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Xu M, Li F, Zhang X, Chen B, Geng Y, Ouyang P, Chen D, Li L, Huang X. Microbiome analysis reveals the intestinal microbiota characteristics and potential impact of Procambarus clarkii. Appl Microbiol Biotechnol 2024; 108:77. [PMID: 38204126 PMCID: PMC10781845 DOI: 10.1007/s00253-023-12914-5] [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: 07/19/2023] [Revised: 11/06/2023] [Accepted: 11/17/2023] [Indexed: 01/12/2024]
Abstract
The intestinal microbiota interacts with the host and plays an important role in the immune response, digestive physiology, and regulation of body functions. In addition, it is also well documented that the intestinal microbiota of aquatic animals are closely related to their growth rate. However, whether it resulted in different sizes of crayfish in the rice-crayfish coculture model remained vague. Here, we analyzed the intestinal microbiota characteristics of crayfish of three sizes in the same typical rice-crayfish coculture field by high-throughput sequencing technology combined with quantitative real-time polymerase chain reaction (qRT-PCR) and enzyme activity, investigating the relationship between intestinal microbiota in crayfish and water and sediments. The results showed that the dominant intestinal microbiota of crayfish was significantly different between the large size group (BS), normal size group (NS), and small size group (SS), where Bacteroides and Candidatus_Bacilloplasma contributed to the growth of crayfish by facilitating food digestion through cellulolysis, which might be one of the potential factors affecting the difference in sizes. Follow-up experiments confirmed that the activity of lipase (LPS) and protease was higher in BS, and the relative expression of development-related genes, including alpha-amylase (α-AMY), myocyte-specific enhancer factor 2a (MEF2a), glutathione reductase (GR), chitinase (CHI), and ecdysone receptor (EcR), in BS was significantly higher than that in SS. These findings revealed the intestinal microbiota characteristics of crayfish of different sizes and their potential impact on growth, which is valuable for managing and manipulating the intestinal microbiota in crayfish to achieve high productivity in practice. KEY POINTS: • Significant differences in the dominant microflora of BS, NS, and SS in crayfish. • Cellulolysis might be a potential factor affecting different sizes in crayfish. • Adding Bacteroides and Candidatus_Bacilloplasma helped the growth of crayfish.
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Affiliation(s)
- Ming Xu
- Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Fulong Li
- Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaoli Zhang
- Fishery Research Institute, Chengdu Academy of Agriculture and Forestry Sciences, Wenjiang, Sichuan, China
| | - Baipeng Chen
- Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yi Geng
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ping Ouyang
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Defang Chen
- Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Liangyu Li
- Fishery Research Institute, Chengdu Academy of Agriculture and Forestry Sciences, Wenjiang, Sichuan, China
| | - Xiaoli Huang
- Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Yang M, Liu Z, Wang A, Nopens I, Hu H, Chen H. High biomass yields of Chlorella protinosa with efficient nitrogen removal from secondary effluent in a membrane photobioreactor. J Environ Sci (China) 2024; 146:272-282. [PMID: 38969455 DOI: 10.1016/j.jes.2023.10.036] [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: 07/16/2023] [Revised: 10/28/2023] [Accepted: 10/29/2023] [Indexed: 07/07/2024]
Abstract
Further treatment of secondary effluents before their discharge into the receiving water bodies could alleviate water eutrophication. In this study, the Chlorella proteinosa was cultured in a membrane photobioreactor to further remove nitrogen from the secondary effluents. The effect of hydraulic retention time (HRT) on microalgae biomass yields and nutrient removal was studied. The results showed that soluble algal products concentration reduced in the suspension at low HRT, thereby alleviating microalgal growth inhibition. In addition, the lower HRT reduced the nitrogen limitation for Chlorella proteinosa's growth through the phase-out of nitrogen-related functional bacteria. As a result, the productivity for Chlorella proteinosa increased from 6.12 mg/L/day at an HRT of 24 hr to 20.18 mg/L/day at an HRT of 8 hr. The highest removal rates of 19.7 mg/L/day, 23.8 mg/L/day, and 105.4 mg/L/day were achieved at an HRT of 8 hr for total nitrogen (TN), ammonia, and chemical oxygen demand (COD), respectively. However, in terms of removal rate, TN and COD were the largest when HRT is 24 hr, which were 74.5% and 82.6% respectively. The maximum removal rate of ammonia nitrogen was 99.2% when HRT was 8 hr.
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Affiliation(s)
- Min Yang
- School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China; Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha 410114, China; BIOMATH, Department of Data Analysis and Mathematical Modelling, Ghent University, Gent B 9000, Belgium
| | - Zhen Liu
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha 410114, China
| | - Aijie Wang
- School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Ingmar Nopens
- BIOMATH, Department of Data Analysis and Mathematical Modelling, Ghent University, Gent B 9000, Belgium
| | - Hairong Hu
- School of Materials Science and Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Hong Chen
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha 410114, China.
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Qi Y, Zhong Y, Luo L, He J, Feng B, Zhang X, Xia Y, Ren H. Feasibility analysis of reclaimed water reuse based on water quality data and microbial community structure study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:174781. [PMID: 39094655 DOI: 10.1016/j.scitotenv.2024.174781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 07/06/2024] [Accepted: 07/12/2024] [Indexed: 08/04/2024]
Abstract
The ecological recharge of urban landscapes with reclaimed water plays a crucial role in alleviating urban water shortage. In Yinchuan, we examined the effects of recharging urban rivers with either Yellow River or reclaimed water on the abundance and diversity of microbial communities. This study aimed to support the effective utilization of reclaimed water. We monitored six sites: three in the reclaimed water recharge area (Lucaowa inlet (ZLJ), Lucaowa channel (ZLH), and Lucaowa outlet (ZLC)) and three in the Yellow River water recharge area (Ningcheng lock (FNCZ), Qingfengjie (FQFJ), and Laifosi (FLFS)). Various indicators (pH, turbidity, temperature (T), dissolved oxygen (DO), electrical conductivity (EC), chemical oxygen demand (COD), total phosphorus (TP), total nitrogen (TN), ammonia nitrogen (NH3-N), and nitrate nitrogen (NO3-N)) were used to assess the water quality. The microbial community abundance and diversity were evaluated using 16S rRNA high-throughput sequencing. The results indicated that throughout the monitoring period, the reclaimed water recharge area exhibited increased water transparency and greater microbial community abundance and diversity than the Yellow River water recharge area. However, the reclaimed water recharge area also showed significantly higher levels of nitrogen, phosphorus, organic matter, and electrical conductivity, along with an increase in Firmicutes. Seasonal changes significantly influenced water quality factors, significantly affecting Cyanobacteria and Campylobacter populations, as demonstrated by RDA analysis, which showed a close relationship between microbial communities and environmental factors. Further comparative analysis revealed that erythrocytic bacteria were predominant in the reclaimed water recharge area, whereas Actinobacteria, Planktonia, and Aspergillus spp. were more significant in the Yellow River water recharge area. Predictive analysis of microbial functions suggested that carbon and nitrogen cycle-related functions were more abundant in the reclaimed water recharge area, indicating that reclaimed water recharge could improve the self-purification capacity of the water body.
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Affiliation(s)
- Yarong Qi
- School of Civil and Hydraulic Engineering, Ningxia University, Yinchuan 750021, People's Republic of China
| | - Yanxia Zhong
- School of Ecology and Environment, Ningxia University, Yinchuan 750021, People's Republic of China; Ningxia University Northwest State Key Laboratory of Land Degradation and Ecological Restoration Cultivation Base, Yinchuan 750021, People's Republic of China.
| | - Lingling Luo
- School of Ecology and Environment, Ningxia University, Yinchuan 750021, People's Republic of China; Ningxia University Northwest State Key Laboratory of Land Degradation and Ecological Restoration Cultivation Base, Yinchuan 750021, People's Republic of China
| | - Jing He
- School of Ecology and Environment, Ningxia University, Yinchuan 750021, People's Republic of China; Ningxia University Northwest State Key Laboratory of Land Degradation and Ecological Restoration Cultivation Base, Yinchuan 750021, People's Republic of China
| | - Bo Feng
- School of Civil and Hydraulic Engineering, Ningxia University, Yinchuan 750021, People's Republic of China
| | - Xin Zhang
- School of Civil and Hydraulic Engineering, Ningxia University, Yinchuan 750021, People's Republic of China
| | - Yuan Xia
- School of Ecology and Environment, Ningxia University, Yinchuan 750021, People's Republic of China
| | - Huiqin Ren
- School of Geography and Planning, Ningxia University, Yinchuan 750021, People's Republic of China
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Jiao G, Huang Y, Tang H, Chen Y, Zhou D, Yu D, Ma Z, Ni S. Unveiling the hidden impact: How human disturbances threaten aquatic microorganisms in cities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175305. [PMID: 39117200 DOI: 10.1016/j.scitotenv.2024.175305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 07/23/2024] [Accepted: 08/03/2024] [Indexed: 08/10/2024]
Abstract
Urban activity emissions have important ecological significance to bacterial communities' spatial and temporal distribution and the mechanism of bacterial community construction. The mechanism of bacterial community construction is the key to community structure and lifestyle, and the influence of this aspect has not been thoroughly studied. This study analyzed the response of bacteria in water and sediment in different seasons to urban activities in Jinsha River. The results showed that the influence of urban activities on bacterial community structure in sediment was greater than that in water. The input of pollution in different regions changed the diversity and abundance of water and sediments bacteria and promoted bacterial community reconstruction to a certain extent. Co-network analysis found that many metal-mediated species are core species within the same module and can be used to mitigate pollution caused by metal or organic pollutants due to interspecific solid interactions. Different potential pollution sources around urban rivers affect the metabolic function of bacteria in aquatic ecosystems and promote the detoxification function of bacteria in different media. The results of this study supplement our understanding of the characteristics of microbial communities in urban river systems and provide clues for understanding the maintenance mechanism of microbial diversity in multi-pollution environments.
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Affiliation(s)
- Ganghui Jiao
- College of Geosciences, Chengdu University of Technology, Sichuan 610059, China; Yunnan Earthquake Agency, Yunnan 650000, China; Observation Station for Field Scientific Research of Crustal Tectonic Activity in Northwest Yunnan, Dali 671000, China
| | - Yi Huang
- College of Geosciences, Chengdu University of Technology, Sichuan 610059, China; State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, College of Ecology and Environment, Chengdu University of Technology, Sichuan 610059, China.
| | - Hua Tang
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, College of Ecology and Environment, Chengdu University of Technology, Sichuan 610059, China
| | - Ying Chen
- College of Geosciences, Chengdu University of Technology, Sichuan 610059, China
| | - Dan Zhou
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, College of Ecology and Environment, Chengdu University of Technology, Sichuan 610059, China
| | - Daming Yu
- Pangang Group Company Limited, Sichuan 617050, China
| | - Zhongjian Ma
- Pangang Group Company Limited, Sichuan 617050, China
| | - Shijun Ni
- College of Geosciences, Chengdu University of Technology, Sichuan 610059, China
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Li W, Yang M, Luo Y, Liu W, Wang Z, Ning Z. Effects of dietary rosemary ultrafine powder supplementation on aged hen health and productivity: a randomized controlled trial. Poult Sci 2024; 103:104133. [PMID: 39180778 PMCID: PMC11385426 DOI: 10.1016/j.psj.2024.104133] [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: 06/02/2024] [Revised: 07/17/2024] [Accepted: 07/24/2024] [Indexed: 08/26/2024] Open
Abstract
Recently, poultry industry has been seeking antibiotic residue-free poultry products and safe nutritious feed additives. Whether rosemary ultrafine powder (RUP) affects productive performance by regulating the intestinal microbiome of aged layers remains unclear. Here, we investigated the effects of dietary RUP supplementation on the production performance, egg quality, antioxidant capacity, intestinal microbial structure, and metabolome of aged hens. The results indicate that RUP had no significant effect on production performance but significantly enhanced Thick albumen height, Haugh unit, yolk color (P < 0.05), daily feed intake, and qualified egg rate. Serum content of non-esterified fatty acids, catalase, and glutathione peroxidase increased significantly (P < 0.05). Furthermore, the liver total protein content was significantly increased (P < 0.05). 16S rRNA sequence analysis revealed that RUP significantly impacted both α- and β-diversity of the caecum microbiota. Linear discriminant analysis of effect size and random forest identified Bacteroides, Muribaculum, Butyricimonas, Odoribacter, and Prevotella as biomarkers in groups A and B. In comparing groups A and C, Barnesiella, Turicibacter, and Acholeplasma were critical bacteria, while comparing groups A and D highlighted Barnesiella and Candidatus Saccharimonas as differential bacteria. FAPROTAX analysis of the caecum microbiota revealed that the functional genes associated with harmful substance biodegradation were significantly increased in the RUP-fed group. Based on Spearman correlation analysis, alterations in microbial genera were associated with divergent metabolites. In summary, dietary RUP can improve egg quality and antioxidant capacity and regulate the intestinal microbiome and metabolome in aged breeders. Therefore, RUP can potentially be used as a feed additive to extend breeder service life at an appropriate level of 1.0 g/kg.
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Affiliation(s)
- Wen Li
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Meixue Yang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yuxing Luo
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wei Liu
- Zhuozhou Mufeng Poultry Company Limited, Zhuozhou 072750, China
| | - Zhong Wang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhonghua Ning
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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6
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Zhang J, Song K, Jin F, Jia F, Liang J, Wang F, Zhang J. A novel strategy of artificially regulating plant rhizosphere microbial community to promote plant tolerance to cold stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175184. [PMID: 39089386 DOI: 10.1016/j.scitotenv.2024.175184] [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: 04/24/2024] [Revised: 07/14/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
Artificial regulation of plant rhizosphere microbial communities through the synthesis of microbial communities is one of the effective ways to improve plant stress resistance. However, the process of synthesizing stress resistant microbial communities with excellent performance is complex, time-consuming, and costly. To address this issue, we proposed a novel strategy for preparing functional microbial communities. We isolated a cultivable cold tolerant bacterial community (PRCBC) from the rhizosphere of peas, and studied its effectiveness in assisting rice to resist stress. The results indicate that PRCBC can not only improve the ability of rice to resist cold stress, but also promote the increase of rice yield after cold stress relieved. This is partly because PRCBC increases the nitrogen content in the rhizosphere soil, and promotes rice's absorption of nitrogen elements, thereby promoting rice growth and enhancing its ability to resist osmotic stress. More importantly, the application of PRCBC drives the succession of rice rhizosphere microbial communities, and promotes the succession of rice rhizosphere microbial communities towards stress resistance. Surprisingly, PRCBC drives the succession of rice rhizosphere microbial communities towards a composition similar to PRCBC. This provides a feasible novel method for artificially and directionally driving microbial succession. In summary, we not only proposed a novel and efficient strategy for preparing stress resistant microbial communities to promote plant stress resistance, but also unexpectedly discovered a possible directionally driving method for soil microbial community succession.
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Affiliation(s)
- Jianfeng Zhang
- College of Life Science, Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Keji Song
- College of Life Science, Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Fengyuan Jin
- College of Life Science, Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Fang Jia
- College of Life Science, Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Jing Liang
- College of Life Science, Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Fudong Wang
- College of Life Science, Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Jiejing Zhang
- College of Life Science, Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun 130118, China.
