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Xu C, Zhang Y, Hu C, Shen C, Li F, Xu Y, Liu W, Shi D. From disinfection to pathogenicity: Occurrence, resistome risks and assembly mechanism of biocide and metal resistance genes in hospital wastewaters. Environ Pollut 2024; 349:123910. [PMID: 38570158 DOI: 10.1016/j.envpol.2024.123910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 03/20/2024] [Accepted: 03/31/2024] [Indexed: 04/05/2024]
Abstract
Hospital wastewaters (HWWs) represent critical reservoir for the accumulation and propagation of resistance genes. However, studies on biocide and metal resistance genes (BMRGs) and their associated resistome risks and driving mechanisms in HWWs are still in their infancy. Here, metagenomic assembly was firstly used to investigate host pathogenicity and transferability profiles of BMGRs in a typical HWWs system. As a result, genes conferring resistance to Ethidium Bromide, Benzylkonium Chloride, and Cetylpyridinium Chloride dominated biocide resistance genes (BRGs), whereas Cu resistance gene was the largest contributor of metal resistance genes (MRGs). Most BMRGs experienced significant reduction from anoxic-aerobic treatment to sedimentation stages but exhibited enrichment after chlorine disinfection. Network analysis indicated intense interactions between BMRGs and virulence factors (VFs). Polar_flagella, belonging to the adherence was identified to play important role in the network. Contig-based analysis further revealed noteworthy shifts in host associations along the treatment processes, with Pseudomonadota emerging as the primary carrier, hosting 91.1% and 85.3% of the BRGs and MRGs. A total of 199 opportunistic pathogens were identified to carry 285 BMRG subtypes, which mainly included Pseudomonas alcaligenes, Pseudomonas lundensis, and Escherichia coli. Notably, ruvB conferring resistance to Cr, Cetylpyridinium Chloride, and Dodine were characterized with the highest frequency carried by pathogens. Diverse co-occurrence patterns between BMRGs and mobile genetic elements (MGEs) were found from the raw influent to final effluent. Overall, 10.5% BRGs and 8.84% MRGs were mobile and among the 4 MGEs, transposase exhibited the greatest potential for the BMRGs dissemination. Furthermore, deterministic processes played a dominant role in bacterial communities and BMRGs assembly in HWWs. Bacterial communities contributed more than MGEs in shaping the resistome. Taken together, this work demonstrated widespread BMRGs pollution throughout the HWWs treatment system, emphasizing the potential for informing resistome risk and ecological mechanism in medical practice.
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Affiliation(s)
- Chenye Xu
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Yibo Zhang
- Department of Infection Control, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chun Hu
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Chensi Shen
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Fang Li
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Yumin Xu
- Department of Infection Control, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Weiping Liu
- MOE Key Laboratory of Environmental Remediation and Ecosystem Health, Institute of Environmental Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China
| | - Dake Shi
- Department of Infection Control, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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Xing H, Chen W, Liu Y, Cahill JF. Local Community Assembly Mechanisms and the Size of Species Pool Jointly Explain the Beta Diversity of Soil Fungi. Microb Ecol 2024; 87:58. [PMID: 38602532 PMCID: PMC11008070 DOI: 10.1007/s00248-024-02374-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/01/2024] [Indexed: 04/12/2024]
Abstract
Fungi play vital regulatory roles in terrestrial ecosystems. Local community assembly mechanisms, including deterministic and stochastic processes, as well as the size of regional species pools (gamma diversity), typically influence overall soil microbial community beta diversity patterns. However, there is limited evidence supporting their direct and indirect effects on beta diversity of different soil fungal functional groups in forest ecosystems. To address this gap, we collected 1606 soil samples from a 25-ha subtropical forest plot in southern China. Our goal was to determine the direct effects and indirect effects of regional species pools on the beta diversity of soil fungi, specifically arbuscular mycorrhizal (AM), ectomycorrhizal (EcM), plant-pathogenic, and saprotrophic fungi. We quantified the effects of soil properties, mycorrhizal tree abundances, and topographical factors on soil fungal diversity. The beta diversity of plant-pathogenic fungi was predominantly influenced by the size of the species pool. In contrast, the beta diversity of EcM fungi was primarily driven indirectly through community assembly processes. Neither of them had significant effects on the beta diversity of AM and saprotrophic fungi. Our results highlight that the direct and indirect effects of species pools on the beta diversity of soil functional groups of fungi can significantly differ even within a relatively small area. They also demonstrate the independent and combined effects of various factors in regulating the diversities of soil functional groups of fungi. Consequently, it is crucial to study the fungal community not only as a whole but also by considering different functional groups within the community.
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Affiliation(s)
- Hua Xing
- ECNU-Alberta Joint Lab for Biodiversity Study, Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, 500 Dongchuan Road, Minhuang District, 200241, Shanghai, China
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Wuwei Chen
- Qingyuan Bureau Natural Resources and Planning, Qingyuan, 323800, China
| | - Yu Liu
- ECNU-Alberta Joint Lab for Biodiversity Study, Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, 500 Dongchuan Road, Minhuang District, 200241, Shanghai, China.
