] [Accepted: 08/05/2024] [Indexed: 08/13/2024] Open
Abstract
The complex interactions between epiphytic bacteria and marine macroalgae are still poorly understood, with limited knowledge about their community structure, interactions, and functions. This study focuses on comparing epiphytic prokaryotes community structure between three seaweed phyla; Chlorophyta, Rhodophyta, and Heterokontophyta in an easternmost rocky intertidal site of the Mediterranean Sea. By taking a snapshot approach and simultaneously collecting seaweed samples from the same habitat, we minimize environmental variations that could affect epiphytic bacterial assembly, thereby emphasizing host specificity. Through 16S rRNA gene amplicon sequencing, we identified that the microbial community composition was more similar within the same seaweed phylum host compared to seaweed host from other phyla. Furthermore, exclusive Amplicon Sequence Variants (ASVs) were identified for each algal phyla despite sharing higher taxonomic classifications across the other phyla. Analysis of niche breadth indices uncovers distinctive affinities and potential specialization among seaweed host phyla, with 39% of all ASVs identified as phylum specialists and 13% as generalists. Using taxonomy function prediction, we observed that the taxonomic variability does not significantly impact functional redundancy, suggesting resilience to disturbance. The study concludes that epiphytic bacteria composition is connected to host taxonomy, possibly influenced by shared morphological and chemical traits among genetically related hosts, implying a potential coevolutionary relationship between specific bacteria and their host seaweeds.
Collapse
Affiliation(s)
- Omri Nahor
- Department of Marine Biology, The Charney School of Marine Sciences, University of Haifa, Haifa, Israel
- Israel Oceanographic and Limnological Research, Tel Shikmona, Haifa, Israel
| | - Álvaro Israel
- Israel Oceanographic and Limnological Research, Tel Shikmona, Haifa, Israel
| | - Nataly Barger
- Department of Marine Biology, The Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Maxim Rubin-Blum
- Department of Marine Biology, The Charney School of Marine Sciences, University of Haifa, Haifa, Israel
- Israel Oceanographic and Limnological Research, Tel Shikmona, Haifa, Israel
| | - Tal Luzzatto-Knaan
- Department of Marine Biology, The Charney School of Marine Sciences, University of Haifa, Haifa, Israel.
| |
Collapse
|
31
|
He JL, Zhao YW, Yang JL, Ju JM, Ye BQ, Huang JY, Huang ZH, Zhao WY, Zeng WF, Xia M, Liu Y. Enhanced interactions among gut mycobiomes with the deterioration of glycemic control. MED 2024; 5:909-925.e7. [PMID: 38670112 DOI: 10.1016/j.medj.2024.03.023] [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: 11/23/2023] [Revised: 02/06/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND The gut mycobiome is closely linked to health and disease; however, its role in the progression of type 2 diabetes mellitus (T2DM) remains obscure. Here, a multi-omics approach was employed to explore the role of intestinal fungi in the deterioration of glycemic control. METHODS 350 participants without hypoglycemic therapies were invited for a standard oral glucose tolerance test to determine their status of glycemic control. The gut mycobiome was identified through internal transcribed spacer sequencing, host genetics were determined by genotyping array, and plasma metabolites were measured with untargeted liquid chromatography mass spectrometry. FINDINGS The richness of fungi was higher, whereas its dissimilarity was markedly lower, in participants with T2DM. Moreover, the diversity and composition of fungi were closely associated with insulin sensitivity and pancreatic β-cell functions. With the exacerbation of glycemic control, the co-occurrence network among fungus taxa became increasingly complex, and the complexity of the interaction network was inversely associated with insulin sensitivity. Mendelian randomization analysis further demonstrated that the Archaeorhizomycetes class, Fusarium genus, and Neoascochyta genus were causally linked to impaired glucose metabolism. Furthermore, integrative analysis with metabolomics showed that increased 4-hydroxy-2-oxoglutaric acid, ketoleucine, lysophosphatidylcholine (20:3/0:0), and N-lactoyl-phenylalanine, but decreased lysophosphatidylcholine (O-18:2), functioned as key molecules linking the adverse effect of Fusarium genus on insulin sensitivity. CONCLUSIONS Our study uncovers a strong association between disturbance in gut fungi and the progression of T2DM and highlights the potential of targeting the gut mycobiome for the management of T2DM. FUNDINGS This study was supported by MOST and NSFC of China.
Collapse
Affiliation(s)
- Jia-Lin He
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, and Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Ya-Wen Zhao
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, and Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Jia-Lu Yang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, and Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Jing-Meng Ju
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, and Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Bing-Qi Ye
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, and Department of Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Jing-Yi Huang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, and Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Zhi-Hao Huang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, and Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Wan-Ying Zhao
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, and Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Wei-Feng Zeng
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, and Department of Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Min Xia
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, and Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China.
| | - Yan Liu
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, and Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China.
| |
Collapse
|
32
|
Xie Z, Li W, Yang K, Wang X, Xiong S, Zhang X. Bacterial and Archaeal Communities in Erhai Lake Sediments: Abundance and Metabolic Insight into a Plateau Lake at the Edge of Eutrophication. Microorganisms 2024; 12:1617. [PMID: 39203459 PMCID: PMC11356345 DOI: 10.3390/microorganisms12081617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 09/03/2024] Open
Abstract
The littoral zones of lakes are potential hotspots for local algal blooms and biogeochemical cycles; however, the microbial communities within the littoral sediments of eutrophic plateau lakes remain poorly understood. Here, we investigated the taxonomic composition, co-occurrence networks, and potential functional roles of both abundant and rare taxa within bacterial and archaeal communities, as well as physicochemical parameters, in littoral sediments from Erhai Lake, a mesotrophic lake transitioning towards eutrophy located in the Yunnan-Guizhou Plateau. 16S rRNA gene sequencing revealed that bacterial communities were dominated by Proteobacteria, Bacteroidetes, and Chloroflexi, while Euryarchaeota was the main archaeal phylum. Co-occurrence network analysis revealed that keystone taxa mainly belonged to rare species in the bacterial domain, but in the archaeal domain, over half of keystone taxa were abundant species, demonstrating their fundamental roles in network persistence. The rare bacterial taxa contributed substantially to the overall abundance (81.52%), whereas a smaller subset of abundant archaeal taxa accounted for up to 82.70% of the overall abundance. Functional predictions highlighted a divergence in metabolic potentials, with abundant bacterial sub-communities enriched in pathways for nitrogen cycling, sulfur cycling, and chlorate reduction, while rare bacterial sub-communities were linked to carbon cycling processes such as methanotrophy. Abundant archaeal sub-communities exhibited a high potential for methanogenesis, chemoheterotrophy, and dark hydrogen oxidation. Spearman correlation analysis showed that genera such as Candidatus competibacter, Geobacter, Syntrophobacter, Methanocella, and Methanosarcina may serve as potential indicators of eutrophication. Overall, this study provides insight into the distinct roles that rare and abundant taxa play in the littoral sediments of mesotrophic plateau lakes.