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Deng D, Yang Z, Yang Y, Wan W, Liu W, Xiong X. Metagenomic insights into nitrogen-cycling microbial communities and their relationships with nitrogen removal potential in the Yangtze River. WATER RESEARCH 2024; 265:122229. [PMID: 39154395 DOI: 10.1016/j.watres.2024.122229] [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: 02/22/2024] [Revised: 08/01/2024] [Accepted: 08/06/2024] [Indexed: 08/20/2024]
Abstract
Nitrogen (N) pollution is a major threat to river ecosystems worldwide. Elucidating the community structure of N-cycling microorganisms in rivers is essential to understanding how ecosystem processes and functions will respond to increasing N inputs. However, previous studies generally focus on limited functional genes through amplicon sequencing or quantitative PCR techniques and cannot cover all N-cycling microorganisms. Here, metagenomic sequencing and genome binning were used to determine N-cycling genes in water, channel sediments, and riparian soils of the Yangtze River, which has been heavily polluted by N. Additionally, the denitrification and anaerobic ammonium oxidation (anammox) rates that reflect N removal potential were measured using 15N isotope pairing technique. Results showed that functional genes involved in organic N metabolism (i.e., organic degradation and synthesis) and nitrate reduction pathways (i.e., dissimilatory and assimilatory nitrate reduction to ammonium and denitrification) were more abundant and diverse than other N-cycling genes. A total of 121 metagenome-assembled genomes (MAGs) were identified to be involved in N-cycling processes, and the key MAGs were mainly taxonomically classified as Alphaproteobacteria and Gammaproteobacteria. The abundance and diversity of most N-cycling genes were higher in soils and sediments than in water, as well as higher in downstream and midstream than in upstream sites. These spatial variations were explained not only by local environment and vegetation but also by geographical and climatic factors. N removal process (i.e., denitrification and anammox) rates were significantly related to the abundance or diversity of several N-cycling genes, and climate and edaphic factors could regulate denitrification and anammox rates directly and indirectly through their effects on functional genes. Overall, these results provide a new avenue for further understanding the biogeographic patterns and environmental drivers of N-cycling microorganisms in rivers from the metagenomic perspective.
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Affiliation(s)
- Danli Deng
- Post Doctoral Research Station of Hydraulic Engineering of Three Gorges University, Hubei Field Observation and Scientific Research Stations for Water Ecosystem in Three Gorges Reservoir, China Three Gorges University, Yichang 443002, China; Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Zhengjian Yang
- Post Doctoral Research Station of Hydraulic Engineering of Three Gorges University, Hubei Field Observation and Scientific Research Stations for Water Ecosystem in Three Gorges Reservoir, China Three Gorges University, Yichang 443002, China
| | - Yuyi Yang
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, The Chinese Academy of Sciences & Hubei Province, Wuhan 430074, China
| | - Wenjie Wan
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, The Chinese Academy of Sciences & Hubei Province, Wuhan 430074, China
| | - Wenzhi Liu
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, The Chinese Academy of Sciences & Hubei Province, Wuhan 430074, China.
| | - Xiang Xiong
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, The Chinese Academy of Sciences & Hubei Province, Wuhan 430074, China.
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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.
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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
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Yang X, Li Y, Pu J, Huang Y, Luan T, Xu M. Effects of cable bacteria on vertical redox profile formation and phenanthrene biodegradation in intertidal sediment responded to tide. WATER RESEARCH 2024; 265:122283. [PMID: 39173361 DOI: 10.1016/j.watres.2024.122283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 08/09/2024] [Accepted: 08/15/2024] [Indexed: 08/24/2024]
Abstract
Periodic oxygen permeation is critical for pollutant removal within intertidal sediments. However, tidal effects on the vertical redox profile associated with cable bacterial activity is not well understood. In this study, we simulated and quantified the effects of tidal flooding, exposing, and their periodic alternation on vertical redox reactions and phenanthrene removal driven by cable bacteria in the riverbank sediment. Results show that electrogenic sulfur oxidation (e-SOx) mediated by cable bacteria during exposing process drove the vertical permeation of oxidation potential characterized by a decrease in Fe(II) and sulfide concentrations. The sulfate produced was observed in deep sediment (5-10 mm) and served as an electron acceptor for anaerobic oxidation, thereby triggering the functional succession of microbial community. About 78.2 % and 80.8 % of phenanthrene was degraded in deep sediment where cable bacteria grew well under exposing and tidal conditions. Anaerobic processes during tidal flood were also found to be important for the survival of cable bacteria. Higher cable bacteria abundance (up to 1.5 %) was observed under tidal conditions compared to that under continuous exposing conditions and flooding conditions. This might be attributed to lower oxidation stress and sulfide replenishment via sulfate reduction while flooding. Under tidal conditions, the cable bacteria interacted with sulfate reduction bacteria (e.g. Desulfobacca spp. and Desulfatiglans spp.) and maintained the dynamic balance of HS- and SO42- in sediment profiles. This HS--SO42- cycle could serve as a "redox connector" that continuously delivers oxidation potential to deep sediments, resulting in the removal of organic pollutants. The findings provide preliminary evidence of the self-purification mechanisms within intertidal sediments and suggest a potential strategy for sediment remediation.
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Affiliation(s)
- Xunan Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Yu Li
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Jia Pu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Youda Huang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Tiangang Luan
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China; School of Environmental and Chemical Engineering, Wuyi University, Jiangmen 529020, China.
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
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10
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Meroz N, Livny T, Toledano G, Sorokin Y, Tovi N, Friedman J. Evolution in microbial microcosms is highly parallel, regardless of the presence of interacting species. Cell Syst 2024; 15:930-940.e5. [PMID: 39419002 DOI: 10.1016/j.cels.2024.09.007] [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: 02/22/2024] [Revised: 07/29/2024] [Accepted: 09/17/2024] [Indexed: 10/19/2024]
Abstract
Evolution often follows similar trajectories in replicate populations, suggesting that it may be predictable. However, populations are naturally embedded in multispecies communities, and the extent to which evolution is contingent on the specific species interacting with the focal population is still largely unexplored. Here, we study adaptations in strains of 11 different species, experimentally evolved both in isolation and in various pairwise co-cultures. Although partner-specific effects are detectable, evolution was mostly shared between strains evolved with different partners; similar changes occurred in strains' growth abilities, in community properties, and in about half of the repeatedly mutated genes. This pattern persisted even in species pre-adapted to the abiotic conditions. These findings indicate that evolution may not always depend strongly on the biotic environment, making predictions regarding coevolutionary dynamics less challenging than previously thought. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Nittay Meroz
- Institute of Environmental Sciences, Hebrew University, Rehovot, Israel.
| | - Tal Livny
- Institute of Environmental Sciences, Hebrew University, Rehovot, Israel
| | - Gal Toledano
- Institute of Environmental Sciences, Hebrew University, Rehovot, Israel; The Rachel and Selim Benin School of Computer Science and Engineering, Hebrew University, Jerusalem, Israel
| | - Yael Sorokin
- Institute of Environmental Sciences, Hebrew University, Rehovot, Israel
| | - Nesli Tovi
- Institute of Environmental Sciences, Hebrew University, Rehovot, Israel
| | - Jonathan Friedman
- Institute of Environmental Sciences, Hebrew University, Rehovot, Israel.
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11
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Liu S, Zhang Z, Hao J, Zhao C, Han F, Xiong Q, Wang X, Du C, Xu H. Plastic debris mediates bacterial community coalescence by breaking dispersal limitation in the sediments of a large river. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 359:124603. [PMID: 39047888 DOI: 10.1016/j.envpol.2024.124603] [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: 05/23/2024] [Revised: 07/21/2024] [Accepted: 07/22/2024] [Indexed: 07/27/2024]
Abstract
Plastic debris has recently been proposed as a novel habitat for bacterial colonization, which can raise perturbations in bacterial ecology after burial in riverine sediments. However, community coalescence, as a prevalent process involving the interrelationships of multiple communities and their surrounding environments, has been rarely discussed to reveal the impact of the plastisphere on sedimentary bacterial community. This study analyzed the bacterial community in plastic debris and sediment along the Nujiang River, elucidating the role of the plastisphere in mediating community coalescence in sediments. Our results demonstrated that the plastisphere and sedimentary bacterial communities exhibited distinct biogeography along the river (r = 0.694, p < 0.01). Based on overlapped taxa and SourceTracker, the extent of coalescence between adjacent communities was in following orders: plastic-plastic (0.589) > plastic-sediment (0.561) > sediment-sediment (0.496), indicating the plastisphere promoted bacterial community coalescence along the river. Flow velocity and geographic distance were the major factors driving the plastisphere changes, suggesting that the plastisphere were vulnerable to dispersal. The null model and the neutral model provided additional support for the higher immigration ability of the plastisphere to overcome dispersal limitation, highlighting the potential importance of the plastisphere in community coalescence. Network analysis indicated the critical role of keystone species (Proteobacteria, Bacteroidetes, and Gemmatimonadetes) in mediating the coalescence between sedimentary bacterial community and the plastisphere. In summary, the plastisphere could mediate the coalescence of bacterial communities by overcoming dispersal limitation, which provides new perspectives on the plastisphere altering bacterial ecology in riverine sediments.
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Affiliation(s)
- Sheng Liu
- School of Civil Engineering, Shandong University, Jinan, Shandong, 250061, China.
| | - Zixuan Zhang
- School of Civil Engineering, Shandong University, Jinan, Shandong, 250061, China
| | - Jie Hao
- School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266000, China
| | - Chuanfu Zhao
- School of Civil Engineering, Shandong University, Jinan, Shandong, 250061, China
| | - Fei Han
- School of Civil Engineering, Shandong University, Jinan, Shandong, 250061, China
| | - Qingrong Xiong
- School of Civil Engineering, Shandong University, Jinan, Shandong, 250061, China
| | - Xun Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Chenggong Du
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huaiyin Normal University, Huai'an, Jiangsu, 223300, China
| | - Hongzhe Xu
- Dept of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, USA
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12
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Wang Y, Liu Y, Xue S, Chai F, Zhang S, Yang K, Liu Y, Li J, Yu F. Comparative analysis of bioaerosol emissions: Seasonal dynamics and exposure risks in hospital vs. municipal wastewater treatment systems. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 359:124608. [PMID: 39053807 DOI: 10.1016/j.envpol.2024.124608] [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: 03/18/2024] [Revised: 07/21/2024] [Accepted: 07/22/2024] [Indexed: 07/27/2024]
Abstract
Hospital wastewater is known to contain various pathogenic microorganisms and harmful substances. During the hospital wastewater treatment process, the bioaerosols released may encapsulate these pathogens, leading to human infection. This study undertook an investigation to compare the dispersion characteristics and seasonal variations of bioaerosols from hospital and municipal sewage. The results indicated that the airborne bacterial concentration from hospital sewage (119 ± 118 CFU/m3) was higher than municipal sewage (46 ± 19 CFU/m3), with the highest concentration observed in summer. The dominant bacterial genera present in bioaerosols from both sewages were alike, with the proportions varied by sewage types and the structure mainly influenced by seasonal factors. Bacteroides, Escherichia-Shigella and Streptococcus were identified as the most prevalent pathogenic genera in spring, summer and winter bioaerosols, respectively, while Pseudomonas and Acinetobacter were abundant in autumn. Although the non-carcinogenic risk associated with bioaerosols was low (<1), the presence of pathogenic species and their potential synergistic interactions elevated the overall exposure risk. The diffusion modeling results demonstrated that bioaerosol emissions from the surface of hospital sewage can reach up to 10570 CFU/m3 in summer and can spread more than 300 m downwind. The potential pathogenicity of bioaerosols was also highest in summer, which may pose a health hazard to populations located downwind. Therefore, the management and control of bioaerosols from sewage should be strengthened, especially in summer.
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Affiliation(s)
- Yanjie Wang
- School of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China.
| | - Yang Liu
- School of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China.
| | - Song Xue
- CSCEC SCIMEE Sci.& Tech. Co., Ltd, Chengdu, 610045, PR China.
| | - Fengguang Chai
- School of Ecology and Environment, Zhengzhou University, Zhengzhou, 450001, PR China.
| | - Song Zhang
- School of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China.
| | - Kai Yang
- School of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China.
| | - Yifan Liu
- School of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China.
| | - Jinlong Li
- School of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China.
| | - Fangfang Yu
- School of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China.
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13
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Peng J, Wang D, He P, Wei P, Zhang L, Lan W, Li Y, Chen W, Zhao Z, Jiang L, Zhou L. Exploring the environmental influences and community assembly processes of bacterioplankton in a subtropical coastal system: Insights from the Beibu Gulf in China. ENVIRONMENTAL RESEARCH 2024; 259:119561. [PMID: 38972345 DOI: 10.1016/j.envres.2024.119561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/09/2024]
Abstract
Due to rapid urbanization, the Beibu Gulf, a semi-closed gulf in the northwestern South China Sea, faces escalating ecological and environmental threats. Understanding the assembly mechanisms and driving factors of bacterioplankton in the Beibu Gulf is crucial for preserving its ecological functions and services. In the present study, we investigated the spatiotemporal dynamics of bacterioplankton communities and their assembly mechanisms in the Beibu Gulf based on the high-throughput sequencing of the bacterial 16 S rRNA gene. Results showed significantly higher bacterioplankton diversity during the wet season compared to the dry season. Additionally, distinct seasonal variations in bacterioplankton composition were observed, characterized by an increase in Cyanobacteria and Thermoplasmatota and a decrease in Proteobacteria and Bacteroidota during the wet season. Null model analysis revealed that stochastic processes governed bacterioplankton community assembly in the Beibu Gulf, with drift and homogenizing dispersal dominating during the dry and wet seasons, respectively. Enhanced deterministic assembly of bacterioplankton was also observed during the wet season. Redundancy and random forest model analyses identified the physical properties (e.g., temperature) and nutrient content (e.g., nitrate) of water as primary environmental drivers influencing bacterioplankton dynamics. Moreover, variation partitioning and distance-decay of similarity revealed that environmental filtering played a significant role in shaping bacterioplankton variations in this rapidly developed coastal ecosystem. These findings advance our understanding of bacterioplankton assembly in coastal ecosystems and establish a theoretical basis for effective ecological health management amidst ongoing global changes.
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Affiliation(s)
- Jinxia Peng
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 53002l, China
| | - Dapeng Wang
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 53002l, China
| | - Pingping He
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 53002l, China
| | - Pinyuan Wei
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 53002l, China
| | - Li Zhang
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 53002l, China
| | - Wenlu Lan
- Beibu Gulf Marine Ecological Environment Field Observation and Research Station of Guangxi, Marine Environmental Monitoring Centre of Guangxi, Beihai, 536000, China
| | - Yusen Li
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 53002l, China
| | - Wenjian Chen
- 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, Guangzhou, 510642, China
| | - Zelong Zhao
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Linyuan Jiang
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 53002l, China.
| | - Lei Zhou
- 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, Guangzhou, 510642, China.