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200082, China.
| | - James F Cahill
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
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Li W, Xia Y, Li N, Chang J, Liu J, Wang P, He X. Temporal assembly patterns of microbial communities in three parallel bioreactors treating low-concentration coking wastewater with differing carbon source concentrations. J Environ Sci (China) 2024; 137:455-468. [PMID: 37980030 DOI: 10.1016/j.jes.2023.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 11/20/2023]
Abstract
Carbon source is an important factor of biological treatment systems, the effects of which on their temporal community assembly patterns are not sufficiently understood currently. In this study, the temporal dynamics and driving mechanisms of the communities in three parallel bioreactors for low-concentration coking wastewater (CWW) treatment with differing carbon source concentrations (S0 with no glucose addition, S1 with 200 mg/L glucose addition and S2 with 400 mg/L glucose addition) were comprehensively studied. High-throughput sequencing and bioinformatics analyses including network analysis and Infer Community Assembly Mechanisms by Phylogenetic bin-based null model (iCAMP) were used. The communities of three systems showed turnover rates of 0.0029∼0.0034 every 15 days. Network analysis results showed that the S0 network showed higher positive correlation proportion (71.43%) and clustering coefficient (0.33), suggesting that carbon source shortage in S0 promoted interactions and cooperation of microbes. The neutral community model analysis showed that the immigration rate increased from 0.5247 in S0 to 0.6478 in S2. The iCAMP analysis results showed that drift (45.89%) and homogeneous selection (31.68%) dominated in driving the assembly of all the investigated microbial communities. The contribution of homogeneous selection increased with the increase of carbon source concentrations, from 27.92% in S0 to 36.08% in S2. The OTUs participating in aerobic respiration and tricarboxylic acid (TCA) cycle were abundant among the bins mainly affected by deterministic processes, while those related to the metabolism of refractory organic pollutants in CWW such as alkanes, benzenes and phenols were abundant in the bins dominated by stochastic processes.
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Affiliation(s)
- Weijia Li
- School of Chemical and Environmental Engineering, China University of Mining and Technology-Beijing, Beijing 100083, China
| | - Yu Xia
- School of Chemical and Environmental Engineering, China University of Mining and Technology-Beijing, Beijing 100083, China.
| | - Na Li
- School of Chemical and Environmental Engineering, China University of Mining and Technology-Beijing, Beijing 100083, China
| | - Jie Chang
- School of Chemical and Environmental Engineering, China University of Mining and Technology-Beijing, Beijing 100083, China
| | - Jing Liu
- School of Chemical and Environmental Engineering, China University of Mining and Technology-Beijing, Beijing 100083, China
| | - Pei Wang
- School of Chemical and Environmental Engineering, China University of Mining and Technology-Beijing, Beijing 100083, China
| | - Xuwen He
- School of Chemical and Environmental Engineering, China University of Mining and Technology-Beijing, Beijing 100083, China
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Niu X, Wang H, Wang T, Zhang P, Zhang H, Wang H, Kong X, Xie S, Xu J. The combination of multiple environmental stressors strongly alters microbial community assembly in aquatic ecosystems. J Environ Manage 2024; 350:119594. [PMID: 37995485 DOI: 10.1016/j.jenvman.2023.119594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 10/14/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023]
Abstract
Microorganisms play a critical role in maintaining the delicate balance of ecosystem services. However, the assembly processes that shape microbial communities are vulnerable to a range of environmental stressors, such as climate change, eutrophication, and the use of herbicides. Despite the importance of these stressors, little is known about their cumulative impacts on microbial community assembly in aquatic ecosystems. To address this knowledge gap, we established 48 mesocosm experiments that simulated shallow lake ecosystems and subjected them to warming (including continuous warming (W) and heat waves (H)), glyphosate-based herbicides (G), and nutrient loading (E). Our study revealed that in the control group, both deterministic and stochastic processes codominated the assembly of microbial communities in water, whereas in sediment, the processes were primarily stochastic. Interestingly, the effects of multiple stress factors on assembly in these two habitats were completely opposite. Specifically, stressors promoted the dominance of stochastic processes in water but increased the importance of deterministic processes in sediment. Furthermore, warming amplified the effects of herbicides but exerted an opposite and stronger influence on assembly compared to nutrients, emphasizing the complexity of these mechanisms and the significance of considering multiple stressors. The interaction of some factors significantly affected assembly (p < 0.05), with the effects of WEG being most pronounced in water. Both water and sediment exhibited homogeneous assembly of microbial communities (mean NTI >0), but the phylogenetic clustering of microbial communities in water was more closely related (NTI >2). Our research revealed the response model of microbial community assembly in aquatic ecosystems to multiple environmental stresses, such as agricultural pollution, climate change, and eutrophication, and indicated that microbial community changes in sediment may be an important predictor of lake ecosystem development. This provides scientific evidence that better environmental management can reduce impacts on aquatic ecosystems under the threat of future warming.
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Affiliation(s)
- Xiaofeng Niu
- School of Marine Biology and Fisheries, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China
| | - Huan Wang
- School of Marine Biology and Fisheries, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China.
| | - Tao Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China
| | - Peiyu Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China
| | - Huan Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China
| | - Hongxia Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China
| | - Xianghong Kong
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China
| | - Songguang Xie
- School of Marine Biology and Fisheries, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China
| | - Jun Xu
- School of Marine Biology and Fisheries, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China.