Collapse
Affiliation(s)
- Zhen Xie
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (Z.X.); (K.Y.)
| | - Wei Li
- National Observation and Research Station of Erhai Lake Ecosystem in Yunnan, Dali 671000, China; (W.L.); (X.W.); (S.X.)
- Yunnan Dali Research Institute, Shanghai Jiao Tong University, Dali 671000, China
| | - Kaiwen Yang
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (Z.X.); (K.Y.)
| | - Xinze Wang
- National Observation and Research Station of Erhai Lake Ecosystem in Yunnan, Dali 671000, China; (W.L.); (X.W.); (S.X.)
- Yunnan Dali Research Institute, Shanghai Jiao Tong University, Dali 671000, China
| | - Shunzi Xiong
- National Observation and Research Station of Erhai Lake Ecosystem in Yunnan, Dali 671000, China; (W.L.); (X.W.); (S.X.)
- Yunnan Dali Research Institute, Shanghai Jiao Tong University, Dali 671000, China
| | - Xiaojun Zhang
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (Z.X.); (K.Y.)
| |
Collapse
|
33
|
Thomas G, Kay WT, Fones HN. Life on a leaf: the epiphyte to pathogen continuum and interplay in the phyllosphere. BMC Biol 2024; 22:168. [PMID: 39113027 PMCID: PMC11304629 DOI: 10.1186/s12915-024-01967-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 08/01/2024] [Indexed: 08/11/2024] Open
Abstract
Epiphytic microbes are those that live for some or all of their life cycle on the surface of plant leaves. Leaf surfaces are a topologically complex, physicochemically heterogeneous habitat that is home to extensive, mixed communities of resident and transient inhabitants from all three domains of life. In this review, we discuss the origins of leaf surface microbes and how different biotic and abiotic factors shape their communities. We discuss the leaf surface as a habitat and microbial adaptations which allow some species to thrive there, with particular emphasis on microbes that occupy the continuum between epiphytic specialists and phytopathogens, groups which have considerable overlap in terms of adapting to the leaf surface and between which a single virulence determinant can move a microbial strain. Finally, we discuss the recent findings that the wheat pathogenic fungus Zymoseptoria tritici spends a considerable amount of time on the leaf surface, and ask what insights other epiphytic organisms might provide into this pathogen, as well as how Z. tritici might serve as a model system for investigating plant-microbe-microbe interactions on the leaf surface.
Collapse
Affiliation(s)
| | - William T Kay
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | |
Collapse
|
34
|
Teles AM, Pina C, Cardoso IL, Tramontana A, Cardoso M, Duarte AS, Bartolomeu M, Noites R. Degree of Contamination of Gutta-Percha Points by Staphylococcus aureus (MRSA/MSSA) Strains. Int J Mol Sci 2024; 25:8566. [PMID: 39201252 PMCID: PMC11354985 DOI: 10.3390/ijms25168566] [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: 07/05/2024] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 09/02/2024] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is considered one of the most harmful bacteria to human health. Dentistry, like all healthcare disciplines, places great emphasis on preventing scenarios that may result in cross-infection. Although various tested and already used materials are suitable for filling the root canal system, Gutta-Percha (GP) remains the preferred and widely accepted gold standard. OBJECTIVE We performed an in vitro analysis of the contamination of GP points, regarding the strains of Methicillin-resistant (MRSA) and Methicillin-sensitive (MSSA) Staphylococcus aureus, using classical microbiology methods and molecular biology techniques. METHODS Gutta-Percha points of two different brands from opened packages (already in use for 1 month) were collected for analysis. The assessment involved incubating the GP points in Brain Heart Infusion (BHI) medium to detect microbial growth. Growing microorganisms were plated on a selective and differential chromogenic medium for MRSA/MSSA strains, and the identification of isolates was confirmed by Polymerase Chain Reaction (PCR). In the case of microbial growth, the GP point was submitted to a disinfection protocol. RESULTS From the 315 collected GP points, only 6 (1.9%) resulted in being positive for microbial growth. After confirmation by PCR, only one sample of the six GP points was contaminated by MRSA, and the remaining five were MSSA-contaminated. The disinfection protocol was effective in all contaminated GP points. CONCLUSIONS The Gutta-Percha points from opened pre-sterilized packages showed a very low degree of contamination by MRSA/MSSA. However, the detection of MSSA and MRSA strains raises concerns about potential contamination in dental clinic environments, and this risk cannot be considered negligible.
Collapse
Affiliation(s)
- Ana Moura Teles
- Faculty of Dental Medicine, Universidade Católica Portuguesa, 3504-505 Viseu, Portugal; (A.M.T.); (M.C.); (A.S.D.); (M.B.)
- Centre for Interdisciplinary Research in Health (CIIS), Universidade Católica Portuguesa, 3504-505 Viseu, Portugal
| | - Cristina Pina
- FCS-UFP, Universidade Fernando Pessoa, Faculdade de Ciências da Saúde, 4200-150 Porto, Portugal; (C.P.); (I.L.C.); (A.T.)