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14
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Wang T, Wang H, Li Z, Li X, Tsybekmitova G, Wang Y. Sulfide addition accelerates anammox sludge granulation and promotes microbial cooperation. WATER RESEARCH 2024; 268:122626. [PMID: 39418804 DOI: 10.1016/j.watres.2024.122626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Revised: 10/04/2024] [Accepted: 10/12/2024] [Indexed: 10/19/2024]
Abstract
The granular anaerobic ammonium oxidation (anammox) system has attractive advantages in tolerance to environmental-stress and enhancement of nitrogen removal capacity. Sulfide addition can improve nitrogen removals in anammox systems via inducing sulfur denitrification, yet its function in the improvement of the property of anammox granular sludge remains unclear. Herein, we investigated the variations in the morphological and microbial properties of the anammox sludge response to different sulfide concentrations (Na2S: 10-100 mg/L) through a long-term experiment. By comparing the sludge diameter and heme c content, it comes that a relatively low sulfide (S/N [nitrate] molar ratio of 0.18-0.50) significantly promoted the average diameter and heme c concentration of sludge by 25-175 % and 75-95 %, respectively, compared to that of both without sulfide addition and a high sulfide addition (S/N > 0.85). This enhancement is primarily because a low amount of sulfide had stimulated the secretion of extracellular polymeric substance, induced slight biogenic sulfur accumulation as microbial nuclei, and facilitated the appropriate amount of filamentous bacteria proliferation. Microbial metabolism functions analyses revealed a robust granular anammox coupled with sulfur denitrification in the sulfide-mediated anammox reactor, and the assembled granules exhibited exceptional tolerance to environmental stress. Significantly, the anammox bacteria (Candidatus_Brocadia) dominating the granules displayed satisfactory anammox activity (21.8 ± 2.1 mg N/g VSS h), and their produced nitrate was efficiently removed by the sulfur-oxidizing bacteria (Thiobacillus) that predominantly occurred in the flocs. This collaboration ensured an efficient sulfide-mediated anammox granules system, achieving nitrogen removal efficiency exceeding 95 %. These results highlight the function of sulfide in improving the morphological property of anammox sludge as well as the creation of a favorable ecological niche for the functional microorganism, which is important to maintain the efficiency and robustness of the anammox process in treating wastewater.
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Affiliation(s)
- Tong Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, PR China
| | - Han Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, PR China.
| | - Zibin Li
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, PR China
| | - Xiang Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, PR China
| | - Gazhit Tsybekmitova
- Institute of Natural Resources, Ecology and Cryology, Siberian Branch of Russian Academy Science Nedorezova, 16a, Chita 672014, Russian Federation
| | - Yayi Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, PR China
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15
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Chen J, Li X, Wang H, Tang L, Xue S, Xin J, Zang Y, Tang X. The contribution of seasonal variations and Zostera marina presence to the bacterial community assembly of seagrass bed sediments. BMC Microbiol 2024; 24:405. [PMID: 39394553 PMCID: PMC11468120 DOI: 10.1186/s12866-024-03558-0] [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: 07/17/2024] [Accepted: 09/30/2024] [Indexed: 10/13/2024] Open
Abstract
BACKGROUND Microorganisms play pivotal roles in seagrass ecosystems by facilitating material and elemental cycling as well as energy flux. However, our understanding of how seasonal factors and seagrass presence influence the assembly of bacterial communities in seagrass bed sediments is limited. Employing high-throughput sequencing techniques, this study investigates and characterizes bacterial communities in the rhizosphere of eelgrass (Zostera marina) and the bulk sediments across different seasons. The research elucidates information on the significance of seasonal variations and seagrass presence in impacting the microbial communities associated with Zostera marina. RESULTS The results indicate that seasonal variations have a more significant impact on the bacterial community in seagrass bed sediments than the presence of seagrass. We observed that the assembly of bacterial communities in bulk sediments primarily occurs through stochastic processes. However, the presence of seagrass leading to a transition from stochastic to deterministic processes in bacterial community assembly. This shift further impacts the complexity and stability of the bacterial co-occurrence network. Through LEfSe analysis, different candidate biomarkers were identified in the bacterial communities of rhizosphere sediments in different seasons, indicating that seagrass may possess adaptive capabilities to the environment during different stages of growth and development. CONCLUSIONS Seasonal variations play a significant role in shaping these communities, while seagrass presence influences the assembly processes and stability of the bacterial community. These insights will provide valuable information for the ecological conservation of seagrass beds.
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Affiliation(s)
- Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
| | - Xinqi Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
| | - Hongzhen Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
| | - Liuqing Tang
- Marine Science Research Institute of Shandong Province, National Oceanographic Center, Qingdao, Shandong, China
| | - Song Xue
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
| | - Jiayi Xin
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
| | - Yu Zang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, Shandong, China.
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, Shandong, China.
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16
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Martoni F, Rako L, Jaroslow D, Selleck C, Kant P, Nancarrow N, Blacket MJ. Diversity and composition of the bacterial communities associated with the Australian spittlebugs Bathyllus albicinctus and Philagra parva (Hemiptera: Aphrophoridae). PLoS One 2024; 19:e0311938. [PMID: 39388461 PMCID: PMC11469610 DOI: 10.1371/journal.pone.0311938] [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: 07/22/2024] [Accepted: 09/28/2024] [Indexed: 10/12/2024] Open
Abstract
Spittlebugs and froghoppers (Hemiptera: Cercopoidea) are insects feeding on xylem, which potentially can cause significant economic damage worldwide by transmitting plant pathogenic bacteria such as Xylella fastidiosa. Australia and New Zealand are currently free from X. fastidiosa, but they are home to at least 45 native spittlebug species. Among these, the Australian natives Bathyllus albicinctus (Erichson, 1842) and Philagra parva (Donovan, 1805) are particularly widespread and can be found across southern and eastern Australia, with B. albicinctus also in New Zealand. The potential that both species might be capable of vectoring Xylella fastidiosa poses a substantial biosecurity risk if the bacterium were to invade these regions. In this study, we examined 87 spittlebug nymphs collected across 12 different host plant species, in five locations in Victoria, Australia. Our objective was to explore the factors influencing bacterial communities within and between these widespread spittlebug species, considering geographic location, insect phylogenetics, and host plant associations. We employed COI barcoding to assess insect genetic variation and 16S high throughput sequencing (HTS) metabarcoding to analyse bacterial microbiome diversity across various host plants. Our findings revealed minimal genetic divergence among spittlebug individuals in the same species, highlighting conspecificity despite conspicuous morphological divergences. On the other hand, we recorded significant variation in bacterial communities harboured by Bathyllus albicinctus nymphs feeding on different plants, even when these were collected within close proximity to each other. Therefore, host plant association appeared to shape the bacterial communities of spittlebugs more than insect genetic divergence or geographical location. These diverse bacterial communities could potentially facilitate transmission of plant pathogenic bacteria, underscoring the risk of widespread transmission among numerous plant hosts through insect-plant interactions. This study emphasizes the critical need to understand these complex interactions, particularly in the context of biosecurity.
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Affiliation(s)
| | - Lea Rako
- Agriculture Victoria, AgriBio Centre, Bundoora, Victoria, Australia
| | - Duncan Jaroslow
- Agriculture Victoria, AgriBio Centre, Bundoora, Victoria, Australia
| | - Caitlin Selleck
- Agriculture Victoria, AgriBio Centre, Bundoora, Victoria, Australia
| | - Pragya Kant
- Agriculture Victoria, AgriBio Centre, Bundoora, Victoria, Australia
| | - Narelle Nancarrow
- Agriculture Victoria, Grains Innovation Park, Horsham, Victoria, Australia
| | - Mark J. Blacket
- Agriculture Victoria, AgriBio Centre, Bundoora, Victoria, Australia
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17
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Girija GK, Tseng LC, Muthu P, Chen YL, Ho YN, Hwang JS. Microbiome flexibility enhances the resilience of the potentially invasive coral Tubastraea aurea to abrupt environmental changes: Insights from a shallow water hydrothermal vent transplantation study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 954:176792. [PMID: 39389143 DOI: 10.1016/j.scitotenv.2024.176792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 09/18/2024] [Accepted: 10/05/2024] [Indexed: 10/12/2024]
Abstract
To comprehend the effects of potentially invasive coral Tubastraea aurea on marine ecosystems, it is crucial to understand their adaptive strategies to survive environmental changes and perturbations. Therefore, a cross-transplantation study was conducted to assess the microbiome's role in the resilience of T. aurea to sudden environmental changes.Hydrographic analyses revealed distinct ecological conditions at two sites: a hydrothermal vent (HV) site, characterized by harsh environmental conditions serving as a natural laboratory for future oceanic changes, and a regular coastal site Fulong (FU). Both sites showed significant differences in pH, temperature, and dissolved oxygen. Using Oxford Nanopore Technologies, we examined bacterial dynamics in coral tissue, mucus and ambient sediment samples following cross-transplantation experiments. We observed a rapid shift in dominant bacterial groups post-transplantation with transplanted corals acquiring microbiomes similar to native corals from their respective sites within 16 days. The bacteria Endozoicomonas euniceicola and Ruegeria profundi were dominant in both native and transplanted corals, suggesting their critical role in coral resilience. Furthermore, the enrichment of certain bacterial taxa post-transplantation suggests that opportunistic species also contribute to host acclimatization. Functional profiling data indicated that there was site-specific adaptation because corals had acquired beneficial bacterial assemblages to assist them cope with environmental stressors. More specifically, there was a switch towards sulfur and nitrogen metabolism in corals that moved to high sulfidic environments, while corals transplanted into normal coastal environments showed enriched photoautotrophic processes due to their symbionts. Our study underscored the highly flexible microbiome of T. aurea and its pivotal role in facilitating host resilience to environmental perturbations, particularly in the context of its potential invasiveness. Hence, these findings contribute to the understanding of coral-microbiome dynamics and emphasize the necessity of considering microbially-mediated resilience in managing potentially invasive coral species in marine ecosystems around the world, especially as ocean conditions continue to change.
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Affiliation(s)
- Gowri Krishna Girija
- Institute of Marine Biology, National Taiwan Ocean University, Keelung 202301, Taiwan
| | - Li-Chun Tseng
- Institute of Marine Biology, National Taiwan Ocean University, Keelung 202301, Taiwan
| | - Priyanka Muthu
- Institute of Marine Biology, National Taiwan Ocean University, Keelung 202301, Taiwan
| | - Yu-Ling Chen
- Institute of Marine Biology, National Taiwan Ocean University, Keelung 202301, Taiwan
| | - Ying-Ning Ho
- Institute of Marine Biology, National Taiwan Ocean University, Keelung 202301, Taiwan; Centre of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202301, Taiwan; Taiwan Ocean Genome Center, National Taiwan Ocean University, Keelung 202301, Taiwan.
| | - Jiang-Shiou Hwang
- Institute of Marine Biology, National Taiwan Ocean University, Keelung 202301, Taiwan; Centre of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202301, Taiwan.
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18
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Gao SM, Wang P, Li Q, Shu WS, Tang LY, Lin ZL, Li JT, Huang LN. Deciphering microbial metabolic interactions and their implications for community dynamics in acid mine drainage sediments. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135478. [PMID: 39137550 DOI: 10.1016/j.jhazmat.2024.135478] [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: 04/16/2024] [Revised: 07/28/2024] [Accepted: 08/08/2024] [Indexed: 08/15/2024]
Abstract
The microbially-mediated reduction processes have potential for the bioremediation of acid mine drainage (AMD), which represents a worldwide environment problem. However, we know little about the microbial interactions in anaerobic AMD sediments. Here we utilized genome-resolved metagenomics to uncover the nature of cooperative and competitive metabolic interactions in 90 AMD sediments across Southern China. Our analyses recovered well-represented prokaryotic communities through the reconstruction of 2625 population genomes. Functional analyses of these genomes revealed extensive metabolic handoffs which occurred more frequently in nitrogen metabolism than in sulfur metabolism, as well as stable functional redundancy across sediments resulting from populations with low genomic relatedness. Genome-scale metabolic modeling showed that metabolic competition promoted microbial co-occurrence relationships, suggesting that community assembly was dominated by habitat filtering in sediments. Notably, communities colonizing more extreme conditions tended to be highly competitive, which was typically accompanied with increased network complexity but decreased stability of the microbiome. Finally, our results demonstrated that heterotrophic Thermoplasmatota associated with ferric iron and sulfate reduction contributed most to the elevated levels of competition. Our study shed light on the cooperative and competitive metabolisms of microbiome in the hazardous AMD sediments, which may provide preliminary clues for the AMD bioremediation in the future.
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Affiliation(s)
- Shao-Ming Gao
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Pandeng Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Qi Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Ling-Yun Tang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Zhi-Liang Lin
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Jin-Tian Li
- School of Life Sciences, South China Normal University, Guangzhou 510631, PR China.
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China.
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19
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Ali Q, Ma S, Farooq U, Liu B, Wang Z, Sun H, Cui Y, Li D, Shi Y. Chronological dynamics of the gut microbiome in response to the pasture grazing system in geese. Microbiol Spectr 2024; 12:e0418823. [PMID: 39189756 PMCID: PMC11448393 DOI: 10.1128/spectrum.04188-23] [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: 12/12/2023] [Accepted: 07/21/2024] [Indexed: 08/28/2024] Open
Abstract
It is commonly accepted that dietary fibers are good for gut health. The effect of fibers on the diversity and metabolic activities of the cecal microflora, however, differ with the passage of time. Therefore, we investigated the time-series impacts of the pasture grazing system (a high dietary fiber source) on the cecal microbiome and short-chain fatty acids in Wanpu geese, comparing it to commercial feeding (a low dietary fiber source). The cecal microbiota composition and SCFA concentrations were evaluated by 16S rRNA gene sequencing and gas chromatography, respectively. We found that pasture produced a generally quick positive response to Bacteroidales, Lactobacillales, Gastranaerophilales (at 45 days), Lachnospirales, and Oscillospirales (at 60 days and 90 days) irrespective of Erysipelotrichales (at 45 days), Clostridia_UCG-014, RF39 (at 60 days), Christensenellales, and Peptostreptococcales-Tissierellales (at 90 days) in geese. Meanwhile, we found that Lactobacillales, Gastranaerophilales, Lachnospirales, and Oscillospirales were significantly correlated with short-chain fatty acids in pasture grazing geese. Indeed, the correlation of cecal microbiota with SCFAs led to altered microbial functions evinced by COG; KEGG pathway levels 1, 2, and 3; BugBase; and FAPROTAX databases. This study emphasizes the importance of dietary fiber sources in influencing beneficial impacts in regulating geese microbiota homeostasis and metabolic functions such as energy and lipid metabolism.IMPORTANCELow dietary fiber diet sources cause gut microbial and short-chain fatty acid alterations that lead to compromised animal health. The establishment of an artificial pasture grazing system at the expense of ryegrass is a good source of dietary fiber for geese. Our results described the importance of pasture in maintaining the gut microbiota, SCFAs, and potential microbial functions reported by COG; KEGG pathway levels 1, 2, and 3; BugBase; and FAPROTAX databases.