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Liu S, Lin Y, Liu T, Xu X, Wang J, Chen Q, Sun W, Dang C, Ni J. Planktonic/benthic Bathyarchaeota as a "gatekeeper" enhance archaeal nonrandom co-existence and deterministic assembling in the Yangtze River. Water Res 2023; 247:120829. [PMID: 37976624 DOI: 10.1016/j.watres.2023.120829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/23/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023]
Abstract
Archaea, the third proposed domain of life, mediate carbon and nutrient cycling in global natural habitats. Compared with bacteria, our knowledge about archaeal ecological modes in large freshwater environments subject to varying natural and human factors is limited. By metabarcoding analysis of 303 samples, we provided the first integrate biogeography about archaeal compositions, co-existence networks, and assembling processes within a 6000 km continuum of the Yangtze River. Our study revealed that, among the major phyla, water samples owned a higher proportion of Thaumarchaeota (62.8%), while sediments had higher proportions of Euryarchaeota (33.4%) and Bathyarchaeota (18.8%). A decline of polarization in phylum abundance profile was observed from plateau/mountain/hill to basin/plain areas, which was attributed to the increase of nutrients and metals. Planktonic and benthic Bathyarchaeota tended to co-occur with both major (e.g., methanogens or Thermoplasmata) and minor (e.g., Asgard or DPANN) taxa in the non-random networks, harboring the highest richness and abundances of keystone species and contributing the most positively to edge number, node degree, and nearest neighbor degree. Furthermore, we noted significantly positive contributions of Bathyarchaeota abundance and network complexity to the dominance of deterministic process in archaeal assembly (water: 65.3%; sediments: 92.6%), since higher carbon metabolic versatility of Bathyarchaeota would benefit archaeal symbiotic relations. Stronger deterministic assembling was identified at the lower-reach plain, and higher concentrations of ammonium and aluminum separately functioning as nutrition and agglomerator were the main environmental drivers. We lastly found that the Three Gorges Dam caused a simultaneous drop of benthic Bathyarchaeota abundance, network co-existence, and deterministic effects immediately downstream due to riverbed erosion as a local interference. These findings highlight that Bathyarchaeota are a "gatekeeper" to promote fluvial archaeal diversity, stability, and predictability under varying macroscopic and microscopic factors, expanding our knowledge about microbial ecology in freshwater biogeochemical cycling globally.
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Affiliation(s)
- Shufeng Liu
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, PR China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing, PR China; College of Resources and Environmental Sciences, China Agricultural University, Beijing, PR China
| | - Yahsuan Lin
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, PR China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing, PR China
| | - Tang Liu
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, PR China
| | - Xuming Xu
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, PR China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing, PR China
| | - Jiawen Wang
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, PR China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing, PR China
| | - Qian Chen
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, PR China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing, PR China
| | - Weiling Sun
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, PR China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing, PR China
| | - Chenyuan Dang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan, PR China
| | - Jinren Ni
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, PR China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing, PR China.
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Zhong S, Zhou S, Liu S, Wang J, Dang C, Chen Q, Hu J, Yang S, Deng C, Li W, Liu J, Borthwick AGL, Ni J. May microbial ecological baseline exist in continental groundwater? Microbiome 2023; 11:152. [PMID: 37468948 PMCID: PMC10355068 DOI: 10.1186/s40168-023-01572-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 05/13/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Microbes constitute almost the entire biological community in subsurface groundwater and play an important role in ecological evolution and global biogeochemical cycles. Ecological baseline as a fundamental reference with less human interference has been investigated in surface ecosystems such as soils, rivers, and ocean, but the existence of groundwater microbial ecological baseline (GMEB) is still an open question so far. RESULTS Based on high-throughput sequencing information derived from national monitoring of 733 newly constructed wells, we find that bacterial communities in pristine groundwater exhibit a significant lateral diversity gradient and gradually approach the topsoil microbial latitudinal diversity gradient with decreasing burial depth of phreatic water. Among 74 phyla dominated by Proteobacteria in groundwater, Patescibacteria act as keystone taxa that harmonize microbes in shallower aquifers and accelerate decline in bacterial diversity with increasing well-depth. Decreasing habitat niche breadth with increasing well-depth suggests a general change in the relationship among key microbes from closer cooperation in shallow to stronger competition in deep groundwater. Unlike surface-water microbes, microbial communities in pristine groundwater are predominantly shaped by deterministic processes, potentially associated with nutrient sequestration under dark and anoxic environments in aquifers. CONCLUSIONS By unveiling the biogeographic patterns and mechanisms controlling the community assembly of microbes in pristine groundwater throughout China, we firstly confirm the existence of GMEB in shallower aquifers and propose Groundwater Microbial Community Index (GMCI) to evaluate anthropogenic impact, which highlights the importance of GMEB in groundwater water security and health diagnosis. Video Abstract.
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Affiliation(s)
- Sining Zhong
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, People's Republic of China
- Fujian Agriculture and Forestry University, College of Resources and Environment, Fujian Provincial Key Laboratory of Soil Environment Health and Regulation, Fuzhou, 350002, People's Republic of China
| | - Shungui Zhou
- Fujian Agriculture and Forestry University, College of Resources and Environment, Fujian Provincial Key Laboratory of Soil Environment Health and Regulation, Fuzhou, 350002, People's Republic of China
| | - Shufeng Liu
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Jiawen Wang
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Chenyuan Dang
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Qian Chen
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China
| | - Jinyun Hu
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Shanqing Yang
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Chunfang Deng
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Wenpeng Li
- Center for Groundwater Monitoring, China Institute of Geo-environmental Monitoring, Beijing, 100081, People's Republic of China
| | - Juan Liu
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Alistair G L Borthwick
- School of Engineering, Computing and Mathematics, University of Plymouth, Drake Circus, Plymouth, PL8 4AA, UK
| | - Jinren Ni
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China.
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, People's Republic of China.