- FP-I3ID, Instituto de Investigação, Inovação e Desenvolvimento, FP-BHS, Universidade Fernando Pessoa, Biomedical and Health Sciences, 4249-004 Porto, Portugal
- CINTESIS.UFP@RISE, Centro de Investigação em Tecnologias e Serviços de Saúde, Rede de Investigação em Saúde, Universidade Fernando Pessoa, 4200-450 Porto, Portugal
| | - Inês Lopes Cardoso
- FCS-UFP, Universidade Fernando Pessoa, Faculdade de Ciências da Saúde, 4200-150 Porto, Portugal; (C.P.); (I.L.C.); (A.T.)
- FP-I3ID, Instituto de Investigação, Inovação e Desenvolvimento, FP-BHS, Universidade Fernando Pessoa, Biomedical and Health Sciences, 4249-004 Porto, Portugal
- CINTESIS.UFP@RISE, Centro de Investigação em Tecnologias e Serviços de Saúde, Rede de Investigação em Saúde, Universidade Fernando Pessoa, 4200-450 Porto, Portugal
| | - Antea Tramontana
- FCS-UFP, Universidade Fernando Pessoa, Faculdade de Ciências da Saúde, 4200-150 Porto, Portugal; (C.P.); (I.L.C.); (A.T.)
| | - Miguel Cardoso
- Faculty of Dental Medicine, Universidade Católica Portuguesa, 3504-505 Viseu, Portugal; (A.M.T.); (M.C.); (A.S.D.); (M.B.)
| | - Ana Sofia Duarte
- Faculty of Dental Medicine, Universidade Católica Portuguesa, 3504-505 Viseu, Portugal; (A.M.T.); (M.C.); (A.S.D.); (M.B.)
- Centre for Interdisciplinary Research in Health (CIIS), Universidade Católica Portuguesa, 3504-505 Viseu, Portugal
| | - Maria Bartolomeu
- Faculty of Dental Medicine, Universidade Católica Portuguesa, 3504-505 Viseu, Portugal; (A.M.T.); (M.C.); (A.S.D.); (M.B.)
- Centre for Interdisciplinary Research in Health (CIIS), Universidade Católica Portuguesa, 3504-505 Viseu, Portugal
| | - Rita Noites
- Faculty of Dental Medicine, Universidade Católica Portuguesa, 3504-505 Viseu, Portugal; (A.M.T.); (M.C.); (A.S.D.); (M.B.)
- Centre for Interdisciplinary Research in Health (CIIS), Universidade Católica Portuguesa, 3504-505 Viseu, Portugal
| |
Collapse
|
35
|
Abbasi E, Akçay E. Host control and species interactions jointly determine microbiome community structure. Theor Popul Biol 2024; 158:185-194. [PMID: 38925487 DOI: 10.1016/j.tpb.2024.06.006] [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: 02/26/2023] [Revised: 03/21/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
The host microbiome can be considered an ecological community of microbes present inside a complex and dynamic host environment. The host is under selective pressure to ensure that its microbiome remains beneficial. The host can impose a range of ecological filters including the immune response that can influence the assembly and composition of the microbial community. How the host immune response interacts with the within-microbiome community dynamics to affect the assembly of the microbiome has been largely unexplored. We present here a mathematical framework to elucidate the role of host immune response and its interaction with the balance of ecological interactions types within the microbiome community. We find that highly mutualistic microbial communities characteristic of high community density are most susceptible to changes in immune control and become invasion prone as host immune control strength is increased. Whereas highly competitive communities remain relatively stable in resisting invasion to changing host immune control. Our model reveals that the host immune control can interact in unexpected ways with a microbial community depending on the prevalent ecological interactions types for that community. We stress the need to incorporate the role of host-control mechanisms to better understand microbiome community assembly and stability.
Collapse
Affiliation(s)
- Eeman Abbasi
- Department of Biology, University of Pennsylvania, 433 S University Ave, Philadelphia, PA 19104, USA.
| | - Erol Akçay
- Department of Biology, University of Pennsylvania, 433 S University Ave, Philadelphia, PA 19104, USA
| |
Collapse
|
36
|
Kristensen TN, Schönherz AA, Rohde PD, Sørensen JG, Loeschcke V. Selection for stress tolerance and longevity in Drosophila melanogaster have strong impacts on microbiome profiles. Sci Rep 2024; 14:17789. [PMID: 39090347 PMCID: PMC11294339 DOI: 10.1038/s41598-024-68753-5] [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: 02/29/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
There is experimental evidence that microbiomes have a strong influence on a range of host traits. Understanding the basis and importance of symbiosis between host and associated microorganisms is a rapidly developing research field, and we still lack a mechanistic understanding of ecological and genetic pressures affecting host-microbiome associations. Here Drosophila melanogaster lines from a large-scale artificial selection experiment were used to investigate whether the microbiota differ in lines selected for different stress resistance traits and longevity. Following multiple generations of artificial selection all selection regimes and corresponding controls had their microbiomes assessed. The microbiome was interrogated based on 16S rRNA sequencing. We found that the microbiome of flies from the different selection regimes differed markedly from that of the unselected control regime, and microbial diversity was consistently higher in selected relative to control regimes. Several common Drosophila bacterial species showed differentially abundance in the different selection regimes despite flies being exposed to similar environmental conditions for two generations prior to assessment. Our findings provide strong evidence for symbiosis between host and microbiomes but we cannot reveal whether the interactions are adaptive, nor whether they are caused by genetic or ecological factors.