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Affiliation(s)
- Qasim Ali
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Sen Ma
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou, China
- Henan Herbage Engineering Technology Research Center, Zhengzhou, China
| | - Umar Farooq
- Department of Poultry Science, University of Agriculture Faisalabad, Sub Campus Toba Tek Singh, Toba Tek Singh, Pakistan
| | - Boshuai Liu
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou, China
- Henan Herbage Engineering Technology Research Center, Zhengzhou, China
| | - Zhichang Wang
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou, China
- Henan Herbage Engineering Technology Research Center, Zhengzhou, China
| | - Hao Sun
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou, China
- Henan Herbage Engineering Technology Research Center, Zhengzhou, China
| | - Yalei Cui
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou, China
- Henan Herbage Engineering Technology Research Center, Zhengzhou, China
| | - Defeng Li
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou, China
- Henan Herbage Engineering Technology Research Center, Zhengzhou, China
| | - Yinghua Shi
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou, China
- Henan Herbage Engineering Technology Research Center, Zhengzhou, China
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20
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Luo X, Yan G, Wang Q, Xing Y. Community structure, diversity and function of endophytic and soil microorganisms in boreal forest. Front Microbiol 2024; 15:1410901. [PMID: 39417072 PMCID: PMC11480031 DOI: 10.3389/fmicb.2024.1410901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 09/23/2024] [Indexed: 10/19/2024] Open
Abstract
Introduction Despite extensive studies on soil microbial community structure and functions, the significance of plant-associated microorganisms, especially endophytes, has been overlooked. To comprehensively anticipate future changes in forest ecosystem function under future climate change scenarios, it is imperative to gain a thorough understanding of the community structure, diversity, and function of both plant-associated microorganisms and soil microorganisms. Methods In our study, we aimed to elucidate the structure, diversity, and function of leaf endophytes, root endophytes, rhizosphere, and soil microbial communities in boreal forest. The microbial structure and composition were determined by high-throughput sequencing. FAPROTAX and FUNGuild were used to analyze the microbial functional groups. Results Our findings revealed significant differences in the community structure and diversity of fungi and bacteria across leaves, roots, rhizosphere, and soil. Notably, we observed that the endophytic fungal or bacterial communities associated with plants comprised many species distinct from those found in the soil microbial communities, challenging the assumption that most of endophytic fungal or bacterial species in plants originate from the soil. Furthermore, our results indicated noteworthy differences in the composition functional groups of bacteria or fungi in leaf endophytes, root endophytes, rhizosphere, and soil, suggesting distinct roles played by microbial communities in plants and soil. Discussion These findings underscore the importance of recognizing the diverse functions performed by microbial communities in both plant and soil environments. In conclusion, our study emphasizes the necessity of a comprehensive understanding of the structure and function microbial communities in both plants and soil for assessing the functions of boreal forest ecosystems.
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Affiliation(s)
- Xi Luo
- School of Life Sciences, Qufu Normal University, Qufu, China
- Library, Qufu Normal University, Qufu, China
| | - Guoyong Yan
- School of Life Sciences, Qufu Normal University, Qufu, China
| | - Qinggui Wang
- School of Life Sciences, Qufu Normal University, Qufu, China
| | - Yajuan Xing
- School of Life Sciences, Qufu Normal University, Qufu, China
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21
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Xiang Y, Song X, Yang Y, Deng S, Fu L, Yang C, Chen M, Pu J, Zhang H, Chai H. Comammox rather than AOB dominated the efficient autotrophic nitrification-denitrification process in an extremely oxygen-limited environment. WATER RESEARCH 2024; 268:122572. [PMID: 39383803 DOI: 10.1016/j.watres.2024.122572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 09/29/2024] [Accepted: 10/02/2024] [Indexed: 10/11/2024]
Abstract
The discovery of complete ammonia oxidizer (comammox) has challenged the traditional understanding of the two-step nitrification process. However, their functions in the oxygen-limited autotrophic nitrification-denitrification (OLAND) process remain unclear. In this study, OLAND was achieved using comammox-dominated nitrifying bacteria in an extremely oxygen-limited environment with a dissolved oxygen concentrations of 0.05 mg/L. The ammonia removal efficiency exceeded 97 %, and the total nitrogen removal efficiency reached 71 % when sodium bicarbonate was used as the carbon source. The pseudo-first- and second-order models were found to best fit the ammonia removal processes under low and high loads, respectively, suggesting distinct ammonia removal pathways. Full-length 16S rRNA gene sequencing and metagenomic results revealed that comammox-dominated under different oxygen levels, in conjunction with anammox and heterotrophic denitrifiers. The abundance of enzymes involved in energy metabolism indicates the coexistence of anammox and autotrophic nitrification-heterotrophic denitrification pathways. The binning results showed that comammox bacteria engaged in horizontal gene transfer with nitrifiers, anammox bacteria, and denitrifiers to adapt to an obligate environments. Therefore, this study demonstrated that comammox, anammox, and heterotrophic denitrifiers play important roles in the OLAND process and provide a reference for further reducing aeration energy in the autotrophic nitrogen removal process.
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Affiliation(s)
- Yu Xiang
- School of Environmental Science and Engineering, Southwest Jiaotong University, Chengdu 611756, PR China; School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 611756, PR China; School of Architecture and Civil Engineering, Xihua University, Chengdu 610039, PR China
| | - Xiaoming Song
- School of Architecture and Civil Engineering, Xihua University, Chengdu 610039, PR China
| | - Yilin Yang
- School of Architecture and Civil Engineering, Xihua University, Chengdu 610039, PR China
| | - Shuai Deng
- School of Architecture and Civil Engineering, Xihua University, Chengdu 610039, PR China
| | - Liwei Fu
- School of Architecture and Civil Engineering, Xihua University, Chengdu 610039, PR China
| | - Cheng Yang
- School of Environmental Science and Engineering, Southwest Jiaotong University, Chengdu 611756, PR China
| | - Mengli Chen
- School of Environmental Science and Engineering, Southwest Jiaotong University, Chengdu 611756, PR China
| | - Jia Pu
- School of Environmental Science and Engineering, Southwest Jiaotong University, Chengdu 611756, PR China
| | - Han Zhang
- School of Environmental Science and Engineering, Southwest Jiaotong University, Chengdu 611756, PR China.
| | - Hongxiang Chai
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China.
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22
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Yan Z, Wei H, Wang H, Ye H. Sediment contamination alters the submersed macrophyte Vallisneria natans and root-associated microbiome profiles during phytoremediation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 284:117012. [PMID: 39243668 DOI: 10.1016/j.ecoenv.2024.117012] [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: 05/15/2024] [Revised: 09/02/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
The submerged plant Vallisneria natans plays an important role in the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated sediments. In this study, V. natans and sediments were collected from different V. natans natural vegetation zones, and sediment mesocosms were set up for phytoremediation tests. In addition, commercial-grade V. natans were obtained from the Fish-Bird-Flower market for comparison with phytoremediation. Phytoremediation using V. natans from natural growth significantly increased the degradation of PAHs in Dashui Harbor (0.0148±0.0015 d-1) and Taihu Lake bay sediments (0.0082±0.0010 d-1) but not in commercial-grade V. natans. Transplanted V. natans from natural growth had a significant (p=0.002) effect on PAH degradation, especially in highly PAH-contaminated sedimentary environments. The distinct bacterial communities were strongly affected by sediment type and V. natans type, which contributed to different phytoremediation patterns. Less complex but more stable microbial co-occurrence networks play key roles in improving PAH phytoremediation potential. In addition, V. natans from natural growth in highly PAH-contaminated sediment could adapt to PAH stress by exuding tryptophan metabolites to assemble health-promoting microbiomes. This study provides novel evidence that initial microbial and physicochemical characteristics of sediment and submerged plant types should be considered in the use of bioremediation management strategies for organic pollutant-contaminated sediments.
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Affiliation(s)
- Zaisheng Yan
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Haoming Wei
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Hongyang Wang
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin 150025, China
| | - Huaxiang Ye
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin 150025, China
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23
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Clifton BE, Alcolombri U, Uechi GI, Jackson CJ, Laurino P. The ultra-high affinity transport proteins of ubiquitous marine bacteria. Nature 2024; 634:721-728. [PMID: 39261732 DOI: 10.1038/s41586-024-07924-w] [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: 03/10/2023] [Accepted: 08/07/2024] [Indexed: 09/13/2024]
Abstract
SAR11 bacteria are the most abundant microorganisms in the surface ocean1 and have global biogeochemical importance2-4. To thrive in their competitive oligotrophic environment, these bacteria rely heavily on solute-binding proteins that facilitate uptake of specific substrates via membrane transporters5,6. The functions and properties of these transport proteins are key factors in the assimilation of dissolved organic matter and biogeochemical cycling of nutrients in the ocean, but they have remained largely inaccessible to experimental investigation. Here we performed genome-wide experimental characterization of all solute-binding proteins in a prototypical SAR11 bacterium, revealing specific functions and general trends in their properties that contribute to the success of SAR11 bacteria in oligotrophic environments. We found that the solute-binding proteins of SAR11 bacteria have extremely high binding affinity (dissociation constant >20 pM) and high binding specificity, revealing molecular mechanisms of oligotrophic adaptation. Our functional data have uncovered new carbon sources for SAR11 bacteria and enable accurate biogeographical analysis of SAR11 substrate uptake capabilities throughout the ocean. This study provides a comprehensive view of the substrate uptake capabilities of ubiquitous marine bacteria, providing a necessary foundation for understanding their contribution to assimilation of dissolved organic matter in marine ecosystems.
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Affiliation(s)
- Ben E Clifton
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan.
| | - Uria Alcolombri
- Department of Plant and Environmental Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gen-Ichiro Uechi
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
- ARC Centre of Excellence in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Paola Laurino
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan.
- Institute for Protein Research, Osaka University, Suita, Japan.
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24
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Chen XL, Wu LJ, Miao LL, Li L, Qiu LM, Zhu HQ, Si XR, Li HF, Zhao QL, Qi PZ, Hou TT. Chronic polystyrene microplastics exposure-induced changes in thick-shell mussel (Mytilus coruscus) metaorganism: A holistic perspective. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 284:116961. [PMID: 39208580 DOI: 10.1016/j.ecoenv.2024.116961] [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: 05/17/2024] [Revised: 08/19/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Microplastics have emerged as a significant global concern, particularly in marine ecosystems. While extensive research has focused on the toxicological effects of microplastics on marine animals and/or their associated microorganisms as two separate entities, the holistic perspective of the adaptability and fitness of a marine animal metaorganism-comprising the animal host and its microbiome-remains largely unexplored. In this study, mussel metaorganisms subjected chronic PS-MPs exposure experienced acute mortality but rapidly adapted. We investigated the response of innate immunity, digestive enzymes and their associated microbiomes to chronic PS-MPs exposure. We found that PS-MPs directly and indirectly interacted with the host and microbe within the exposure system. The adaptation was a joint effort between the physiological adjustments of mussel host and genetic adaptation of its microbiome. The mussel hosts exhibited increased antioxidant activity, denser gill filaments and increased immune cells, enhancing their innate immunity. Concurrently, the gill microbiome and the digestive gland microbiome respective selectively enriched for plastic-degrading bacteria and particulate organic matter-utilizing bacteria, facilitating the microbiome's adaptation. The microbial adaptation to chronic PS-MPs exposure altered the ecological roles of mussel microbiome, as evidenced by alterations in microbial interactions and nutrient cycling functions. These findings provided new insights into the ecotoxicological impact of microplastics on marine organisms from a metaorganism perspective.
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Affiliation(s)
- Xing-Lu Chen
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Lin-Jun Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Li-Li Miao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei Li
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China; East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China
| | - Long-Mei Qiu
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Hui-Qiang Zhu
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Xi-Rui Si
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Hong-Fei Li
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Qiao-Ling Zhao
- Zhoushan Institute for Food and Drug Control, Zhoushan, Zhejiang 316000, China
| | - Peng-Zhi Qi
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Ting-Ting Hou
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China.
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Romero F, Labouyrie M, Orgiazzi A, Ballabio C, Panagos P, Jones A, Tedersoo L, Bahram M, Guerra CA, Eisenhauer N, Tao D, Delgado-Baquerizo M, García-Palacios P, van der Heijden MGA. Soil health is associated with higher primary productivity across Europe. Nat Ecol Evol 2024; 8:1847-1855. [PMID: 39192006 DOI: 10.1038/s41559-024-02511-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 07/19/2024] [Indexed: 08/29/2024]
Abstract
Soil health is expected to be of key importance for plant growth and ecosystem functioning. However, whether soil health is linked to primary productivity across environmental gradients and land-use types remains poorly understood. To address this gap, we conducted a pan-European field study including 588 sites from 27 countries to investigate the link between soil health and primary productivity across three major land-use types: woodlands, grasslands and croplands. We found that mean soil health (a composite index based on soil properties, biodiversity and plant disease control) in woodlands was 31.4% higher than in grasslands and 76.1% higher than in croplands. Soil health was positively linked to cropland and grassland productivity at the continental scale, whereas climate best explained woodland productivity. Among microbial diversity indicators, we observed a positive association between the richness of Acidobacteria, Firmicutes and Proteobacteria and primary productivity. Among microbial functional groups, we found that primary productivity in croplands and grasslands was positively related to nitrogen-fixing bacteria and mycorrhizal fungi and negatively related to plant pathogens. Together, our results point to the importance of soil biodiversity and soil health for maintaining primary productivity across contrasting land-use types.
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Affiliation(s)
- Ferran Romero
- Plant-Soil Interactions group, Agroscope, Zurich, Switzerland.
| | - Maëva Labouyrie
- Plant-Soil Interactions group, Agroscope, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- European Commission, Joint Research Centre, Ispra, Italy
| | - Alberto Orgiazzi
- European Commission, Joint Research Centre, Ispra, Italy
- European Dynamics, Brussels, Belgium
| | | | - Panos Panagos
- European Commission, Joint Research Centre, Ispra, Italy
| | - Arwyn Jones
- European Commission, Joint Research Centre, Ispra, Italy
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Mohammad Bahram
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | - Carlos A Guerra
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
- Departamento de Geografía, Universidade de Coimbra, Coimbra, Portugal
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Dongxue Tao
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Seville, Spain
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Seville, Spain
| | - Pablo García-Palacios
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Marcel G A van der Heijden
- Plant-Soil Interactions group, Agroscope, Zurich, Switzerland.
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.
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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.
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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.
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27
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Litchman E, Villéger S, Zinger L, Auguet JC, Thuiller W, Munoz F, Kraft NJB, Philippot L, Violle C. Refocusing the microbial rare biosphere concept through a functional lens. Trends Ecol Evol 2024; 39:923-936. [PMID: 38987022 DOI: 10.1016/j.tree.2024.06.005] [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: 10/06/2023] [Revised: 06/04/2024] [Accepted: 06/11/2024] [Indexed: 07/12/2024]
Abstract
The influential concept of the rare biosphere in microbial ecology has underscored the importance of taxa occurring at low abundances yet potentially playing key roles in communities and ecosystems. Here, we refocus the concept of rare biosphere through a functional trait-based lens and provide a framework to characterize microbial functional rarity, a combination of numerical scarcity across space or time and trait distinctiveness. We demonstrate how this novel interpretation of the rare biosphere, rooted in microbial functions, can enhance our mechanistic understanding of microbial community structure. It also sheds light on functionally distinct microbes, directing conservation efforts towards taxa harboring rare yet ecologically crucial functions.