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Yu Q, Han Q, Shi S, Sun X, Wang X, Wang S, Yang J, Su W, Nan Z, Li H. Metagenomics reveals the response of antibiotic resistance genes to elevated temperature in the Yellow River. Sci Total Environ 2023; 859:160324. [PMID: 36410491 DOI: 10.1016/j.scitotenv.2022.160324] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/08/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
Climate warming may aggravate the threat of antibiotic resistance genes (ARGs) to environmental and human health. However, whether temperature can predict ARGs and influence their assembly processes remains unknown. Here, we used metagenomic sequencing to explore how gradually elevated water temperature (23 °C, 26 °C, 29 °C, 32 °C, 35 °C) influences ARG and mobile genetic element (MGE) profiles in the Yellow River. In total, 30 ARG types including 679 subtypes were detected in our water samples. Gradually increased temperature remarkably reduced ARG diversity but increased ARG abundance. Approximately 37 % of ARGs and 42 % of MGEs were predicted by temperature, while most others were not sensitive to temperature. For each 1 °C increase in temperature, the ARG abundance rose by 2133 TPM (Transcripts Per kilobase of exon model per Million mapped reads) abundance, and multidrug, tetracycline and peptide resistance genes had the fastest increases. Proteobacteria and Actinobacteria were the primary ARG hosts, with 558 and 226 ARG subtypes, respectively. Although ARG profiles were mainly governed by stochastic process, elevated temperature increased the deterministic process of ARGs in the Yellow River. The abundance of five high-risk ARGs (tetM, mecA, bacA, vatE and tetW) significantly increased with elevated water temperature, and these ARGs co-occurred with several opportunistic pathogens (Delftia, Legionella and Pseudomonas), implying that antibiotic resistance risk may increase under climate warming. Our study explored the possibility of predicting resistomes and their health risks through temperature, providing a novel approach to predict and control ARGs in water environments under climate warming.
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Affiliation(s)
- Qiaoling Yu
- College of Pastoral Agriculture Science and Technology, State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microiome, Lanzhou University, Lanzhou 730000, China
| | - Qian Han
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Shunqin Shi
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xiaofang Sun
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xiaochen Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Sijie Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Jiawei Yang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Wanghong Su
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Zhibiao Nan
- College of Pastoral Agriculture Science and Technology, State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microiome, Lanzhou University, Lanzhou 730000, China
| | - Huan Li
- College of Pastoral Agriculture Science and Technology, State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microiome, Lanzhou University, Lanzhou 730000, China; School of Public Health, Lanzhou University, Lanzhou 730000, China.
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Shi L, Xia P, Lin T, Li G, Wang T, Du X. Temporal Succession of Bacterial Community Structure, Co-occurrence Patterns, and Community Assembly Process in Epiphytic Biofilms of Submerged Plants in a Plateau Lake. Microb Ecol 2023; 85:87-99. [PMID: 34997308 DOI: 10.1007/s00248-021-01956-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
In shallow macrophytic lakes, epiphytic biofilms are formed on the surface of submerged plant stems and leaves because of algae and bacterial accumulation. Epiphytic biofilms significantly impact the health of the host vegetation and the biogeochemical cycling of lake elements. However, community diversity, species interactions, and community assembly mechanisms in epiphytic bacterial communities (EBCs) of plants during different growth periods are not well understood. We investigated the successional dynamics, co-occurrence patterns, and community assembly processes of epiphytic biofilm bacterial communities of submerged plants, Najas marina and Potamogeton lucens, from July to November 2020. The results showed a significant seasonal variation in EBC diversity and richness. Community diversity and richness increased from July to November, and the temperature was the most important driving factor for predicting seasonal changes in EBC community structure. Co-occurrence network analysis revealed that the average degree and graph density of the network increased from July to November, indicating that the complexity of the EBC network increased. The bacterial community co-occurrence network was limited by temperature, pH, and transparency. The phylogeny-based null model analysis showed that deterministic processes dominated the microbial community assembly in different periods, increasing their contribution. In addition, we found that as the dominance of deterministic processes increased, the microbial co-occurrence links increased, and the potential interrelationships between species became stronger. Thus, the findings provide insights into the seasonal variability of EBC assemblage and co-occurrence patterns in lacustrine ecosystems.
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Affiliation(s)
- Lei Shi
- Guizhou Province Key Laboratory for Information System of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, No. 116 Baoshan Road (N), Guiyang, 550001, Guizhou, China
| | - Pinhua Xia
- Guizhou Province Key Laboratory for Information System of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, No. 116 Baoshan Road (N), Guiyang, 550001, Guizhou, China.
| | - Tao Lin
- Guizhou Province Key Laboratory for Information System of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, No. 116 Baoshan Road (N), Guiyang, 550001, Guizhou, China
| | - Guoqing Li
- Guizhou Province Key Laboratory for Information System of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, No. 116 Baoshan Road (N), Guiyang, 550001, Guizhou, China
| | - Tianyou Wang
- Guizhou Province Key Laboratory for Information System of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, No. 116 Baoshan Road (N), Guiyang, 550001, Guizhou, China
| | - Xin Du
- Guizhou Province Key Laboratory for Information System of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, No. 116 Baoshan Road (N), Guiyang, 550001, Guizhou, China
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Pearman JK, Thomson-Laing G, Thompson L, Waters S, Vandergoes MJ, Howarth JD, Duggan IC, Hogg ID, Wood SA. Human access and deterministic processes play a major role in structuring planktonic and sedimentary bacterial and eukaryotic communities in lakes. PeerJ 2022; 10:e14378. [PMID: 36389411 PMCID: PMC9661969 DOI: 10.7717/peerj.14378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/20/2022] [Indexed: 11/13/2022] Open
Abstract
Lakes provide habitat for a diverse array of species and offer a wide range of ecosystem services for humanity. However, they are highly vulnerable as they are not only impacted by adverse actions directly affecting them, but also those on the surrounding environment. Improving knowledge on the processes responsible for community assembly in different biotic components will aid in the protection and restoration of lakes. Studies to date suggested a combination of deterministic (where biotic/abiotic factors act on fitness differences amongst taxa) and stochastic (where dispersal plays a larger factor in community assembly) processes are responsible for structuring biotic communities, but there is no consensus on the relative roles these processes play, and data is lacking for lakes. In the present study, we sampled different biotic components in 34 lakes located on the South Island of New Zealand. To obtain a holistic view of assembly processes in lakes we used metabarcoding to investigate bacteria in the sediment and surface waters, and eukaryotes in the sediment and two different size fractions of the water column. Physicochemical parameters were collected in parallel. Results showed that deterministic processes dominated the assembly of lake communities although the relative importance of variable and homogeneous selection differed among the biotic components. Variable selection was more important in the sediment (SSbact and SSeuks) and for the bacterioplankton (Pbact) while the assembly of the eukaryotic plankton (SPeuks, LPeuks) was driven more by homogeneous selection. The ease of human access to the lakes had a significant effect on lake communities. In particular, clade III of SAR11 and Daphnia pulex were only present in lakes with public access. This study provides insights into the distribution patterns of different biotic components and highlights the value in understanding the drivers of different biological communities within lakes.