Collapse
Affiliation(s)
- Torsten Nygaard Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark.
| | - Anna A Schönherz
- Department of Animal and Veterinary Sciences, Aarhus University, Tjele, Denmark
| | - Palle Duun Rohde
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | | | | |
Collapse
|
37
|
Qian Z, Hou D, Gao S, Wang X, Yu J, Dong J, Sun C. Toxic effects and mechanisms of chronic cadmium exposure on Litopenaeus vannamei growth performance based on combined microbiome and metabolome analysis. CHEMOSPHERE 2024; 361:142578. [PMID: 38857631 DOI: 10.1016/j.chemosphere.2024.142578] [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: 03/20/2024] [Revised: 05/28/2024] [Accepted: 06/08/2024] [Indexed: 06/12/2024]
Abstract
Cadmium (Cd) pollution seriously affects marine organisms' health and poses a threat to food safety. Although Cd pollution has attracted widespread attention in aquaculture, little is known about the toxic mechanisms of chronic Cd exposure on shrimp growth performance. The study investigated the combined effects of chronic exposure to Cd of different concentrations including 0, 75, 150, and 300 μg/L for 30 days on the growth performance, tissue bioaccumulation, intestinal microbiology, and metabolic responses of Litopenaeus vannamei. The results revealed that the growth was significantly inhibited under exposure to 150 and 300 μg/L Cd2+. The bioaccumulation in gills and intestines respectively showed an increasing and inverted "U" shaped trend with increasing Cd2+ concentration. Chronic Cd altered the intestinal microflora with a significant decrease in microbial richness and increasing trends in the abundances of the potentially pathogenic bacteria Vibrio and Maribacter at exposure to 75 and 150 μg/L Cd2+, and Maribacter at 300 μg/L. In addition, chronic Cd interfered with intestinal metabolic processes. The expressions of certain metabolites associated with growth promotion and enhanced antioxidant power, including N-methyl-D-aspartic acid, L-malic acid, guanidoacetic acid, betaine, and gluconic acid were significantly down-regulated, especially at exposure to 150 and 300 μg/L Cd2+, and were negatively correlated with Vibrio and Maribacter abundance levels. In summary, chronic Cd exposure resulted in severe growth inhibition and increased Cd accumulation in shrimp tissues. Increased levels of intestinal pathogenic bacteria and decreased levels of growth-promoting metabolites may be the key causes of growth inhibition. Harmful bacteria Vibrio and Maribacter may be associated with the inhibition of growth-promoting metabolite expression and may be involved in disrupting intestinal metabolic functions, ultimately impairing shrimp growth potential. This study sheds light on the potential toxicological mechanisms of chronic Cd inhibition on shrimp growth performance, offering new insights into Cd toxicity studies in aquaculture.
Collapse
Affiliation(s)
- Zhaoying Qian
- School of Economics, Guizhou University of Finance and Economics, Guiyang, 550025, Guizhou, China
| | - Danqing Hou
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524000, Guangdong, China
| | - Shan Gao
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524000, Guangdong, China
| | - Xuejie Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524000, Guangdong, China
| | - Jianbo Yu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524000, Guangdong, China
| | - Jiaxin Dong
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524000, Guangdong, China
| | - Chengbo Sun
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524000, Guangdong, China.
| |
Collapse
|
38
|
Pawlowska TE. Symbioses between fungi and bacteria: from mechanisms to impacts on biodiversity. Curr Opin Microbiol 2024; 80:102496. [PMID: 38875733 PMCID: PMC11323152 DOI: 10.1016/j.mib.2024.102496] [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: 07/10/2023] [Revised: 05/20/2024] [Accepted: 05/31/2024] [Indexed: 06/16/2024]
Abstract
Symbiotic interactions between fungi and bacteria range from positive to negative. They are ubiquitous in free-living as well as host-associated microbial communities worldwide. Yet, the impact of fungal-bacterial symbioses on the organization and dynamics of microbial communities is uncertain. There are two reasons for this uncertainty: (1) knowledge gaps in the understanding of the genetic mechanisms underpinning fungal-bacterial symbioses and (2) prevailing interpretations of ecological theory that favor antagonistic interactions as drivers stabilizing biological communities despite the existence of models emphasizing contributions of positive interactions. This review synthesizes information on fungal-bacterial symbioses common in the free-living microbial communities of the soil as well as in host-associated polymicrobial biofilms. The interdomain partnerships are considered in the context of the relevant community ecology models, which are discussed critically.
Collapse
Affiliation(s)
- Teresa E Pawlowska
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
39
|
An Q, Zheng N, Pan J, Ji Y, Wang S, Li X, Chen C, Peng L, Wang B. Association between plant microbiota and cadmium uptake under the influence of microplastics with different particle sizes. ENVIRONMENT INTERNATIONAL 2024; 190:108938. [PMID: 39111171 DOI: 10.1016/j.envint.2024.108938] [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: 06/12/2024] [Revised: 08/01/2024] [Accepted: 08/03/2024] [Indexed: 08/28/2024]
Abstract
Plant microbiota are an important factor impacting plant cadmium (Cd) uptake. However, little is known about how plant microbiota affects the Cd uptake by plants under the influence of microplastics (MPs) with different particle sizes. In this study, bacterial structure and assembly in the rhizosphere and endosphere in pakchoi were analyzed by amplicon sequencing of 16S rRNA genes under the influence of different particle sizes of polystyrene microplastics (PS-MPs) combined with Cd treatments. Results showed that there were no significant differences observed in the shoot endophytes among different treatments. However, compared to Cd treatment, larger-sized PS-MPs (2 and 20 μm) significantly increased community diversity and altered the structural composition of rhizosphere bacteria and root endophytes, while smaller-sized PS-MPs (0.2 μm) did not. Under the treatment of larger-sized PS-MPs, the niche breadth of rhizosphere bacteria and root endophytes were significantly increased. And larger-sized PS-MPs also maintained stability and complexity of bacterial co-occurrence networks, while smaller-sized PS-MPs reduced them. Furthermore, compared to Cd treatment, the addition of larger particle size PS-MPs decreased the proportion of homogeneous section, while increased the proportion of drift in root endophytic bacterial community assembly. The role of larger-sized MPs in the community assembly of rhizosphere bacteria was opposite. Using random forest and structural equation models, the study found that larger-sized PS-MPs can promote the colonization of specific bacterial taxa, such as Brevundimonas, AKAU4049, SWB02, Ellin6055, Porphyrobacter, Sphingorhabdus, Rhodobacter, Erythrobacter, Devosia and some other bacteria belonging to Alphaproteobacteria, in the rhizosphere and root endosphere. The colonization of these taxa can may induce the formation of biofilms in the roots, immobilize heavy metals through oxidation processes, and promote plant growth, thereby reducing Cd uptake by pakchoi. The findings of this study provide important insights into the microbial mechanisms underlying the influence of MPs with different particle sizes on plant Cd uptake.