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Affiliation(s)
- Elena Litchman
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA; Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA.
| | | | - Lucie Zinger
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France; Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300, CNRS, Institut de Recherche pour le Développement (IRD), Toulouse INP, Université Toulouse 3 Paul Sabatier, Toulouse, France
| | | | - Wilfried Thuiller
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - François Munoz
- Université Grenoble Alpes, CNRS, LIPhy, F-38000 Grenoble, France
| | - Nathan J B Kraft
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Laurent Philippot
- Université Bourgogne Franche-Comté, INRAE, Institut Agro Dijon, Agroecology, Dijon, France
| | - Cyrille Violle
- CEFE, Université Montpellier, CNRS, IRD, EPHE, Montpellier, France
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Zhang Z, Lu J, Zhang S, Tian Z, Feng C, Liu Y. Analysis of bacterial community structure, functional variation, and assembly mechanisms in multi-media habitats of lakes during the frozen period. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 284:116903. [PMID: 39205354 DOI: 10.1016/j.ecoenv.2024.116903] [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: 05/19/2024] [Revised: 08/13/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024]
Abstract
Ice, water, and sediment represent three interconnected habitats in lake ecosystems, and bacteria are crucial for maintaining ecosystem equilibrium and elemental cycling across these habitats. However, the differential characteristics and driving mechanisms of bacterial community structures in the ice, water, and sediments of seasonally frozen lakes remain unclear. In this study, high-throughput sequencing technology was used to analyze and compare the structure, function, network characteristics, and assembly mechanisms of bacterial communities in the ice, water, and sediment of Wuliangsuhai, a typical cold region in Inner Mongolia. The results showed that the bacterial communities in the ice and water phases had similar diversity and composition, with Proteobacteria, Bacteroidota, Actinobacteria, Campilobacterota, and Cyanobacteria as dominant phyla. The bacterial communities in sediments displayed significant differences from ice and water, with Chloroflexi, Proteobacteria, Firmicutes, Desulfobacterota, and Acidobacteriota being the dominant phyla. Notably, the bacterial communities in water exhibited higher spatial variability in their distribution than those in ice and sediment. This study also revealed that during the frozen period, the bacterial community species in the ice, water, and sediment media were dominated by cooperative relationships. Community assembly was primarily influenced by stochastic processes, with dispersal limitation and drift identified as the two most significant factors within this process. However, heterogeneous selection also played a significant role in the community composition. Furthermore, functions related to nitrogen, phosphorus, sulfur, carbon, and hydrogen cycling vary among bacterial communities in ice, water, and sediment. These findings elucidate the intrinsic mechanisms driving variability in bacterial community structure and changes in water quality across different media phases (ice, water, and sediment) in cold-zone lakes during the freezing period, offering new insights for water environmental protection and ecological restoration efforts in such environments.
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Affiliation(s)
- Zixuan Zhang
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Junping Lu
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Inner Mongolia Autonomous Region Key Laboratory of Water Resources Protection and Utilization, Hohhot 010018, China; Collaborative Innovation Center for Integrated Management of Water Resources and Water Environment in Inner Mongolia Section of the Yellow River Basin, Hohhot 010018, China.
| | - Sheng Zhang
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Inner Mongolia Autonomous Region Key Laboratory of Water Resources Protection and Utilization, Hohhot 010018, China; Collaborative Innovation Center for Integrated Management of Water Resources and Water Environment in Inner Mongolia Section of the Yellow River Basin, Hohhot 010018, China
| | - Zhiqiang Tian
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Chen Feng
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yinghui Liu
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
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29
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Ljubešić Z, Mihanović H, Matek A, Mucko M, Achterberg EP, Omand M, Pestorić B, Lučić D, Čižmek H, Čolić B, Balestra C, Casotti R, Janeković I, Orlić M. Marine plankton community and net primary production responding to island-trapped waves in a stratified oligotrophic ecosystem. Heliyon 2024; 10:e37788. [PMID: 39323781 PMCID: PMC11422578 DOI: 10.1016/j.heliyon.2024.e37788] [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: 01/20/2024] [Revised: 08/31/2024] [Accepted: 09/10/2024] [Indexed: 09/27/2024] Open
Abstract
The oligotrophic Adriatic Sea is characterized during a typical summer by low productivity caused by strong water column stratification, which inhibits vertical mixing and nutrient supply to the euphotic zone. These conditions can be disrupted by transient physical forcing, which enhances nutrient fluxes and creates localized hotspots of relatively high net primary production. In this study, plankton abundance and diversity were investigated in relation to the physical forcing and nutrient concentrations in an area affected by island-trapped waves (ITWs) near Lastovo Island (Adriatic Sea). The episodic ITW events resulted in enhanced uplift and vertical excursion of the thermocline, marked by anomalously higher nutrient concentrations and a corresponding increase in net primary production in the thermocline layer. Physicochemical properties explained 11.7 % (p = 0.002) of the variability in micro- and nanophytoplankton and 88.9 % (p = 0.001) in the picoplankton community. A significant response to the ITW phenomenon in the plankton community composition (p = 0.001) was observed for bacterioplankton. Among the identified amplicon sequence variances, primary producers were scarce and mainly represented cyanobacteria (Synechococcus strain CC9902), stramenopiles (Pelagomonas), and chlorophytes (Ostreococcus). The remaining amplicon sequence variances were assigned to the classes Copepoda, parasitic fungi (Meyerozyma spp.), mixotrophic dinoflagellates (family Peridiniales, mostly the genus Blastodinium), and parasitic Ciliophora (Scuticociliata). Bacterial ecological functions corresponded to chemoheterotrophic, degradation, and fermentation processes, whereas samples collected after the most intense ITW episode also showed abundant bacteria linked to microplastic degradation and parasitosis. These results highlight the ecological role of localized physical phenomena in enhancing nearshore primary productivity and fine shifts in plankton taxa in oligotrophic systems.
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Affiliation(s)
- Zrinka Ljubešić
- University of Zagreb, Faculty of Science, Department of Biology, Horvatovac 102A, 10000, Zagreb, Croatia
| | - Hrvoje Mihanović
- Institute of Oceanography and Fisheries, Šetalište I. Meštrovića 63, 21000, Split, Croatia
| | - Antonija Matek
- University of Zagreb, Faculty of Science, Department of Biology, Horvatovac 102A, 10000, Zagreb, Croatia
| | - Maja Mucko
- University of Zagreb, Faculty of Science, Department of Biology, Horvatovac 102A, 10000, Zagreb, Croatia
| | - Eric P. Achterberg
- GEOMAR Helmholtz Centre for Ocean Research, Kiel Wischhofstraße 1-3, D-24148, Kiel, Germany
| | - Melissa Omand
- University of Rhode Island, Graduate School of Oceanography, 215 South Ferry Rd, Narragansett, RI, 02882, USA
| | - Branka Pestorić
- University of Montenegro, Institute of Marine Biology, Put I Bokeljske brigade 68, 85330, Kotor, Montenegro
| | - Davor Lučić
- University of Dubrovnik, Institute for Marine and Coastal Research, Kneza Damjana Jude 12, 20000 Dubrovnik, Croatia
| | - Hrvoje Čižmek
- Marine Explorers Society 20.000 leagues, Put Bokanjca 26A, 23000, Zadar, Croatia
| | - Barbara Čolić
- Marine Explorers Society 20.000 leagues, Put Bokanjca 26A, 23000, Zadar, Croatia
| | - Cecilia Balestra
- National Institute of Oceanography and Applied Geophysics – OGS, Borgo Grotta Gigante 42/C, 34010 Sgonico (TS), Italy
| | - Raffaella Casotti
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Ivica Janeković
- Ocean Graduate School and the UWA Oceans Institute, The University of Western Australia, Cnr Fairway and Service Road 4, M470, Crawley, WA, 6009, Australia
- GEKOM (Geophysical and Ecological Modelling) Ltd, Fallerovo šetalište 22, 10000, Zagreb, Croatia
| | - Mirko Orlić
- University of Zagreb, Faculty of Science, Department of Geophysics, Horvatovac 95, 10000, Zagreb, Croatia
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30
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Kolda A, Mucko M, Rapljenović A, Ljubešić Z, Pikelj K, Kwokal Ž, Fajković H, Cuculić V. Beach wracks microbiome and its putative function in plastic polluted Mediterranean marine ecosystem. MARINE ENVIRONMENTAL RESEARCH 2024; 202:106769. [PMID: 39369653 DOI: 10.1016/j.marenvres.2024.106769] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/18/2024] [Accepted: 09/24/2024] [Indexed: 10/08/2024]
Abstract
The coasts of the world's oceans and seas accumulate various types of floating debris, commonly known as beach wracks, including organic seaweeds, seagrass, and ubiquitous anthropogenic waste, mainly plastic. Beach wrack microbiome (MB), surviving in the form of a biofilm, ensures decomposition and remineralization of wracks, but can also serve as a vector of potential pathogens in the environment. Through the interdisciplinary approach and comprehensive sampling design that includes geological analysis of the sediment, plastic debris composition analysis (ATR-FTIR) and application of 16S rRNA gene metabarcoding of beach wrack MBs, this study aims to describe MB in relation to beach exposure, sediment type and plastic pollution. Major contributors in beach wrack MB were Proteobacteria, Bacteroidetes, Actinobacteria, Planctomycetes, Verrucomicrobia and Firmicutes and there was significant dissimilarity between sample groups with Vibrio, Cobetia and Planococcus shaping the Exposed beach sample group and Cyclobacteriaceae and Flavobacterium shaping the Sheltered beach sample group. Our results suggest plastisphere MB is mostly shaped by beach exposure, type of seagrass, sediment type and probably beach naturalness with heavy influence of seawater MB and shows no significant dissimilarity between MBs from a variety of microplastics (MP). Putative functional analysis of MB detected plastic degradation and potential human pathogen bacteria in both beach wrack and seawater MB. The research provides the next crucial step in beach wrack MP accumulation research, MB composition and functional investigation with focus on beach exposure as an important variable.
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Affiliation(s)
- Anamarija Kolda
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Zagreb, Croatia
| | - Maja Mucko
- University of Zagreb, Faculty of Science, Department of Biology, Zagreb, Croatia.
| | - Ana Rapljenović
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Zagreb, Croatia
| | - Zrinka Ljubešić
- University of Zagreb, Faculty of Science, Department of Biology, Zagreb, Croatia
| | - Kristina Pikelj
- University of Zagreb, Faculty of Science, Department of Geology, Zagreb, Croatia
| | - Željko Kwokal
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Zagreb, Croatia
| | - Hana Fajković
- University of Zagreb, Faculty of Science, Department of Geology, Zagreb, Croatia
| | - Vlado Cuculić
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Zagreb, Croatia
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31
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Xu H, Wang S, Sun Y, Yu T, Yang H, Xu G. Enhancing nitrogen removal by simultaneous nitritation and denitritation in a multi-cycle SBR with supplementation of solid carbon sources. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 370:122672. [PMID: 39326074 DOI: 10.1016/j.jenvman.2024.122672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 08/30/2024] [Accepted: 09/24/2024] [Indexed: 09/28/2024]
Abstract
Simultaneous nitritation and denitritation have the potential to significantly improve nitrogen removal in sewage treatment processes. However, their application in low-strength sewage treatment systems presents challenges. This study explored the impact of four solid carbon sources (SCSs) on N-removal via nitrite in a multi-cycle SBR with biocarriers. Results showed that both N-removal efficiencies and nitrite accumulation rates increased with higher COD/N ratios, indicating that high COD/N ratios can improve the competition between denitrifiers and nitrite-oxidizing bacteria for nitrite, leading to stable simultaneous nitritation and denitritation. The supplementation of SCSs further enhanced this high-efficiency N-removal process, with polybutylene succinate (PBS) and polycaprolactone (PCL) showing greater increases in N-removal via nitrite than poly-hydroxybutyrate (PHB) and poly-hydroxyalkanoate (PHA). Moreover, PBS showed the most significant increase in denitrification efficiency in anoxic conditions, while PHA was the most effective external SCS at a moderate level of dissolved oxygen. These findings suggest that the incorporation of external SCSs can facilitate the simultaneous nitritation and denitrification process in multi-cycle SBRs, underscoring the importance of selecting an appropriate SCS for optimizing nitrogen removal in sewage treatment projects.
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Affiliation(s)
- Huchun Xu
- College of Marine Technology and Environment, Dalian Ocean University, Dalian, 116023, PR China; Key Laboratory of Nearshore Marine Environmental Science and Technology in Liaoning Province, Dalian Ocean University, Dalian, 116023, PR China
| | - Siya Wang
- College of Marine Technology and Environment, Dalian Ocean University, Dalian, 116023, PR China; Key Laboratory of Nearshore Marine Environmental Science and Technology in Liaoning Province, Dalian Ocean University, Dalian, 116023, PR China
| | - Yuxin Sun
- College of Marine Technology and Environment, Dalian Ocean University, Dalian, 116023, PR China; Key Laboratory of Nearshore Marine Environmental Science and Technology in Liaoning Province, Dalian Ocean University, Dalian, 116023, PR China
| | - Ting Yu
- College of Marine Technology and Environment, Dalian Ocean University, Dalian, 116023, PR China; Key Laboratory of Nearshore Marine Environmental Science and Technology in Liaoning Province, Dalian Ocean University, Dalian, 116023, PR China
| | - Hui Yang
- College of Marine Technology and Environment, Dalian Ocean University, Dalian, 116023, PR China; Key Laboratory of Nearshore Marine Environmental Science and Technology in Liaoning Province, Dalian Ocean University, Dalian, 116023, PR China
| | - Guangjing Xu
- College of Marine Technology and Environment, Dalian Ocean University, Dalian, 116023, PR China; Key Laboratory of Nearshore Marine Environmental Science and Technology in Liaoning Province, Dalian Ocean University, Dalian, 116023, PR China.
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32
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Li D, Wang L, Jiang F, Zeng X, Xu Q, Zhang X, Zheng Q, Shao Z. Unveiling the microbial diversity across the northern Ninety East Ridge in the Indian Ocean. Front Microbiol 2024; 15:1436735. [PMID: 39380675 PMCID: PMC11458393 DOI: 10.3389/fmicb.2024.1436735] [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: 05/22/2024] [Accepted: 09/03/2024] [Indexed: 10/10/2024] Open
Abstract
Prokaryotes play a crucial role in marine ecosystem health and drive biogeochemical processes. The northern Ninety East Ridge (NER) of the Indian Ocean, a pivotal yet understudied area for these cycles, has been the focus of our study. We employed high-throughput 16S rRNA gene sequencing to analyze 35 water samples from five stations along the ridge, categorized into three depth- and dissolved oxygen-level-based groups. Our approach uncovered a clear stratification of microbial communities, with key bioindicators such as Prochlorococcus MIT9313, Sva0996 marine group, and Candidatus Actinomarina in the upper layer; Ketobacter, Pseudophaeobacter, Nitrospina, and SAR324 clade in the middle layer; and Methylobacterium-Methylorubrum, Sphingomonas, Sphingobium, and Erythrobacter in the deep layer. Methylobacterium-Methylorubrum emerged as the most abundant bacterial genus, while Nitrosopumilaceae predominated among archaeal communities. The spatial and depth-wise distribution patterns revealed that Ketobacter was unique to the northern NER, whereas Methylobacterium-Methylorubrum, UBA10353, SAR324 clade, SAR406, Sva0996_marine_group, Candidatus Actinomarina were ubiquitous across various marine regions, exhibiting niche differentiation at the OTU level. Environmental factors, especially dissolved oxygen (DO), silicate, nitrate, and salinity, significantly influence community structure. These findings not only reveal the novelty and adaptability of the microbial ecosystem in the northern NER but also contribute to the broader understanding of marine microbial diversity and its response to environmental heterogeneity.