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Affiliation(s)
| | | | | | | | | | | | | | - Ian D. Hogg
- University of Waikato, Hamilton, New Zealand,Canadian High Arctic Research Station, Nunavut, Canada
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10
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Zhao B, Jiao C, Wang S, Zhao D, Jiang C, Zeng J, Wu QL. Contrasting assembly mechanisms explain the biogeographic patterns of benthic bacterial and fungal communities on the Tibetan Plateau. Environ Res 2022; 214:113836. [PMID: 35810809 DOI: 10.1016/j.envres.2022.113836] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 06/22/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
The Tibetan Plateau characterized by high altitude and low temperature, where a great number of lakes are located, is a hotspot of global biodiversity research. Both bacterial and fungal communities are vital participants of biogeochemical cycling in lake ecosystems. However, we know very little about the large-scale biogeographic patterns and the underlying assembly mechanisms of lake benthic microbial communities on the Tibetan Plateau. To investigate the biogeographic patterns and their underlying assembly mechanisms of benthic bacterial and fungal communities, we collected sediment samples from 11 lakes on the Tibetan Plateau (maximum geographic distance between lakes over 1100 km). Benthic community diversity and composition were determined using the high-throughput sequencing technique. Our results indicated that there were contrasting distance-decay relationships between benthic bacterial and fungal communities on a regional scale. Benthic bacterial communities showed a significant distance-decay relationship, whereas no significant relationship was observed for benthic fungal communities. Deterministic processes dominated the bacterial community assembly, whereas fungal community assembly was more stochastic. pH was a dominant factor in influencing the geographic distribution of benthic microbial communities. Co-occurrence network analysis revealed that bacterial communities showed higher complexity and greater stability than those of the fungal communities. Taken together, this study contributes to a novel understanding of the assembly mechanisms underlying the biogeographic distribution of plateau benthic bacterial and fungal communities at a large scale.
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Affiliation(s)
- Baohui Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
| | - Congcong Jiao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Shuren Wang
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
| | - Cuiling Jiang
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, 100049, China
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11
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Xiao Z, Li H, Li XC, Li RH, Huo SL, Yu GL. Geographic pattern of phytoplankton community and their drivers in lakes of middle and lower reaches of Yangtze River floodplain, China. Environ Sci Pollut Res Int 2022; 29:83993-84005. [PMID: 35778664 DOI: 10.1007/s11356-022-21657-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
Disentangling the relative contributions of deterministic and stochastic processes was critical to compressive understanding of underlying mechanism governing geographic pattern and assembly of phytoplankton community, while it was seldom performed in connected lakes under human pressure. Here, we investigated phytoplankton community pattern in relation to environmental and spatial factors over 81 lakes located in the middle and lower reaches of Yangtze River (MLYR) floodplain, where many lakes suffered from eutrophication and cyanobacterial blooms. A majority of MLYR lakes had higher phytoplankton abundance surpassing 107 cells/L and were dominated by common bloom-forming cyanobacterial genera, including Pseudanabaena, Microcystis, Merismopedia, Dolichospermum, Limnothrix, and Raphidiopsis. Phytoplankton community exhibited a striking geographical pattern both for taxonomic and functional compositions, while functional groups were less sensitive, and dissimilarity in communities displayed no significant increases with increasing geographical distance. Further, species richness explained much higher percentage of community variations than species turnover, indicating a reduced effect of environmental filtering of phytoplankton species with tolerance to similar environments in connected MLYR lakes. Both deterministic and stochastic processes governed assembly and biogeographic of phytoplankton community. Variation partition analysis showed that spatial factors exhibited greater influence on phytoplankton community compared to environmental variables. The stronger influence of spatial factors was further demonstrated by Mantel test and neutral community model. These findings indicate that deterministic and stochastic processes exhibited similar biogeographic patterns for phytoplankton community in MLYR lakes, but stochastic process was overwhelmingly dominated. Moreover, a large proportion of unexplained variation implies that complex interactions exist to shape assembly mechanism of phytoplankton community in MLYR lakes.
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Affiliation(s)
- Zhe Xiao
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Hua Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Xiao-Chuang Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Ren-Hui Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, Zhejiang, China
| | - Shou-Liang Huo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Gong-Liang Yu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China.
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12
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Sha H, Li L, Lu J, Xiong J. High nutrient induces virulence in the AHPND-causing Vibrio parahaemolyticus, interpretation from the ecological assembly of shrimp gut microbiota. Fish Shellfish Immunol 2022; 127:758-765. [PMID: 35835385 DOI: 10.1016/j.fsi.2022.07.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/03/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Shrimp diseases frequently occur during the later farming stages, when the rearing water is eutrophic. This observation provides clue that the virulence of pathogens could be induced by elevated nutrient, whereas the underlying ecological mechanism remains limited. To address this pressing knowledge, we explored how gut microbiota responded to the infection of oligotrophic (OVp) or eutrophic (EVp) pre-cultured Vibrio parahaemolyticus, a causing pathogen of shrimp acute hepatopancreatic necrosis disease (AHPND). Resulted revealed that OVp and EVp infections caused dysbiosis in the gut microbiota and compromised shrimp immunity, while the later infection led to earlier and higher mortality. Significant associations were detected between the gut microbiota and each of the measured immune activities. Neutral community model showed that the assembly of gut microbiota was more strongly governed by deterministic processes in EVp infection, followed by EVp infected and control shrimp. Additionally, there were significantly lower temporal turnover rate and average variation degree in the gut microbiota in EVp infected shrimp compared with control individuals. Notably, we identified 22 infection-discriminatory taxa after ruling out the ontogenic effect. Using profiles of the 22 indicators as independent variables, the diagnosis model accurately distinguished (an overall 85.9% accuracy) the infected status (control, OVp or EVp infected shrimp), with 81.3% accuracy at the initial infection stage. The convergent and deterministic gut microbiota in EVp infected shrimp could partially explain why it is challenge to cure APHND from an ecological viewpoint. In addition, we provided a sensitive approach for diagnosing the onset of infection, when disease symptom is unobservable.