Collapse
Affiliation(s)
- Qirui An
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, College of New Energy and Environment, Jilin University, China
| | - Na Zheng
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, College of New Energy and Environment, Jilin University, China.
| | - Jiamin Pan
- Northeast Institute of Geography and Agricultural Ecology, Chinese Academy of Sciences, Changchun, Jilin, China
| | - Yining Ji
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, College of New Energy and Environment, Jilin University, China
| | - Sujing Wang
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, College of New Energy and Environment, Jilin University, China
| | - Xiaoqian Li
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, College of New Energy and Environment, Jilin University, China
| | - Changcheng Chen
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, College of New Energy and Environment, Jilin University, China
| | - Liyuan Peng
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, College of New Energy and Environment, Jilin University, China
| | - Bo Wang
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, College of New Energy and Environment, Jilin University, China
| |
Collapse
|
40
|
Fu R, Cao C, Liu L, Zhu H, Malghani S, Yu Y, Liao Y, Delgado-Baquerizo M, Li X. Limited dependence on soil nitrogen fixation as subtropical forests develop. Microbiol Res 2024; 285:127757. [PMID: 38759379 DOI: 10.1016/j.micres.2024.127757] [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: 02/08/2024] [Revised: 04/14/2024] [Accepted: 05/09/2024] [Indexed: 05/19/2024]
Abstract
Soil nitrogen (N) fixation, driven by microbial reactions, is critical to support the entrance of nitrogen in nutrient poor and pioneer ecosystems. However, how and why N fixation and soil diazotrophs evolve as forests develop remain poorly understood. Here, we used a 60-year forest rewilding chronosequence and found that soil N fixation activity gradually decreased with increasing forest age, experiencing dramatic drops of 64.8% in intermediate stages and 93.0% in the oldest forests. Further analyses revealed loses in diazotrophic diversity and a significant reduction in the abundance of important diazotrophs (e.g., Desulfovibrio and Pseudomonas) as forest develops. This reduction in N fixation, and associated shifts in soil microbes, was driven by acidification and increases in N content during forest succession. Our results provide new insights on the life history of one of the most important groups of soil organisms in terrestrial ecosystems, with consequences for understanding the buildup of nutrients as forest soil develops.
Collapse
Affiliation(s)
- Ruoxian Fu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; College of Ecology and Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Chaoyang Cao
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; College of Ecology and Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Li Liu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; College of Ecology and Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Hongguang Zhu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; College of Ecology and Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Saadat Malghani
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1017, Denmark
| | - Yuanchun Yu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; College of Ecology and Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Yangwenke Liao
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; College of Ecology and Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Xiaogang Li
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; College of Ecology and Environment, Nanjing Forestry University, Nanjing 210037, China.
| |
Collapse
|
41
|
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.
Collapse
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
| |
Collapse
|
42
|
Bai C, Wang Q, Xu J, Zhang H, Huang Y, Cai L, Zheng X, Yang M. Impact of Nutrient Enrichment on Community Structure and Co-Occurrence Networks of Coral Symbiotic Microbiota in Duncanopsammia peltata: Zooxanthellae, Bacteria, and Archaea. Microorganisms 2024; 12:1540. [PMID: 39203380 PMCID: PMC11356306 DOI: 10.3390/microorganisms12081540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/24/2024] [Accepted: 07/24/2024] [Indexed: 09/03/2024] Open
Abstract
Symbiotic microorganisms in reef-building corals, including algae, bacteria, archaea, fungi, and viruses, play critical roles in the adaptation of coral hosts to adverse environmental conditions. However, their adaptation and functional relationships in nutrient-rich environments have yet to be fully explored. This study investigated Duncanopsammia peltata and the surrounding seawater and sediments from protected and non-protected areas in the summer and winter in Dongshan Bay. High-throughput sequencing was used to characterize community changes, co-occurrence patterns, and factors influencing symbiotic coral microorganisms (zooxanthellae, bacteria, and archaea) in different environments. The results showed that nutrient enrichment in the protected and non-protected areas was the greatest in December, followed by the non-protected area in August. In contrast, the August protected area had the lowest nutrient enrichment. Significant differences were found in the composition of the bacterial and archaeal communities in seawater and sediments from different regions. Among the coral symbiotic microorganisms, the main dominant species of zooxanthellae is the C1 subspecies (42.22-56.35%). The dominant phyla of bacteria were Proteobacteria, Cyanobacteria, Firmicutes, and Bacteroidota. Only in the August protected area did a large number (41.98%) of SAR324_cladeMarine_group_B exist. The August protected and non-protected areas and December protected and non-protected areas contained beneficial bacteria as biomarkers. They were Nisaea, Spiroplasma, Endozoicomonas, and Bacillus. No pathogenic bacteria appeared in the protected area in August. The dominant phylum in Archaea was Crenarchaeota. These symbiotic coral microorganisms' relative abundances and compositions vary with environmental changes. The enrichment of dissolved inorganic nitrogen in environmental media is a key factor affecting the composition of coral microbial communities. Co-occurrence analysis showed that nutrient enrichment under anthropogenic disturbances enhanced the interactions between coral symbiotic microorganisms. These findings improve our understanding of the adaptations of coral holobionts to various nutritional environments.
Collapse
Affiliation(s)
- Chuanzhu Bai
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China; (C.B.); (Y.H.)