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Affiliation(s)
- Ding Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen, China
| | - Liping Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Fan Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen, China
| | - Xiang Zeng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Qinzeng Xu
- First Institute of Oceanography, Ministry of Natural Resources of PR China, Qingdao, Shandong, China
| | - Xuelei Zhang
- First Institute of Oceanography, Ministry of Natural Resources of PR China, Qingdao, Shandong, China
| | - Qiang Zheng
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen, China
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33
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Karavaeva V, Sousa FL. Navigating the archaeal frontier: insights and projections from bioinformatic pipelines. Front Microbiol 2024; 15:1433224. [PMID: 39380680 PMCID: PMC11459464 DOI: 10.3389/fmicb.2024.1433224] [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: 05/15/2024] [Accepted: 08/28/2024] [Indexed: 10/10/2024] Open
Abstract
Archaea continues to be one of the least investigated domains of life, and in recent years, the advent of metagenomics has led to the discovery of many new lineages at the phylum level. For the majority, only automatic genomic annotations can provide information regarding their metabolic potential and role in the environment. Here, genomic data from 2,978 archaeal genomes was used to perform automatic annotations using bioinformatics tools, alongside synteny analysis. These automatic classifications were done to assess how good these different tools perform in relation to archaeal data. Our study revealed that even with lowered cutoffs, several functional models do not capture the recently discovered archaeal diversity. Moreover, our investigation revealed that a significant portion of archaeal genomes, approximately 42%, remain uncharacterized. In comparison, within 3,235 bacterial genomes, a diverse range of unclassified proteins is obtained, with well-studied organisms like Escherichia coli having a substantially lower proportion of uncharacterized regions, ranging from <5 to 25%, and less studied lineages being comparable to archaea with the range of 35-40% of unclassified regions. Leveraging this analysis, we were able to identify metabolic protein markers, thereby providing insights into the metabolism of the archaea in our dataset. Our findings underscore a substantial gap between automatic classification tools and the comprehensive mapping of archaeal metabolism. Despite advances in computational approaches, a significant portion of archaeal genomes remains unexplored, highlighting the need for extensive experimental validation in this domain, as well as more refined annotation methods. This study contributes to a better understanding of archaeal metabolism and underscores the importance of further research in elucidating the functional potential of archaeal genomes.
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Affiliation(s)
- Val Karavaeva
- Genome Evolution and Ecology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Ecology and Evolution, University of Vienna, Vienna, Austria
| | - Filipa L. Sousa
- Genome Evolution and Ecology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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34
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Li L, Li B, Li Q, Wang L, Yang H. Root Endophytic Microorganisms Contribute to the Attribute of Full-Year Shooting in Woody Bamboo Cephalostachyum pingbianense. Microorganisms 2024; 12:1927. [PMID: 39338601 PMCID: PMC11434196 DOI: 10.3390/microorganisms12091927] [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: 08/19/2024] [Revised: 09/18/2024] [Accepted: 09/19/2024] [Indexed: 09/30/2024] Open
Abstract
Cephalostachyum pingbianense (Hsueh & Y.M. Yang ex Yi et al.) D.Z. Li & H.Q. Yang is unique among bamboo species for its ability to produce bamboo shoots in all seasons under natural conditions. Apart from the physiological mechanism, information regarding the effects of endophytic microorganisms on this full-year shooting characteristic is limited. We hypothesize that root endophytic microorganisms will have a positive impact on the full-year bamboo shooting characteristic of C. pingbianense by increasing the availability or supply of nutrients. To identify the seasonal variations in the root endophytic bacterial and fungal communities of C. pingbianense, and to assess their correlation with bamboo shoot productivity, the roots of C. pingbianense were selected as research materials, and the 16S rRNA and ITS rDNA genes of root endophytic microorganisms were sequenced using the Illumina platform. Following this sequencing, raw sequencing reads were processed, and OTUs were annotated. Alpha and beta diversity, microbial composition, and functional predictions were analyzed, with correlations to bamboo shoot numbers assessed. The results showed that seasonal changes significantly affected the community diversity and structure of root endophytic microbes of C. pingbianense. Bacterial communities in root samples from all seasons contained more nitrogen-fixing microorganisms, with members of the Burkholderiales and Rhizobiales predominating. The relative abundances of ectomycorrhizal and arbuscular mycorrhizal fungi in the autumn sample were significantly higher than in other seasons. Correlation analysis revealed that the bamboo shoot productivity was significantly and positively correlated with bacterial functions of nitrogen fixation, arsenate detoxification, and ureolysis, as well as with symbiotrophic fungi, ectomycorrhizal fungi, and arbuscular mycorrhizal fungi. At the genus level, the bacterial genus Herbaspirillum and the fungal genera Russula, unclassified_f_Acaulosporaceae, and unclassified_f_Glomeraceae were found to have a significant positive correlation with bamboo shoot number. Our study provides an ecological perspective for understanding the highly productive attribute of C. pingbianense and offers new insights into the forest management of woody bamboos.
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Affiliation(s)
- Lushuang Li
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China;
- Forestry College, Southwest Forestry University, Kunming 650224, China
| | - Bin Li
- Horticultural Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China;
| | - Qing Li
- Yunnan Forestry Double Center, Yunnan Forestry and Grassland Bureau, Kunming 650051, China;
| | - Lianchun Wang
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China;
| | - Hanqi Yang
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650233, China
- Key Laboratory of Breeding and Utilization of Resource Insects, National Forestry and Grassland Administration, Kunming 650233, China
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35
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Li M, Li Q, Wang S, Wang X, Li Q, Liu W, Yu J, Zhang G, Wang J, Wu QL, Zeng J. The diversity and biogeography of bacterial communities in lake sediments across different climate zones. ENVIRONMENTAL RESEARCH 2024; 263:120028. [PMID: 39307222 DOI: 10.1016/j.envres.2024.120028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 09/05/2024] [Accepted: 09/17/2024] [Indexed: 09/29/2024]
Abstract
Bacteria are diverse and play important roles in biogeochemical cycling of aquatic ecosystems, but the global distribution patterns of bacterial communities in lake sediments across different climate zones are still obscure. Here we integrated the high-throughput sequencing data of 750 sediment samples from published literature to investigate the distribution of bacterial communities in different climate zones and the potential driving mechanisms. The obtained results indicated that the diversity and richness of bacterial community were notably higher in temperate and cold zones than those in other climate zones. In addition, the bacterial community composition varied significantly in different climate zones, which further led to changes in bacterial functional groups. Specifically, the relative abundance of nitrogen cycling functional groups in polar zones was notably higher compared to other climate zones. Regression analysis revealed that climate (mean annual precipitation, MAP; and mean annual temperature, MAT), vegetation, and geography together determined the diversity pattern of sediment bacterial community on a global scale. The results of partial least squares path modeling further demonstrated that climate was the most significant factor affecting the composition and diversity of bacterial communities, and MAP was the most important climate factor affecting the composition of bacteria community (R2 = 0.443, P < 0.001). It is worth noting that a strong positive correlation was observed between the abundance of the dominant bacterial group uncultured_f_Anaerolineaceae and the normalized difference vegetation index (NDVI; P < 0.001), suggesting that vegetation could affect bacterial community diversity by influencing dominant bacterial taxa. This study enhances our understanding of the global diversity patterns and biogeography of sediment bacteria.
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Affiliation(s)
- Mengyuan Li
- School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China; Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Qiang Li
- National Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Shuren Wang
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xiujun Wang
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Qisheng Li
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Wan Liu
- National Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jianghua Yu
- School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Guoqing Zhang
- National Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jianjun Wang
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Qinglong L Wu
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Jin Zeng
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; Poyang Lake Wetland Research Station, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Jiujiang, 332899, China.
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36
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Shi G, Li H, Fu Q, Li T, Hou R, Chen Q, Xue P. Effects of biochar and compost on the abundant and rare microbial communities assembly and multifunctionality in pesticide-contaminated soil under freeze‒thaw cycles. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 362:125003. [PMID: 39307339 DOI: 10.1016/j.envpol.2024.125003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 08/27/2024] [Accepted: 09/19/2024] [Indexed: 09/27/2024]
Abstract
Biochar and compost are effective ways to improve soil quality and reduce pesticide pollution. However, the effects of them on the abundant and rare microbial communities in freeze‒thaw soil need to be further clarified. Therefore, this study took biochar, compost, and their combination as examples to explore their effects on the abundant and rare microbial communities and multifunctionality in glyphosate, imidacloprid and pyraclostrobin contaminated soil under freeze‒thaw cycles. We found that freeze‒thaw cycles enhanced the functional groups and surface aromaticity of biochar and compost, thereby improving the adsorption capacity. Biochar and compost reduced the concentration and half-life of three pesticides and enhanced the degradation function of rare taxa in soil. Biochar and compost improved the structure composition and co-occurrence relationship of abundant and rare taxa. Meanwhile, the assembly processes of abundant and rare sub-communities were mainly driven by stochastic processes and the Combined treatment promoted the transition from dispersal limitation to homogenizing dispersal and homogeneous selection. Moreover, the Combined treatment significantly improved the multifunctionality before and after freezing and thawing by increasing the diversity of rare taxa and assembly processes. The results provide new insights for farmland soil remediation in seasonal frozen areas, especially the soil functional cycle of abundant and rare microorganisms.
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Affiliation(s)
- Guoxin Shi
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China; Key Laboratory of Effective Utilization of Agricultural Water Resources of Ministry of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China; Heilongjiang Provincial Key Laboratory of Water Resources and Water Conservancy Engineering in Cold Region, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China; College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
| | - Heng Li
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China; Key Laboratory of Effective Utilization of Agricultural Water Resources of Ministry of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China; Heilongjiang Provincial Key Laboratory of Water Resources and Water Conservancy Engineering in Cold Region, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
| | - Qiang Fu
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China; Key Laboratory of Effective Utilization of Agricultural Water Resources of Ministry of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China; Heilongjiang Provincial Key Laboratory of Water Resources and Water Conservancy Engineering in Cold Region, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China.
| | - Tianxiao Li
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China; Key Laboratory of Effective Utilization of Agricultural Water Resources of Ministry of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China; Heilongjiang Provincial Key Laboratory of Water Resources and Water Conservancy Engineering in Cold Region, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
| | - Renjie Hou
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China; Key Laboratory of Effective Utilization of Agricultural Water Resources of Ministry of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China; Heilongjiang Provincial Key Laboratory of Water Resources and Water Conservancy Engineering in Cold Region, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
| | - Ping Xue
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China; Key Laboratory of Effective Utilization of Agricultural Water Resources of Ministry of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China; Heilongjiang Provincial Key Laboratory of Water Resources and Water Conservancy Engineering in Cold Region, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
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Xie G, Yin Z, Zhang Z, Wang X, Sun C. Microbial diversity and potential functional dynamics within the rhizocompartments of Dendrobium huoshanense. FRONTIERS IN PLANT SCIENCE 2024; 15:1450716. [PMID: 39372857 PMCID: PMC11449778 DOI: 10.3389/fpls.2024.1450716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 09/02/2024] [Indexed: 10/08/2024]
Abstract
Introduction Understanding the microbial diversity and potential functional dynamics within the rhizocompartments of Dendrobium huoshanense is crucial for unraveling the plant-microbe interactions that influence its medicinal properties. Methods This study is the first to characterize the microbiome associated with the rhizocompartments of D. huoshanense, including its cultivation medium, rhizosphere, rhizoplane, and root endosphere, using high-throughput sequencing and subsequent bioinformatic analysis. Results Bacterial phylogenetic diversity was significantly higher in the endosphere than in the rhizosphere, while fungal α-diversity significantly decreased from the cultivation medium to the endosphere. Both bacterial and fungal niche widths decreased from the cultivation medium to the endosphere. β-Diversity analysis revealed distinct spatial patterns in both bacterial and fungal communities across the rhizocompartments, with the most pronounced differences between the cultivation medium and the endosphere. Taxonomically, Proteobacteria and Ascomycota were predominant in the endosphere for bacterial and fungal communities, respectively. Functional predictions showed significant enrichment of pathways related to xenobiotics biodegradation, lipid metabolism, and nitrogen fixation in the endosphere, while functions associated with plant pathogens and saprotrophs were significantly reduced. Discussion The results indicate a shift from generalist to specialist microbes from the cultivation medium to the endosphere, suggesting that D. huoshanense exerts strong selective pressure for endophytic fungi. Interestingly, a high proportion of fungi with unknown functions were found in the endosphere, highlighting an area for further research regarding the medicinal efficacy of D. huoshanense. Overall, this study provides foundational data for understanding the adaptive evolution of these microbial communities in response to specific microhabitats.
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Affiliation(s)
- Guijuan Xie
- College of Biology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Province Key Laboratory for Quality Evaluation and Improvement of Traditional Chinese Medicine, Lu’an, China
- Anhui Engineering Technology Center for Conservation and Utilization of Traditional Chinese Medicine Resource, Lu’an, China
| | - Zhichao Yin
- College of Biology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Zhenlin Zhang
- College of Biology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Xinyu Wang
- College of Biology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Chuanbo Sun
- College of Biology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Province Key Laboratory for Quality Evaluation and Improvement of Traditional Chinese Medicine, Lu’an, China
- Anhui Engineering Technology Center for Conservation and Utilization of Traditional Chinese Medicine Resource, Lu’an, China
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Ramirez LYA, Angell IL, Nilsen T, Rudi K. Delayed Shift in Microbiota Composition in a Marine Microcosm Pollution Experiment. Curr Microbiol 2024; 81:365. [PMID: 39292287 PMCID: PMC11410848 DOI: 10.1007/s00284-024-03869-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 08/21/2024] [Indexed: 09/19/2024]
Abstract
Benthic habitats are the largest habitats on Earth, being essential for marine ecosystem functioning. Benthic habitats are particularly vulnerable towards pollution and anthropogenetic influence due to general oligotrophic nature. We, therefore, simulated pollution events involving nitrate and sulphate, in combination with organic carbon. We then observed the microbiota composition the following month. Surprisingly, upon nitrate addition, an abrupt response was observed between two and three weeks after the pollution event. We observed a threefold reduction in species richness, with a dominance of the genus Pseudarchobacter within the Campylobacteriota phylum, concurring with a decrease in nitrification potential and an increase in Dissimilatory Nitrate Reduction to Ammonium (DNRA) and a regain in denitrification. Likewise, addition of sulphate contributed to a delayed response with reduction in species richness albeit weaker than for nitrate, leading to a shift towards potential spore-forming Firmicutes. There was also an increase in DNRA, but only for the oxic conditions, concurring with a regain in sulphate reductio and denitrification. For the nitrate addition experiments, the delay in response could potentially be attributed to the genus Pseudarchobacter which rely on sulphides for denitrification, while for the sulphate addition experiments, the delayed response might be explained by the germination of spores. The late increase of DNRA may indicate a shift towards a different metabolic regime for nitrogen. In conclusion, our microcosm experiments revealed delayed abrupt microbiota shifts resembling tipping points that can potentially be overlooked in natural ecosystems.