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Affiliation(s)
- Haonan Sha
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Luyue Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiaqi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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13
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Yu Q, Zhou R, Wang Y, Su W, Yang J, Feng T, Dou Y, Li H. Carcass decay deteriorates water quality and modifies the nirS denitrifying communities in different degradation stages. Sci Total Environ 2021; 785:147185. [PMID: 33933763 DOI: 10.1016/j.scitotenv.2021.147185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/19/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
Corpse degradation may release amounts of hazardous materials (e.g., cadaverine, putrescine and ammonia) into surrounding areas, which deteriorate environments and result in nitrogen contamination. Nitrate or nitrite can be reduced to nitrogen gas by denitrifying bacteria, thus alleviating nitrogen contamination and purifying aquatic environments. However, the reaction of nirS-encoding denitrifiers to carcass degradation is less studied. Therefore, water physiochemical analysis and high-throughput sequencing were applied to explore the successional pattern of nirS denitrifying communities in the Yellow River water and tap water during three stages of animal cadaver decay (submerged fresh, advanced floating decay as well as sunken remains) and relevant control group. Nitrate nitrogen (NO3-N) and ammonia nitrogen (NH4+-N) concentration in corpse groups were highly elevated compared with control groups. The dominant phylum for nirS denitrifying communities was Proteobacteria. Abundant denitrifying genera Paracoccus, Alicycliphilus and Diaphorobacter were detected, and these genera have been reported to participate in the degradation of organic pollutants. Particularly, nirS-type community structures were remarkably influenced by corpse decay and became similar with succession. Water total dissolved solids (TDS), salinity, conductivity (CON) and phosphate were primary impacting factors driving the community structures, but the effect of water type was almost negligible. Notably, denitrifying community assembly was dominated by deterministic processes rather than stochastic processes, and the relative importance of deterministic processes among most corpse groups was higher than that in control groups, indicating that environmental filtering regulates the denitrifying communities. Our results provide new insight into environmental purification for hazardous materials produced by corpse degradation, thereby providing valuable advice to environmental administration.
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Affiliation(s)
- Qiaoling Yu
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Rui Zhou
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Yijie Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Wanghong Su
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Jiawei Yang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Tianshu Feng
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Yaqi Dou
- Hubei Aquaculture Technology Extension Center (Hubei Aquatic Breeds Introduction and Breeding Center), Wuhan 430070, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou 730000, China; Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China..
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14
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Li S, Li Y, Hu C, Zheng X, Zhang J, Zhang H, Bai N, Zhang H, Tian M, Ban S, Wu G, Pan A, Li P, Lv W. Stochastic processes drive bacterial and fungal community assembly in sustainable intensive agricultural soils of Shanghai, China. Sci Total Environ 2021; 778:146021. [PMID: 34030362 DOI: 10.1016/j.scitotenv.2021.146021] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 06/12/2023]
Abstract
Sustainable intensive cropping systems have been implemented for three decades in suburban agricultural districts of Shanghai, China. These human-managed soils have been developed from paleosol or alluvial soils across different regions. However, little is known about the geographical distribution patterns of microbes and microbial community assembly in the sustainable intensive soils after decades of anthropogenic disturbances. Here, we investigated the impact of local geochemical properties and geographic distance on stochastic/deterministic microbial community assembly processes using high-throughput sequencing and phylogenetic null modeling analysis. Our results showed that soil pH was the most important environmental factor determining bacterial and fungal community structure. Importantly, only soil organic matter was positively correlated with fungal α-diversity, suggesting the efficient use of carbon substrates in sustainable agricultural systems, compensating for the lack of chemical fertilization and reduced tillage in these systems. Both bacterial and fungal communities had robust distance-decay patterns, but the rate of turnover of bacterial taxa was faster than that of fungi. Variation in bacterial and fungal communities was mostly attributed to the simultaneous effects of environmental variables and spatial factors. We also mapped the spatial distributions of the dominant bacterial and fungal taxa across the sustainable agricultural fields, making it possible to forecast the responses of agricultural ecosystems to anthropogenic disturbance. Based on the patterns of the β-nearest taxon index, this study demonstrated that stochastic processes shaped substantial bacterial and fungal community variation in sustainable intensive agricultural soils of the Shanghai suburbs. This variation may be attributed to the increasing microbial dispersal caused by hydrological connectivity in the agricultural fields or the release from environmental stress and weakened environmental filtering across the suitable pH range preferable for most soil microbes. These results unveil assembly mechanisms of soil microbial community after several decades of sustainable intensive management, and contribute to understand the role of microbes in ecosystems in establishing a functional equilibrium which may enable sustainability to be preserved.