- Key Laboratory of Marine Ecology Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; (Q.W.); (H.Z.); (X.Z.)
| | - Qifang Wang
- Key Laboratory of Marine Ecology Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; (Q.W.); (H.Z.); (X.Z.)
| | - Jinyan Xu
- Fujian Key Laboratory of Island Monitoring and Ecological Development (Island Research Center, MNR), Pingtan 350400, China;
| | - Han Zhang
- Key Laboratory of Marine Ecology Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; (Q.W.); (H.Z.); (X.Z.)
| | - Yuxin Huang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China; (C.B.); (Y.H.)
- Key Laboratory of Marine Ecology Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; (Q.W.); (H.Z.); (X.Z.)
| | - Ling Cai
- Key Laboratory of Marine Ecology Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; (Q.W.); (H.Z.); (X.Z.)
- Observation and Research Station of Island and Coastal Ecosystems in the Western Taiwan Strait, Ministry of Natural Resources, Xiamen 361005, China
| | - Xinqing Zheng
- Key Laboratory of Marine Ecology Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; (Q.W.); (H.Z.); (X.Z.)
- Observation and Research Station of Island and Coastal Ecosystems in the Western Taiwan Strait, Ministry of Natural Resources, Xiamen 361005, China
- Fujian Provincial Station for Field Observation and Research of Island and Coastal Zone, Zhangzhou 363216, China
| | - Ming Yang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China; (C.B.); (Y.H.)
| |
Collapse
|
43
|
Veseli I, Chen YT, Schechter MS, Vanni C, Fogarty EC, Watson AR, Jabri BA, Blekhman R, Willis AD, Yu MK, Fernandez-Guerra A, Fussel J, Eren AM. Microbes with higher metabolic independence are enriched in human gut microbiomes under stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.10.540289. [PMID: 37293035 PMCID: PMC10245760 DOI: 10.1101/2023.05.10.540289] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A wide variety of human diseases are associated with loss of microbial diversity in the human gut, inspiring a great interest in the diagnostic or therapeutic potential of the microbiota. However, the ecological forces that drive diversity reduction in disease states remain unclear, rendering it difficult to ascertain the role of the microbiota in disease emergence or severity. One hypothesis to explain this phenomenon is that microbial diversity is diminished as disease states select for microbial populations that are more fit to survive environmental stress caused by inflammation or other host factors. Here, we tested this hypothesis on a large scale, by developing a software framework to quantify the enrichment of microbial metabolisms in complex metagenomes as a function of microbial diversity. We applied this framework to over 400 gut metagenomes from individuals who are healthy or diagnosed with inflammatory bowel disease (IBD). We found that high metabolic independence (HMI) is a distinguishing characteristic of microbial communities associated with individuals diagnosed with IBD. A classifier we trained using the normalized copy numbers of 33 HMI-associated metabolic modules not only distinguished states of health versus IBD, but also tracked the recovery of the gut microbiome following antibiotic treatment, suggesting that HMI is a hallmark of microbial communities in stressed gut environments.
Collapse
|
44
|
Xie G, Sun C, Luo W, Gong Y, Tang X. Distinct ecological niches and community dynamics: understanding free-living and particle-attached bacterial communities in an oligotrophic deep lake. Appl Environ Microbiol 2024; 90:e0071424. [PMID: 38940583 PMCID: PMC11267872 DOI: 10.1128/aem.00714-24] [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: 04/11/2024] [Accepted: 06/05/2024] [Indexed: 06/29/2024] Open
Abstract
Oligotrophic deep-water lakes are unique and sensitive ecosystems with limited nutrient availability. Understanding bacterial communities within these lakes is crucial for assessing ecosystem health, biogeochemical cycling, and responses to environmental changes. In this study, we investigated the seasonal and vertical dynamics of both free-living (FL) and particle-attached (PA) bacteria in Lake Fuxian, a typical oligotrophic deep freshwater lake in southeast China. Our findings revealed distinct seasonal and vertical dynamics of FL and PA bacterial communities, driven by similar physiochemical environmental factors. PA bacteria exhibited higher α- and β-diversity and were enriched with Proteobacteria, Cyanobacteria, Firmicutes, Patescibacteria, Planctomycetota, and Verrucomicrobiota, while FL bacteria were enriched with Actinobacteria and Bacteroidota. FL bacteria showed enrichment in putative functions related to chemoheterotrophy and aerobic anoxygenic photosynthesis, whereas the PA fraction was enriched with intracellular parasites (mainly contributed by Rickettsiales, Chlamydiales, and Legionellales) and nitrogen metabolism functions. Deterministic processes predominantly shaped the assembly of both FL and PA bacterial communities, with stochastic processes playing a greater role in the FL fraction. Network analysis revealed extensive species interactions, with a higher proportion of positively correlated edges in the PA network, indicating mutualistic or cooperative interactions. Cyanobium, Comamonadaceae, and Roseomonas were identified as keystone taxa in the PA network, underscoring potential cooperation between autotrophic and heterotrophic bacteria in organic particle microhabitats. Overall, the disparities in bacterial diversity, community composition, putative function, and network characteristics between FL and PA fractions highlight their adaptation to distinct ecological niches within these unique lake ecosystems.IMPORTANCEUnderstanding the diversity of microbial communities, their assembly mechanisms, and their responses to environmental changes is fundamental to the study of aquatic microbial ecology. Oligotrophic deep-water lakes are fragile ecosystems with limited nutrient resources, rendering them highly susceptible to environmental fluctuations. Examining different bacterial types within these lakes offers valuable insights into the intricate mechanisms governing community dynamics and adaptation strategies across various scales. In our investigation of oligotrophic deep freshwater Lake Fuxian in China, we explored the seasonal and vertical dynamics of two bacterial types: free-living (FL) and particle-attached (PA). Our findings unveiled distinct patterns in the diversity, composition, and putative functions of these bacteria, all shaped by environmental factors. Understanding these subtleties provides insight into bacterial interactions, thereby influencing the overall ecosystem functioning. Ultimately, our research illuminates the adaptation and roles of FL and PA bacteria within these unique lake environments, contributing significantly to our broader comprehension of ecosystem stability and health.