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Affiliation(s)
- Luis Yndy Ariem Ramirez
- Faculty of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway
| | - Inga Leena Angell
- Faculty of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway
| | - Tonje Nilsen
- Faculty of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway
| | - Knut Rudi
- Faculty of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway.
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Xie YP, Zhao HF, Lin S, Wang XL, Liu YF, Xie BY. Suppression of certain intestinal microbiota metabolites may lead to gestational diabetes in mice fed a high-fat diet. Front Microbiol 2024; 15:1473441. [PMID: 39351297 PMCID: PMC11439706 DOI: 10.3389/fmicb.2024.1473441] [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: 07/31/2024] [Accepted: 09/02/2024] [Indexed: 10/04/2024] Open
Abstract
Background We aim to establish a gestational diabetes mellitus (GDM) mouse model with mice fed with a high-fat diet (HFD) in comparison with pregnant mice with normal blood glucose levels to investigate the role of intestinal microbiota in the development of HFD-induced GDM. Methods We divided healthy 6-week-old female C57BL mice into an HFD-induced GDM group and a normal diet group. Their bacterial flora and metabolites in intestinal fecal exosomes were co-analyzed using 16 s multi-region sequencing and compared. Findings Alpha (α) diversity was lower within the model group compared to the control group. Beta (β) diversity was significantly different between the two groups. The relative abundances of Lactobacillus, Actinomyces, Rothia, and Bacteroidetes were significantly different between the two groups. Fermentation and nitrate consumption were significantly higher in the GDM group. Multiple bacteria were associated with glycerophosphocholine, S-methyl-5'-thioadenosine, quinolinate, galactinol, deoxyadenosine, DL-arginine, and 2-oxoadenic acid. Interpretation Imbalances in the production of Lactobacillus, Bacteroidetes, Actinomyces, and Rothia and their related metabolites may lead to metabolic disturbances in GDM. These indicators may be used to assess changes affecting the intestinal microbiota during pregnancy and thus help modulate diet and alter blood glucose.
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Affiliation(s)
- Ya-ping Xie
- Nursing Department, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Hui-fen Zhao
- Nursing Department, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Shu Lin
- Centre of Neurological and Metabolic Research, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
- Group of Neuroendocrinology, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Xian-long Wang
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China
| | - Yi-fei Liu
- Central Laboratory, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Bao-yuan Xie
- Nursing Department, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
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Huang R, Zhang P, Zhang X, Chen S, Sun J, Jiang X, Zhang D, Li H, Yi X, Qu L, Wang T, Gao K, Hall-Spencer JM, Adams J, Gao G, Lin X. Ocean acidification alters microeukaryotic and bacterial food web interactions in a eutrophic subtropical mesocosm. ENVIRONMENTAL RESEARCH 2024; 257:119084. [PMID: 38823617 DOI: 10.1016/j.envres.2024.119084] [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: 10/26/2023] [Revised: 05/03/2024] [Accepted: 05/04/2024] [Indexed: 06/03/2024]
Abstract
Ocean acidification (OA) is known to influence biological and ecological processes, mainly focusing on its impacts on single species, but little has been documented on how OA may alter plankton community interactions. Here, we conducted a mesocosm experiment with ambient (∼410 ppmv) and high (1000 ppmv) CO2 concentrations in a subtropical eutrophic region of the East China Sea and examined the community dynamics of microeukaryotes, bacterioplankton and microeukaryote-attached bacteria in the enclosed coastal seawater. The OA treatment with elevated CO2 affected taxa as the phytoplankton bloom stages progressed, with a 72.89% decrease in relative abundance of the protist Cercozoa on day 10 and a 322% increase in relative abundance of Stramenopile dominated by diatoms, accompanied by a 29.54% decrease in relative abundance of attached Alphaproteobacteria on day 28. Our study revealed that protozoans with different prey preferences had differing sensitivity to high CO2, and attached bacteria were more significantly affected by high CO2 compared to bacterioplankton. Our findings indicate that high CO2 changed the co-occurrence network complexity and stability of microeukaryotes more than those of bacteria. Furthermore, high CO2 was found to alter the proportions of potential interactions between phytoplankton and their predators, as well as microeukaryotes and their attached bacteria in the networks. The changes in the relative abundances and interactions of microeukaryotes between their predators in response to high CO2 revealed in our study suggest that high CO2 may have profound impacts on marine food webs.
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Affiliation(s)
- Ruiping Huang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; State Key Laboratory of Marine Resources Utilization in South China Sea, School of Marine Biology and Fisheries, Hainan University, Haikou, China
| | - Ping Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; Xiamen City Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen, China
| | - Xu Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; Xiamen City Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen, China
| | - Shouchang Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Jiazhen Sun
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xiaowen Jiang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Di Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - He Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xiangqi Yi
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Liming Qu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Tifeng Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Kunshan Gao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Jason M Hall-Spencer
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka 415-0025, Japan; School of Geography and Oceanography, Nanjing University, Nanjing, China
| | - Jonathan Adams
- School of Geography and Oceanography, Nanjing University, Nanjing, China
| | - Guang Gao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; Xiamen City Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen, China.
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Xie G, Zhang Y, Gong Y, Luo W, Tang X. Extreme trophic tales: deciphering bacterial diversity and potential functions in oligotrophic and hypereutrophic lakes. BMC Microbiol 2024; 24:348. [PMID: 39277721 PMCID: PMC11401395 DOI: 10.1186/s12866-024-03488-x] [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: 02/18/2024] [Accepted: 09/02/2024] [Indexed: 09/17/2024] Open
Abstract
BACKGROUND Oligotrophy and hypereutrophy represent the two extremes of lake trophic states, and understanding the distribution of bacterial communities across these contrasting conditions is crucial for advancing aquatic microbial research. Despite the significance of these extreme trophic states, bacterial community characteristics and co-occurrence patterns in such environments have been scarcely interpreted. To bridge this knowledge gap, we collected 60 water samples from Lake Fuxian (oligotrophic) and Lake Xingyun (hypereutrophic) during different hydrological periods. RESULTS Employing 16S rRNA gene sequencing, our findings revealed distinct community structures and metabolic potentials in bacterial communities of hypereutrophic and oligotrophic lake ecosystems. The hypereutrophic ecosystem exhibited higher bacterial α- and β-diversity compared to the oligotrophic ecosystem. Actinobacteria dominated the oligotrophic Lake Fuxian, while Cyanobacteria, Proteobacteria, and Bacteroidetes were more prevalent in the hypereutrophic Lake Xingyun. Functions associated with methanol oxidation, methylotrophy, fermentation, aromatic compound degradation, nitrogen/nitrate respiration, and nitrogen/nitrate denitrification were enriched in the oligotrophic lake, underscoring the vital role of bacteria in carbon and nitrogen cycling. In contrast, functions related to ureolysis, human pathogens, animal parasites or symbionts, and phototrophy were enriched in the hypereutrophic lake, highlighting human activity-related disturbances and potential pathogenic risks. Co-occurrence network analysis unveiled a more complex and stable bacterial network in the hypereutrophic lake compared to the oligotrophic lake. CONCLUSION Our study provides insights into the intricate relationships between trophic states and bacterial community structure, emphasizing significant differences in diversity, community composition, and network characteristics between extreme states of oligotrophy and hypereutrophy. Additionally, it explores the nuanced responses of bacterial communities to environmental conditions in these two contrasting trophic states.
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Affiliation(s)
- Guijuan Xie
- College of Biology and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yuqing Zhang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
- The Third Construction Company of CCCC second Harbor Engineering Co., Ltd, Zhenjiang, 212000, China
| | - Yi Gong
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Wenlei Luo
- Taihu Laboratory for Lake Ecosystem Research, 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, Yunnan, 653100, Yuxi, China
| | - Xiangming Tang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
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Jiang H, Okoye CO, Chen X, Zhang F, Jiang J. High-throughput 16S rRNA gene-based amplicon sequencing reveals the functional divergence of halophilic bacterial communities in the Suaeda salsa root compartments on the eastern coast of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 942:173775. [PMID: 38844238 DOI: 10.1016/j.scitotenv.2024.173775] [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: 04/04/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/13/2024]
Abstract
The rhizosphere environment of plants, which harbors halophilic bacterial communities, faces significant challenges in coping with environmental stressors, particularly saline soil properties. This study utilizes a high-throughput 16S rRNA gene-based amplicon sequencing to investigate the variations in bacterial community dynamics in rhizosphere soil (RH), root surface soil (RS), root endophytic bacteria (PE) compartments of Suaeda salsa roots, and adjoining soils (CK) across six locations along the eastern coast of China: Nantong (NT), Yancheng (YC), Dalian (DL), Tianjin (TJ), Dongying (DY), and Qingdao (QD), all characterized by chloride-type saline soil. Variations in the physicochemical properties of the RH compartment were also evaluated. The results revealed significant changes in pH, electrical conductivity, total salt content, and ion concentrations in RH samples from different locations. Notably, the NT location exhibited the highest alkalinity and nitrogen availability. The pH variations were linked to HCO3- accumulation in S. salsa roots, while salinity stress influenced soil pH through H+ discharge. Despite salinity stress, enzymatic activities such as catalase and urease were higher in soils from various locations. The diversity and richness of bacterial communities were higher in specific locations, with Proteobacteria dominating PE samples from the DL location. Additionally, Vibrio and Marinobacter were prevalent in RH samples. Significant correlations were found between soil pH, salinity, nutrient content, and the abundance and diversity of bacterial taxa in RH samples. Bioinformatics analysis revealed the prevalence of halophilic bacteria, such as Bacillus, Halomonas, and Streptomyces, with diverse metabolic functions, including amino acid and carbohydrate metabolisms. Essential genes, such as auxin response factor (ARF) and GTPase-encoding genes, were abundant in RH samples, suggesting adaptive strategies for harsh environments. Likewise, proline/betaine transport protein genes were enriched, indicating potential bioremediation mechanisms against high salt stress. These findings provide insight into the metabolic adaptations facilitating resilience in saline ecosystems and contribute to understanding the complex interplay between soil conditions, bacterial communities, and plant adaptation.
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Affiliation(s)
- Huifang Jiang
- Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Charles Obinwanne Okoye
- Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China; School of Life Sciences, Jiangsu University, Zhenjiang 212013, China; Department of Zoology & Environmental Biology, University of Nigeria, Nsukka 410001, Nigeria
| | - Xunfeng Chen
- Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Fusheng Zhang
- Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jianxiong Jiang
- Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
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Wang W, Portal-Gonzalez N, Wang X, Li J, Li H, Portieles R, Borras-Hidalgo O, He W, Santos-Bermudez R. Metabolome-driven microbiome assembly determining the health of ginger crop (Zingiber officinale L. Roscoe) against rhizome rot. MICROBIOME 2024; 12:167. [PMID: 39244625 PMCID: PMC11380783 DOI: 10.1186/s40168-024-01885-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 07/27/2024] [Indexed: 09/09/2024]
Abstract
BACKGROUND Plant-associated microorganisms can be found in various plant niches and collectively comprise the plant microbiome. The plant microbiome assemblages have been extensively studied, primarily in model species. However, a deep understanding of the microbiome assembly associated with plant health is still needed. Ginger rhizome rot has been variously attributed to multiple individual causal agents. Due to its global relevance, we used ginger and rhizome rot as a model to elucidate the metabolome-driven microbiome assembly associated with plant health. RESULTS Our study thoroughly examined the biodiversity of soilborne and endophytic microbiota in healthy and diseased ginger plants, highlighting the impact of bacterial and fungal microbes on plant health and the specific metabolites contributing to a healthy microbial community. Metabarcoding allowed for an in-depth analysis of the associated microbial community. Dominant genera represented each microbial taxon at the niche level. According to linear discriminant analysis effect size, bacterial species belonging to Sphingomonas, Quadrisphaera, Methylobacterium-Methylorubrum, Bacillus, as well as the fungal genera Pseudaleuria, Lophotrichus, Pseudogymnoascus, Gymnoascus, Mortierella, and Eleutherascus were associated with plant health. Bacterial dysbiosis related to rhizome rot was due to the relative enrichment of Pectobacterium, Alcaligenes, Klebsiella, and Enterobacter. Similarly, an imbalance in the fungal community was caused by the enrichment of Gibellulopsis, Pyxidiophorales, and Plectosphaerella. Untargeted metabolomics analysis revealed several metabolites that drive microbiome assembly closely related to plant health in diverse microbial niches. At the same time, 6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)oxane-2,3,4,5-tetrol was present at the level of the entire healthy ginger plant. Lipids and lipid-like molecules were the most significant proportion of highly abundant metabolites associated with ginger plant health versus rhizome rot disease. CONCLUSIONS Our research significantly improves our understanding of metabolome-driven microbiome structure to address crop protection impacts. The microbiome assembly rather than a particular microbe's occurrence drove ginger plant health. Most microbial species and metabolites have yet to be previously identified in ginger plants. The indigenous microbial communities and metabolites described can support future strategies to induce plant disease resistance. They provide a foundation for further exploring pathogens, biocontrol agents, and plant growth promoters associated with economically important crops. Video Abstract.
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Affiliation(s)
- Wenbo Wang
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan, Shandong, 250022, People's Republic of China
| | - Nayanci Portal-Gonzalez
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan, Shandong, 250022, People's Republic of China
| | - Xia Wang
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan, Shandong, 250022, People's Republic of China
| | - Jialin Li
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan, Shandong, 250022, People's Republic of China
| | - Hui Li
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan, Shandong, 250022, People's Republic of China
| | - Roxana Portieles
- Joint R&D Center of Biotechnology, RETDA, Yota Bio-Engineering Co., Ltd., 99 Shenzhen Road, Rizhao, Shandong, 276826, People's Republic of China
| | - Orlando Borras-Hidalgo
- Joint R&D Center of Biotechnology, RETDA, Yota Bio-Engineering Co., Ltd., 99 Shenzhen Road, Rizhao, Shandong, 276826, People's Republic of China
| | - Wenxing He
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan, Shandong, 250022, People's Republic of China.
| | - Ramon Santos-Bermudez
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan, Shandong, 250022, People's Republic of China.
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Camuy-Vélez LA, Banerjee S, Sedivec K. Grazing intensity alters network complexity and predator-prey relationships in the soil microbiome. Appl Environ Microbiol 2024:e0042524. [PMID: 39235241 DOI: 10.1128/aem.00425-24] [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: 03/05/2024] [Accepted: 08/13/2024] [Indexed: 09/06/2024] Open
Abstract
Grasslands are recognized as important reservoirs of soil biodiversity. Livestock grazing is implemented as a grassland management strategy to improve soil quality and enhance plant diversity. Soil microbial communities play a pivotal role in grassland ecosystems, so it is important to examine whether grazing practices affect the soil microbiome. Previous studies on grazing have primarily focused on bacteria and fungi, overlooking an important group-protists. Protists are vital in soil microbiomes as they drive nutrient availability and trophic interactions. Determining the impact of grazing on protists and their relationships with bacterial and fungal communities is important for understanding soil microbiome dynamics in grazed ecosystems. In this study, we investigated soil bacterial, fungal, and protist communities under four grazing levels: no grazing, moderate-use grazing, full-use grazing, and heavy-use grazing. Our results showed that heavy grazing led to a greater diversity of protists with specific groups, such as Discoba and Conosa, increasing in abundance. We also found strong associations between protist and bacterial/fungal members, indicating their intricate relationships within the soil microbiome. For example, the abundance of predatory protists increased under grazing while arbuscular mycorrhizal fungi decreased. Notably, arbuscular mycorrhizae were negatively associated with predatory groups. Furthermore, we observed that microbial network complexity increased with grazing intensity, with fungal members playing an important role in the network. Overall, our study reports the impact of temporal grazing intensity on soil microbial dynamics and highlights the importance of considering protist ecology when evaluating the effects of grazing on belowground communities in grassland ecosystems. IMPORTANCE The significance of this study lies in its exploration of the effects of temporal grazing intensity on the dynamics of the soil microbiome, specifically focusing on the often-neglected role of protists. Our findings provide insights into the complex relationships between protists, bacteria, and fungi, emphasizing their impact on trophic interactions in the soil. Gaining a better understanding of these dynamics is essential for developing effective strategies for grassland management and conservation, underscoring the importance of incorporating protist ecology into microbiome studies in grasslands.