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Affiliation(s)
- Shuangxi Li
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Yujie Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Cong Hu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Xianqing Zheng
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Juanqin Zhang
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Hanlin Zhang
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Naling Bai
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Haiyun Zhang
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Minglu Tian
- Information Research Institute of Science and Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Songtao Ban
- Information Research Institute of Science and Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Guogan Wu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Aihu Pan
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Peng Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.
| | - Weiguang Lv
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
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15
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He Q, Wang S, Hou W, Feng K, Li F, Hai W, Zhang Y, Sun Y, Deng Y. Temperature and microbial interactions drive the deterministic assembly processes in sediments of hot springs. Sci Total Environ 2021; 772:145465. [PMID: 33571767 DOI: 10.1016/j.scitotenv.2021.145465] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/22/2021] [Accepted: 01/24/2021] [Indexed: 06/12/2023]
Abstract
Terrestrial geothermal ecosystems, as a representative of extreme environments, exhibit a variety of geochemical gradients, and their microbes are thought to be under high stress through environmental selection. However, it is still unclear how stochasticity and biotic interactions contribute to the microbial community assembly in hot springs. Here, we investigated the assembly processes and co-occurrence patterns of microbiota (i.e. bacteria and archaea) in both water and sediments sampled from fifteen hot springs in the Tengchong area, Southwestern of China, using 16S rRNA gene sequencing combined with multivariate ecological and statistical methods. These hot springs harbored more specialists than non-geothermal ecosystems, which are well-adapted to the extreme conditions, as shown by extremely high nearest-taxon index (NTI) and narrower niche width. Habitat differentiation led to the differences in microbial diversity, species-interactions, and community assembly between water and sediment communities. The sediment community showed stronger phylogenetic clustering and was primarily governed by heterogeneous selection, while undominated stochastic processes and dispersal limitation were the major assembly processes in the water community. Temperature and ferrous iron were the major factors mediating the balance of stochastic and deterministic assembly processes in sediment communities, as evidenced by how divergences in temperature and ferrous iron increased the proportion of determinism. Microbial interactions in sediments contributed to deterministic community assembly, as indicated by more complex associations and greater responsiveness to environmental change than water community. These findings uncover the ecological processes underlying microbial communities in hot springs, and provide potential insight into understanding the mechanism to maintain microbial diversity in extreme biospheres.
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Affiliation(s)
- Qing He
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Shang Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China.
| | - Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Fangru Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Wanming Hai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Yidi Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Yuxuan Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
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16
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Mo Y, Peng F, Gao X, Xiao P, Logares R, Jeppesen E, Ren K, Xue Y, Yang J. Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir. Microbiome 2021; 9:128. [PMID: 34082826 PMCID: PMC8176698 DOI: 10.1186/s40168-021-01079-w] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/15/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND Freshwater salinization may result in significant changes of microbial community composition and diversity, with implications for ecosystem processes and function. Earlier research has revealed the importance of large shifts in salinity on microbial physiology and ecology, whereas studies on the effects of smaller or narrower shifts in salinity on the microeukaryotic community in inland waters are scarce. Our aim was to unveil community assembly mechanisms and the stability of microeukaryotic plankton networks at low shifts in salinity. RESULTS Here, we analyzed a high-resolution time series of plankton data from an urban reservoir in subtropical China over 13 consecutive months following one periodic salinity change ranging from 0 to 6.1‰. We found that (1) salinity increase altered the community composition and led to a significant decrease of plankton diversity, (2) salinity change influenced microeukaryotic plankton community assembly primarily by regulating the deterministic-stochastic balance, with deterministic processes becoming more important with increased salinity, and (3) core plankton subnetwork robustness was higher at low-salinity levels, while the satellite subnetworks had greater robustness at the medium-/high-salinity levels. Our results suggest that the influence of salinity, rather than successional time, is an important driving force for shaping microeukaryotic plankton community dynamics. CONCLUSIONS Our findings demonstrate that at low salinities, even small increases in salinity are sufficient to exert a selective pressure to reduce the microeukaryotic plankton diversity and alter community assembly mechanism and network stability. Our results provide new insights into plankton ecology of inland urban waters and the impacts of salinity change in the assembly of microbiotas and network architecture. Video abstract.
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Affiliation(s)
- Yuanyuan Mo
- Aquatic Ecohealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Feng Peng
- Aquatic Ecohealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
| | - Xiaofei Gao
- Aquatic Ecohealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Peng Xiao
- Aquatic Ecohealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
| | - Ramiro Logares
- Institute of Marine Sciences, CSIC, Passeig Marítim de la Barceloneta 37-49, ES08003 Barcelona, Spain
| | - Erik Jeppesen
- Department of Bioscience, Aarhus University, 8600 Silkeborg, Denmark
- Sino-Danish Centre for Education and Research, Beijing, 100049 China
- Limnology Laboratory, Department of Biological Sciences and Centre for Ecosystem Research and Implementation, Middle East Technical University, 06800 Ankara, Turkey
- Institute of Marine Sciences, Middle East Technical University, 33731 Erdemli-Mersin, Turkey
| | - Kexin Ren
- Aquatic Ecohealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
| | - Yuanyuan Xue
- Aquatic Ecohealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
| | - Jun Yang
- Aquatic Ecohealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
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17
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Lu Z, Liu Z, Zhang C, Wei Q, Zhang S, Li M. Spatial and seasonal variations of sediment bacterial communities in a river-bay system in South China. Appl Microbiol Biotechnol 2021; 105:1979-1989. [PMID: 33544213 DOI: 10.1007/s00253-021-11142-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/18/2021] [Accepted: 01/25/2021] [Indexed: 12/25/2022]
Abstract
River-bay systems are transitional areas that hold important roles in biogeochemical processes between continents and oceans. However, composition and structure of microbial communities shaped by such environments have not been clear yet. In this study, we used high-throughput sequencing of 16S rRNA genes to analyze the diversity and composition of sediment bacterial communities from the Shenzhen river-bay system during dry and wet seasons. The results showed that sediment bacterial community structure was varied according to habitats (river vs. estuary) and seasons (wet season vs. dry season). The alpha diversity of sediment bacterial community was significantly higher in the dry season than in the wet season, while no significant difference of alpha diversity was found between river and estuary. Neutral community model revealed a significant influence of stochastic processes on sediment bacterial community assembly, especially in the wet season. However, the beta nearest-taxon index indicated that deterministic processes were more responsible for the assembly of sediment bacterial community. Additionally, redundancy analysis suggested strong links between sediment bacterial communities and environmental factors in Shenzhen river-bay system, with the environmental factors explaining 63.5% of the bacterial community variation. Specifically, NH4+, pH, and salinity were the three most important contributing factors that shaped the sediment bacterial communities. Overall, this study provides a valuable reference to get insights into the spatiotemporal pattern of sediment bacterial communities in a typical river-bay system. KEY POINTS: • Stochastic processes contribute sediment bacterial community assembly. • Deterministic processes dominate sediment bacterial community assembly. • Environmental factors shape sediment bacterial communities.