Collapse
Affiliation(s)
- Guijuan Xie
- College of Biology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Chuanbo Sun
- College of Biology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Wenlei Luo
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- The Fuxianhu Station of Plateau Deep Lake Field Scientific Observation and Research, Yunnan, Yuxi, China
| | - Yi Gong
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
45
|
Akram MZ, Sureda EA, Comer L, Corion M, Everaert N. Assessing the impact of hatching system and body weight on the growth performance, caecal short-chain fatty acids, and microbiota composition and functionality in broilers. Anim Microbiome 2024; 6:41. [PMID: 39049129 PMCID: PMC11271025 DOI: 10.1186/s42523-024-00331-6] [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: 04/24/2024] [Accepted: 07/17/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Variations in body weight (BW) remain a significant challenge within broiler flocks, despite uniform management practices. Chicken growth traits are influenced by gut microbiota, which are in turn shaped by early-life events like different hatching environments and timing of first feeding. Chicks hatched in hatcheries (HH) experience prolonged feed deprivation, which could adversely impact early microbiota colonization. Conversely, hatching on-farm (HOF) allows early feeding, potentially fostering a more favorable gut environment for beneficial microbial establishment. This study investigates whether BW differences among broilers are linked to the disparities in gut microbiota characteristics and whether hatching systems (HS) impact the initial microbial colonization of broilers differing in BW, which in turn affects their growth patterns. Male Ross-308 chicks, either hatched in a hatchery or on-farm, were categorized into low (LBW) and high (HBW) BW groups on day 7, making a two-factorial design (HS × BW). Production parameters were recorded periodically. On days 7, 14, and 38, cecal volatile fatty acid (VFA) and microbiota composition and function (using 16 S rRNA gene sequencing and PICRUSt2) were examined. RESULTS HOF chicks had higher day 1 BW, but HH chicks caught up within first week, with no further HS-related performance differences. The HBW chicks remained heavier attributed to higher feed intake rather than improved feed efficiency. HBW group had higher acetate concentration on day 14, while LBW group exhibited higher isocaproate on day 7 and isobutyrate on days 14 and 38. Microbiota analyses revealed diversity and composition were primarily influenced by BW than by HS, with HS having minimal impact on BW-related microbiota. The HBW group on various growth stages was enriched in VFA-producing bacteria like unclassified Lachnospiraceae, Alistipes and Faecalibacterium, while the LBW group had higher abundances of Lactobacillus, Akkermansia and Escherichia-Shigella. HBW microbiota presented higher predicted functional potential compared to the LBW group, with early colonizers exhibiting greater metabolic activity than late colonizers. CONCLUSIONS Despite differences in hatching conditions, the effects of HS on broiler performance were transient, and barely impacting BW-related microbiota. BW variations among broilers are likely linked to differences in feed intake, VFA profiles, and distinct microbiota compositions and functions.
Collapse
Affiliation(s)
- Muhammad Zeeshan Akram
- Nutrition and Animal-Microbiota Ecosystems Laboratory, Department of Biosystems, KU Leuven, Heverlee, 3000, Belgium
- Precision Livestock and Nutrition Laboratory, Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, University of Liège, Gembloux, B-5030, Belgium
| | - Ester Arévalo Sureda
- Nutrition and Animal-Microbiota Ecosystems Laboratory, Department of Biosystems, KU Leuven, Heverlee, 3000, Belgium
| | - Luke Comer
- Nutrition and Animal-Microbiota Ecosystems Laboratory, Department of Biosystems, KU Leuven, Heverlee, 3000, Belgium
| | - Matthias Corion
- Nutrition and Animal-Microbiota Ecosystems Laboratory, Department of Biosystems, KU Leuven, Heverlee, 3000, Belgium
| | - Nadia Everaert
- Nutrition and Animal-Microbiota Ecosystems Laboratory, Department of Biosystems, KU Leuven, Heverlee, 3000, Belgium.
| |
Collapse
|
46
|
Xie G, Sun C, Gong Y, Luo W, Tang X. Beyond the Bloom: Unraveling the Diversity, Overlap, and Stability of Free-Living and Particle-Attached Bacterial Communities in a Cyanobacteria-Dominated Hypereutrophic Lake. MICROBIAL ECOLOGY 2024; 87:96. [PMID: 39046558 PMCID: PMC11269507 DOI: 10.1007/s00248-024-02410-2] [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: 04/13/2024] [Accepted: 07/15/2024] [Indexed: 07/25/2024]
Abstract
In aquatic ecosystems with low nutrient levels, organic aggregates (OAs) act as nutrient hotspots, hosting a diverse range of microbial species compared to those in the water column. Lake eutrophication, marked by intensified and prolonged cyanobacterial blooms, significantly impacts material and energy cycling processes, potentially altering the ecological traits of both free-living (FL) and particle-attached (PA) bacteria. However, the extent to which observed patterns of FL and PA bacterial diversity, community assembly, and stability extend to hypereutrophic lakes remains understudied. To address this gap, we investigated bacterial diversity, composition, assembly processes, and stability within hypereutrophic Lake Xingyun. Our results revealed that FL bacterial communities exhibited higher α-diversity than PA counterparts, coupled with discernible taxonomic compositions. Both bacterial communities showed distinct seasonality, influenced by cyanobacterial bloom intensity. Environmental factors accounted for 71.1% and 54.2% of the variation among FL and PA bacteria, respectively. The assembly of the PA bacterial community was predominantly stochastic, while FL assembly was more deterministic. The FL network demonstrated greater stability, complexity, and negative interactions, indicative of competitive relationships, while the PA network showed a prevalence of positive correlations, suggesting mutualistic interactions. Importantly, these findings differ from observations in oligotrophic, mesotrophic, and eutrophic lakes. Overall, this research provides valuable insights into the interplay among bacterial fractions, enhancing our understanding of nutrient status and cyanobacterial blooms in shaping bacterial communities.