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Affiliation(s)
- Lennel A Camuy-Vélez
- Microbiological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Samiran Banerjee
- Microbiological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Kevin Sedivec
- School of Natural Resource Science, North Dakota State University, Fargo, North Dakota, USA
- Central Grasslands Research Extension Center, North Dakota State University, Streeter, North Dakota, USA
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Wang Z, Gao Z, Yu Y, Li H, Luo W, Ji Z, Ding H. New insights into the structure and function of microbial communities in Maxwell Bay, Antarctica. Front Microbiol 2024; 15:1463144. [PMID: 39296290 PMCID: PMC11408308 DOI: 10.3389/fmicb.2024.1463144] [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: 07/11/2024] [Accepted: 08/23/2024] [Indexed: 09/21/2024] Open
Abstract
The microbial communities inhabiting polar ecosystems, particularly in Maxwell Bay, Antarctica, play a pivotal role in nutrient cycling and ecosystem dynamics. However, the diversity of these microbial communities remains underexplored. In this study, we aim to address this gap by investigating the distribution, environmental drivers, and metabolic potential of microorganisms in Maxwell Bay. We analyzed the prokaryotic and eukaryotic microbiota at 11 stations, revealing distinctive community structures and diverse phylum dominance by using high-throughput sequencing. Spatial analysis revealed a significant impact of longitude on microbial communities, with microeukaryotes exhibiting greater sensitivity to spatial factors than microprokaryotes. We constructed co-occurrence networks to explore the stability of microbial communities, indicating the complexity and stability of microprokaryotic communities compared with those of microeukaryotes. Our findings suggest that the microeukaryotic communities in Maxwell Bay are more susceptible to disturbances. Additionally, this study revealed the spatial correlations between microbial communities, diversity, and environmental variables. Redundancy analysis highlighted the significance of pH and dissolved oxygen in shaping microprokaryotic and microeukaryotic communities, indicating the anthropogenic influence near the scientific research stations. Functional predictions using Tax4Fun2 and FUNGuild revealed the metabolic potential and trophic modes of the microprokaryotic and microeukaryotic communities, respectively. Finally, this study provides novel insights into the microbial ecology of Maxwell Bay, expanding the understanding of polar microbiomes and their responses to environmental factors.
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Affiliation(s)
- Zheng Wang
- Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, China
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, China
| | - Zhiwei Gao
- Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, China
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, China
| | - Yong Yu
- Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, China
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Huirong Li
- Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, China
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Luo
- Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, China
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Zhongqiang Ji
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Haitao Ding
- Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, China
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
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Fang K, Kou YP, Tang N, Liu J, Zhang XY, He HL, Xia RX, Zhao WQ, Li DD, Liu Q. Differential responses of soil bacteria, fungi and protists to root exudates and temperature. Microbiol Res 2024; 286:127829. [PMID: 39018940 DOI: 10.1016/j.micres.2024.127829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 06/30/2024] [Indexed: 07/19/2024]
Abstract
The impact of climate warming on soil microbes has been well documented, with studies revealing its effects on diversity, community structure and network dynamics. However, the consistency of soil microbial community assembly, particularly in response to diverse plant root exudates under varying temperature conditions, remains an unresolved issue. To address this issue, we employed a growth chamber to integrate temperature and root exudates in a controlled experiment to examine the response of soil bacteria, fungi, and protists. Our findings revealed that temperature independently regulated microbial diversity, with distinct patterns observed among bacteria, fungi, and protists. Both root exudates and temperature significantly influenced microbial community composition, yet interpretations of these factors varied among prokaryotes and eukaryotes. In addition to phototrophic bacteria and protists, as well as protistan consumers, root exudates determined to varying degrees the enrichment of other microbial functional guilds at specific temperatures. The effects of temperature and root exudates on microbial co-occurrence patterns were interdependent; root exudates primarily simplified the network at low and high temperatures, while responses to temperature varied between single and mixed exudate treatments. Moreover, temperature altered the composition of keystone species within the microbial network, while root exudates led to a decrease in their number. These results emphasize the substantial impact of plant root exudates on soil microbial community responses to temperature, underscoring the necessity for future climate change research to incorporate additional environmental variables.
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Affiliation(s)
- Kai Fang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China; College of Agriculture and Biological Sciences, Dali University, Dali 671003, China
| | - Yong-Ping Kou
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China.
| | - Na Tang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Jia Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Xiao-Ying Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - He-Liang He
- College of Agriculture, Forestry and Food Engineering, Yibin University, Yibin 644007, China
| | - Rui-Xue Xia
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Wen-Qiang Zhao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Dan-Dan Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Qing Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China.
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Shao Q, Ran Q, Li X, Dong C, Zhang Y, Han Y. Differential responses of the phyllosphere abundant and rare microbes of Eucommia ulmoides to phytohormones. Microbiol Res 2024; 286:127798. [PMID: 38964073 DOI: 10.1016/j.micres.2024.127798] [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: 04/04/2024] [Revised: 05/26/2024] [Accepted: 06/05/2024] [Indexed: 07/06/2024]
Abstract
Phyllosphere microbiota play a crucial role in plant productivity and adaptation, and the abundant and rare microbial taxa often possess distinct characteristics and ecological functions. However, it is unclear whether the different subcommunities of phyllosphere microbiota respond variably to the factors that influence their formation, which limits the understanding of community assembly. The effects of two phytohormones, namely, indole-3-acetic acid (IAA) and N6-(delta 2-isopentenyl)-adenine (IP), on the phyllosphere microbial subcommunities of Eucommia ulmoides were investigated using potted experiments. The results demonstrated that the phytohormones induced significant variations in the composition, diversity, and function of the abundant microbial subcommunity in the phyllosphere of E. ulmoides, however, their effects on the rare subcommunity were negligible, and their effects on the moderate subcommunity were between those of the abundant and rare taxa. The phytohormones also induced significant alterations in the phenotypic and physiological properties of E. ulmoides, which indirectly affected the phyllosphere microbial community. Leaf thickness and average leaf area were the main phenotypic variables that affected the composition of the phyllosphere microbial community. The total alkaloid content and activity of superoxide dismutase (SOD) were the main physiological variables that affected the composition of the phyllosphere microbial community. The phenotypic and physiological indices of E. ulmoides explained the variations in the phyllosphere microbial subcommunities in descending order: abundant > moderate > rare taxa. These variables explained a significant proportion of the variations in the abundant taxa, and an insignificant proportion of the variations in the rare taxa. This study improves our understanding of the assembly of the phyllosphere microbiota, which provides important theoretical knowledge for future sustainable agriculture and forestry management based on the precise regulation of phyllosphere microbiota.
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Affiliation(s)
- Qiuyu Shao
- 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, Guizhou 550025, 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, Guizhou 550025, China
| | - Xu 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, Guizhou 550025, 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, Guizhou 550025, China
| | - Yanwei Zhang
- Key Laboratory of Development and Utilization of Biological Resources in Colleges and Universities of Guizhou Province, Guizhou Education University, Guiyang, Guizhou 550018, 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, Guizhou 550025, China.
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Yi P, Li Q, Zhou X, Liang R, Ding X, Wu M, Wang K, Li J, Wang W, Lu G, Zhu T. Inoculation of Saccharomyces cerevisiae for facilitating aerobic composting of acidified food waste. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:55507-55521. [PMID: 39231841 DOI: 10.1007/s11356-024-34876-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 08/27/2024] [Indexed: 09/06/2024]
Abstract
In aerobic composting of food waste, acidification of the material (acidified food waste, AFW) often occurs and consequently leads to failure of fermentation initiation. In this study, we solved this problem by adding Saccharomyces cerevisiae inoculants. The results showed that the inoculation with S. cerevisiae effectively promoted the composting process. In 2 kg composting, inoculation with S. cerevisiae significantly elevated the pile temperatures by 4 ~ 14 °C, accompanied by a rapid increase in pH from 4.5 to 6.0. In 15 kg composting, total acid decreased faster and the thermophilic stage above 50 °C was prolonged by 3 days longer than in the control. The residual oxygen content in the reactor indicated that S. cerevisiae, which proliferated during composting, increased microbial activity and reduced ammonia emission during the thermophilic phase. Cell density analysis showed that compost inoculated with S. cerevisiae promoted thermophilic bacterial propagation. Metagenomic analysis showed that the dominant bacteria in the AFW compost were Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria, and the relative abundance of Bacillus, Thermobacillus, and Thermobifida increased when inoculated with S. cerevisiae. These results indicate that the inoculation of S. cerevisiae is an effective strategy to improve the aerobic composting process of AFW by accelerating the initial phase and altering microbial community structure in the thermophilic phase. Our findings suggest that S. cerevisiae can be applied to aerobic composting of organic wastes to effectively address the problem of acidification.
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Affiliation(s)
- Puhong Yi
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Qinping Li
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xueli Zhou
- Qinghai Grassland Improvement Experimental Station, Gonghe, 813000, China
| | - Ruiqi Liang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xiaoyan Ding
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, 215000, China
| | - Ming Wu
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, 215000, China
| | - Kun Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Ji Li
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, 215000, China
| | - Weixia Wang
- China National Rice Research Institute, Hangzhou, 310006, China
| | - Guangxin Lu
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, 810016, China
| | - Tingheng Zhu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China.
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, 215000, China.
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Xia F, Liu Z, Zhang Y, Li Q, Zhao M, He H, Bao Q, Chen B, He Q, Lai C, He X, Ma Z, Zhou Y. Calcium regulates the interactions between dissolved organic matter and planktonic bacteria in Erhai Lake, Yunnan Province, China. WATER RESEARCH 2024; 261:121982. [PMID: 38936236 DOI: 10.1016/j.watres.2024.121982] [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: 02/21/2024] [Revised: 05/27/2024] [Accepted: 06/20/2024] [Indexed: 06/29/2024]
Abstract
In recent years, the global carbon cycle has garnered significant research attention. However, details of the intricate relationship between planktonic bacteria, hydrochemistry, and dissolved organic matter (DOM) in inland waters remain unclear, especially their effects on lake carbon sequestration. In this study, we analyzed 16S rRNA, chromophoric dissolved organic matter (CDOM), and inorganic nutrients in Erhai Lake, Yunnan Province, China. The results revealed that allochthonous DOM (C3) significantly regulated the microbial community, and that autochthonous DOM, generated via microbial mineralization (C2), was not preferred as a food source by lake bacteria, and neither was allochthonous DOM after microbial mineralization (C4). Specifically, the correlation between the fluorescence index and functional genes (FAPRPTAX) showed that the degree of utilization of DOM was a critical factor in regulating planktonic bacteria associated with the carbon cycle. Further examination of the correlation between environmental factors and planktonic bacteria revealed that Ca2+ had a regulatory influence on the community structure of planktonic bacteria, particularly those linked to the carbon cycle. Consequently, the utilization strategy of DOM by planktonic bacteria was also determined by elevated Ca2+ levels. This in turn influenced the development of specific recalcitrant autochthonous DOM within the high Ca2+ environment of Erhai Lake. These findings are significant for the exploration of the stability of DOM within karst aquatic ecosystems, offering a new perspective for the investigation of terrestrial carbon sinks.
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Affiliation(s)
- Fan Xia
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, CAS, Guiyang 550081, China
| | - Zaihua Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, CAS, Guiyang 550081, China; CAS Center for Excellence in Quaternary Science and Global Change, Xi'an 710061, China.
| | - Yunling Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Qiang Li
- Key Laboratory of Karst Dynamics, Ministry of Nature Resources/Guangxi, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China
| | - Min Zhao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, CAS, Guiyang 550081, China
| | - Haibo He
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, CAS, Guiyang 550081, China
| | - Qian Bao
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest (Sichuan Normal University), Ministry of Education, Chengdu, 610068, China
| | - Bo Chen
- Guizhou University of Finance and Economics, Guiyang 550025, China
| | - Qiufang He
- Chongqing Key Laboratory of Karst Environment & School of Geographical Sciences, Southwest University, Chongqing 400700, China; Key Laboratory of Karst Dynamics, Ministry of Nature Resources/Guangxi, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China
| | - Chaowei Lai
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, CAS, Guiyang 550081, China
| | - Xuejun He
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, CAS, Guiyang 550081, China
| | - Zhen Ma
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, CAS, Guiyang 550081, China
| | - Yongqiang Zhou
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
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Ayayee PA, Wong RY. Zebrafish ( Danio rerio) behavioral phenotypes are not underscored by different gut microbiomes. Ecol Evol 2024; 14:e70237. [PMID: 39219576 PMCID: PMC11362613 DOI: 10.1002/ece3.70237] [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: 06/04/2024] [Revised: 07/25/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024] Open
Abstract
Although bold and shy behavioral phenotypes in zebrafish (Danio rerio) have been selectively bred and maintained over multiple generations, it is unclear if they are underscored by different gut microbiota. Using the microbiota-gut-brain concept, we examined the relationship between gut microbiota and the behavioral phenotypes within this model animal system to assess possible gut microbe-mediated effects on host behavior. To this end, we amplified and sequenced 16S rRNA gene amplicons from the guts of bold and shy zebrafish individuals using the Illumina Miseq platform. We did not record any significant differences in within-group microbial diversity nor between-group community composition of the two behavioral phenotypes. Interestingly, though not statistically different, we determined that the gut microbial community of the bold phenotype was dominated by Burkholderiaceae, Micropepsaceae, and Propionibacteriaceae. In contrast, the shy phenotype was dominated by Beijerinckaceae, Pirelullacaeae, Rhizobiales_Incertis_Sedis, and Rubinishaeraceae. The absence of any significant difference in gut microbiome profiles between the two phenotypes would suggest that in this species, there might exist a stable core gut microbiome, regardless of behavioral phenotypes, and possibly, a limited role for the gut microbiota in modulating this selected-for host behavior. This study characterized the gut microbiomes of distinct innate behavioral phenotypes of the zebrafish (that are not considered dysbiotic states) and did not rely on antibiotic or probiotic treatments to induce changes in behavior. Such studies are crucial to our understanding of the modulating impacts of the gut microbiome on normative animal behavior.
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Affiliation(s)
- Paul A. Ayayee
- Department of BiologyUniversity of Nebraska at OmahaOmahaNebraskaUSA
| | - Ryan Y. Wong
- Department of BiologyUniversity of Nebraska at OmahaOmahaNebraskaUSA
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