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Affiliation(s)
- Zhongyi Lu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Zongbao Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Cuijing Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Qiaoyan Wei
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.,School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, 541004, China
| | - Siyu Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
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Dai W, Zhang J, Tu Q, Deng Y, Qiu Q, Xiong J. Bacterioplankton assembly and interspecies interaction indicating increasing coastal eutrophication. Chemosphere 2017; 177:317-325. [PMID: 28319885 DOI: 10.1016/j.chemosphere.2017.03.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/26/2017] [Accepted: 03/09/2017] [Indexed: 06/06/2023]
Abstract
Anthropogenic perturbations impose negative effects on coastal ecosystems, such as increasing levels of eutrophication. Given the biogeochemical significance of microorganisms, understanding the processes and mechanisms underlying their spatial distribution under changing environmental conditions is critical. To address this question, we examined how coastal bacterioplankton communities respond to increasing eutrophication levels created by anthropogenic perturbations. The results showed that the magnitude of changes in the bacterioplankton community compositions (BCCs) and the importance of deterministic processes that constrained bacterial assembly were closely associated with eutrophication levels. Moreover, increasing eutrophication significantly (P < 0.001) attenuated the distance decay rate, with a random spatial distribution of BCCs in the undisturbed location. In contrast, the complexity of interspecies interaction was enhanced under moderate eutrophication levels but declined under heavy eutrophication. Changes in the relative abundances of 27 bacterial families were significantly correlated with eutrophication levels. Notably, the pattern of enrichment or decrease for a given bacterial family was consistent with its known ecological functions. Our findings demonstrate that the magnitude of changes in BCCs and underlying determinism are dependent on eutrophication levels. However, the buffer capacity of bacterioplankton community is limited, with disrupted interspecies interaction occurring under heavy eutrophication. As such, bacterial assemblages are sensitive to changes in environmental conditions and could thus potentially serve as bio-indicators for increasing eutrophication.
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Affiliation(s)
- Wenfang Dai
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Jinjie Zhang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Qichao Tu
- Department of Marine Sciences, Ocean College, Zhejiang University, Hangzhou, 310058, China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, CAS, Beijing, 100085, China
| | - Qiongfen Qiu
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jinbo Xiong
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China.
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19
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Ferrenberg S, Martinez AS, Faist AM. Aboveground and belowground arthropods experience different relative influences of stochastic versus deterministic community assembly processes following disturbance. PeerJ 2016; 4:e2545. [PMID: 27761333 PMCID: PMC5068348 DOI: 10.7717/peerj.2545] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 09/08/2016] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Understanding patterns of biodiversity is a longstanding challenge in ecology. Similar to other biotic groups, arthropod community structure can be shaped by deterministic and stochastic processes, with limited understanding of what moderates the relative influence of these processes. Disturbances have been noted to alter the relative influence of deterministic and stochastic processes on community assembly in various study systems, implicating ecological disturbances as a potential moderator of these forces. METHODS Using a disturbance gradient along a 5-year chronosequence of insect-induced tree mortality in a subalpine forest of the southern Rocky Mountains, Colorado, USA, we examined changes in community structure and relative influences of deterministic and stochastic processes in the assembly of aboveground (surface and litter-active species) and belowground (species active in organic and mineral soil layers) arthropod communities. Arthropods were sampled for all years of the chronosequence via pitfall traps (aboveground community) and modified Winkler funnels (belowground community) and sorted to morphospecies. Community structure of both communities were assessed via comparisons of morphospecies abundance, diversity, and composition. Assembly processes were inferred from a mixture of linear models and matrix correlations testing for community associations with environmental properties, and from null-deviation models comparing observed vs. expected levels of species turnover (Beta diversity) among samples. RESULTS Tree mortality altered community structure in both aboveground and belowground arthropod communities, but null models suggested that aboveground communities experienced greater relative influences of deterministic processes, while the relative influence of stochastic processes increased for belowground communities. Additionally, Mantel tests and linear regression models revealed significant associations between the aboveground arthropod communities and vegetation and soil properties, but no significant association among belowground arthropod communities and environmental factors. DISCUSSION Our results suggest context-dependent influences of stochastic and deterministic community assembly processes across different fractions of a spatially co-occurring ground-dwelling arthropod community following disturbance. This variation in assembly may be linked to contrasting ecological strategies and dispersal rates within above- and below-ground communities. Our findings add to a growing body of evidence indicating concurrent influences of stochastic and deterministic processes in community assembly, and highlight the need to consider potential variation across different fractions of biotic communities when testing community ecology theory and considering conservation strategies.
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Affiliation(s)
- Scott Ferrenberg
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, CO, United States
| | - Alexander S. Martinez
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, CO, United States
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Akasha M. Faist
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, CO, United States
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