Collapse
Affiliation(s)
- Guijuan Xie
- College of Biology and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Chuanbo Sun
- College of Biology and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
| | - Yi Gong
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Wenlei Luo
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
- The Fuxianhu Station of Plateau Deep Lake Field Scientific Observation and Research, Yuxi, 653100, Yunnan, China
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
47
|
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.
Collapse
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.
| |
Collapse
|
48
|
Yang Y, Zhang F, Yu X, Wang L, Wang Z. Integrating microbial 16S rRNA sequencing and non-targeted metabolomics to reveal sexual dimorphism of the chicken cecal microbiome and serum metabolome. Front Microbiol 2024; 15:1403166. [PMID: 39101039 PMCID: PMC11294938 DOI: 10.3389/fmicb.2024.1403166] [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: 03/18/2024] [Accepted: 06/24/2024] [Indexed: 08/06/2024] Open
Abstract
Background The gut microbiome plays a key role in the formation of livestock and poultry traits via serum metabolites, and empirical evidence has indicated these traits are sex-linked. Methods We examined 106 chickens (54 male chickens and 52 female chickens) and analyzed cecal content samples and serum samples by 16S rRNA gene sequencing and non-targeted metabolomics, respectively. Results The cecal microbiome of female chickens was more stable and more complex than that of the male chickens. Lactobacillus and Family XIII UCG-001 were enriched in male chickens, while Eubacterium_nodatum_group, Blautia, unclassified_Anaerovoraceae, Romboutsia, Lachnoclostridium, and norank_Muribaculaceae were enriched in female chickens. Thirty-seven differential metabolites were identified in positive mode and 13 in negative mode, showing sex differences. Sphingomyelin metabolites possessed the strongest association with cecal microbes, while 11β-hydroxytestosterone showed a negative correlation with Blautia. Conclusion These results support the role of sexual dimorphism of the cecal microbiome and metabolome and implicate specific gender factors associated with production performance in chickens.
Collapse
Affiliation(s)
| | | | | | | | - Zhong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
| |
Collapse
|
49
|
Wilde J, Slack E, Foster KR. Host control of the microbiome: Mechanisms, evolution, and disease. Science 2024; 385:eadi3338. [PMID: 39024451 DOI: 10.1126/science.adi3338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/29/2024] [Indexed: 07/20/2024]
Abstract
Many species, including humans, host communities of symbiotic microbes. There is a vast literature on the ways these microbiomes affect hosts, but here we argue for an increased focus on how hosts affect their microbiomes. Hosts exert control over their symbionts through diverse mechanisms, including immunity, barrier function, physiological homeostasis, and transit. These mechanisms enable hosts to shape the ecology and evolution of microbiomes and generate natural selection for microbial traits that benefit the host. Our microbiomes result from a perpetual tension between host control and symbiont evolution, and we can leverage the host's evolved abilities to regulate the microbiota to prevent and treat disease. The study of host control will be central to our ability to both understand and manipulate microbiotas for better health.
Collapse
Affiliation(s)
- Jacob Wilde
- Department of Biology, University of Oxford, Oxford, UK
| | - Emma Slack
- Institute for Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Basel Institute for Child Health, Basel, Switzerland
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Kevin R Foster
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| |
Collapse
|
50
|
Li S, Zhang L, Fang W, Shen Z. Variations in bacterial community succession and assembly mechanisms with mine age across various habitats in coal mining subsidence water areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174822. [PMID: 39029748 DOI: 10.1016/j.scitotenv.2024.174822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/21/2024]
Abstract
Microorganisms play a pivotal role as catalysts in the biogeochemical cycles of aquatic ecosystems within coal mining subsidence areas. Despite their importance, the succession of microbial communities with increasing mine age, particularly across different habitats, and variations in phylogenetically-based community assembly mechanisms are not well understood. To address this knowledge gap, we collected 72 samples from lake sediments, water, and surrounding topsoil (0-20 cm) at various mining stages (early: 16 years, middle: 31 years, late: 40 years). We analyzed these samples using 16S rRNA gene sequencing and multivariate statistical methods to explore the dynamics and assembly mechanisms of bacterial communities. Our findings reveal that increases in phosphorus and organic matter in sediments, correlating with mining age, significantly enhance bacterial alpha diversity while reducing species richness (P < 0.001). Homogenizing selection (49.9 %) promotes species asynchrony-complementarity, augmenting the bacterial community's ability to metabolize sulfur, phosphorus, and organic matter, resulting in more complex-stable co-occurrence networks. In soil, elevated nitrogen and organic carbon levels markedly influence bacterial community composition (Adonis R2 = 0.761), yet do not significantly alter richness or diversity (P > 0.05). The lake's high connectivity with surrounding soil leads to substantial species drift and organic matter accumulation, thereby increasing bacterial richness in later stages (P < 0.05) and enhancing the ability to metabolize dissolved organic matter, including humic-like substances, fulvic acids, and protein-like materials. The assembly of soil bacterial communities is largely governed by stochastic processes (79.0 %) with species drift (35.8 %) significantly shaping these communities over a broad spatial scale, also affecting water bacterial communities. However, water bacterial community assembly is primarily driven by stochastic processes (51.2 %), with a substantial influence from habitat quality (47.6 %). This study offers comprehensive insights into the evolution of microbial community diversity within coal mining subsidence water areas, with significant implications for enhancing environmental management and protection strategies for these ecosystems.
Collapse
Affiliation(s)
- Shuo Li
- School of Earth and Environment, Anhui University of Science and Technology, Huainan, 232001, China
| | - Lei Zhang
- College of Civil and Architecture Engineering, Chuzhou University, Chuzhou, 239000, China.
| | - Wangkai Fang
- School of Earth and Environment, Anhui University of Science and Technology, Huainan, 232001, China
| | - Zhen Shen
- Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| |
Collapse
|