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Wang L, Zhu M, Li Y, Zhao Z, Hu T. Deterministic assembly process dominates bacterial antibiotic resistome in wastewater effluents receiving river. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:90207-90218. [PMID: 35864403 DOI: 10.1007/s11356-022-22096-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Antibiotic resistance has become a concerning global health challenge, such as the dissemination of bacteria and genes between humans and the environments. Wastewater treatment plants (WWTPs) effluents, as significant reservoirs for antimicrobial resistant bacteria and antibiotic resistance genes (ARGs), pose critical risks to public health. However, whether wastewater effluent prominently contributes to the abundance of ARGs and their community assembly processes in receiving river has yet been unclear. Here we investigated the effects of the effluent discharge on the ARGs and their associate microbial community in the receiving river (Qinhuai River, Nanjing) of upstream and 2000 m downstream of one WWTPs discharge point. Results revealed that the total antibiotic concentrations of all sediment samples ranged from 37.86 to 76.11 µg/kg dw, while antibiotic concentrations and ARG abundances in the river near the wastewater discharge site were significantly higher than that of the downstream receiving river. The metagenomic assembly obtained 245 ARGs associated with 19 antibiotic types in the receiving river. Network analyses confirmed that Proteobacteria, Firmicutes, Acidobacteria, and Bacteroides were the key phylum and positively correlated with the antibiotic resistome. Additionally, the bacterial pathogens of the receiving river were identified as the most frequent strains of clinically relevant antibacterial resistance, such as Streptococcus pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii. Using null modeling analysis to determine the quantification of ecological processes, the results showed that heterogeneous environmental selection (81.81%) was a dominate role of the ecological mechanisms determining the ARG community reconstruction in the receiving river. Our results may contribute to control the environmental dissemination of antimicrobial resistance risks in aquatic environments.
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Affiliation(s)
- Linqiong Wang
- College of Oceanography, Hohai University, Nanjing, China.
| | - Mengjie Zhu
- College of Environment, Hohai University, Nanjing, China
| | - Yi Li
- College of Environment, Hohai University, Nanjing, China
| | - Zhe Zhao
- College of Oceanography, Hohai University, Nanjing, China
| | - Tong Hu
- College of Environment, Hohai University, Nanjing, China
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Liu Q, Yang J, Wang B, Liu W, Hua Z, Jiang H. Influence of salinity on the diversity and composition of carbohydrate metabolism, nitrogen and sulfur cycling genes in lake surface sediments. Front Microbiol 2022; 13:1019010. [PMID: 36519167 PMCID: PMC9742235 DOI: 10.3389/fmicb.2022.1019010] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/08/2022] [Indexed: 08/23/2023] Open
Abstract
Exploring functional gene composition is essential for understanding the biogeochemical functions of lakes. However, little is known about the diversity and composition of biogeochemical cycling genes and their influencing factors in saline lakes. In this study, metagenomic analysis was employed to characterize the diversity and composition of microbial functions predicted from genes involved in carbohydrate metabolisms, nitrogen, and sulfur cycles in 17 surface sediments of Qinghai-Tibetan lakes with salinity ranging from 0.7 to 31.5 g L-1. The results showed that relative abundances of carbohydrate-active enzyme (CAZy), nitrogen, and sulfur cycling genes were 92.7-116.5, 15.1-18.7, 50.8-63.9 per 1,000 amino acid coding reads, respectively. The Shannon diversity indices of CAZy and sulfur cycling genes decreased with increasing salinity, whereas nitrogen cycling gene diversity showed an opposite trend. Relative abundances of many CAZy (i.e., carbohydrate-binding module and carbohydrate esterase), nitrogen (i.e., anammox and organic degradation and synthesis) and sulfur (i.e., dissimilatory sulfur reduction and oxidation, link between inorganic and organic sulfur transformation, sulfur disproportionation and reduction) cycling gene categories decreased with increasing salinity, whereas some CAZy (i.e., auxiliary activity), nitrogen (i.e., denitrification) and sulfur (i.e., assimilatory sulfate reduction and sulfur oxidation) gene categories showed an increasing trend. The compositions of CAZy, nitrogen, and sulfur cycling genes in the studied lake sediments were significantly (p < 0.05) affected by environmental factors such as salinity, total organic carbon, total nitrogen, and total phosphorus, with salinity having the greatest influence. Together, our results suggest that salinity may regulate the biogeochemical functions of carbohydrate metabolisms, nitrogen, and sulfur cycles in lakes through changing the diversity and composition of microbial functional genes. This finding has great implications for understanding the impact of environmental change on microbial functions in lacustrine ecosystems.
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Affiliation(s)
- Qing Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Beichen Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Wen Liu
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Zhengshuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, China
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Xiang Q, Chen QL, Yang XR, Li G, Zhu D. Soil mesofauna alter the balance between stochastic and deterministic processes in the plastisphere during microbial succession. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 849:157820. [PMID: 35932868 DOI: 10.1016/j.scitotenv.2022.157820] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/30/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
Plastic debris, as a novel substrate, provides an avenue for enriching microbial growth. Although the structure of the aquatic plastisphere microbial community is well-characterised, linkages between microbial community assembly and species co-existence in the soil plastisphere vary and remain poorly understood, particularly when soil fauna is involved. This study investigated the soil plastisphere community, including bacteria, fungi, and protists, focusing on microbial succession and community assembly processes impacted by soil mesofauna. Certain soil plastisphere microbial taxa thrived at particular time points (e.g. Actinobacteria at 60 d), indicating the irreplaceable role of microplastic selection for time-sensitive taxa. Additionally, the biodiversity of keystone ecological clusters in the soil plastisphere was significantly associated with incubation time. Furthermore, the slopes of bacterial and fungal time-decay curves in soil plastisphere were steeper when treated with soil mesofauna than without soil mesofauna, whereas protist time-decay curves (total and abundant taxa) exhibited the opposite trend. Soil mesofauna increased the relative importance of determinacy in the soil plastisphere bacterial assembly process, while enhancing the stochasticity of fungal and protistan community assemblages. The study demonstrates the complex assembly patterns of soil plastisphere microbial communities, emphasising the importance of interactions between the plastisphere and local soil fauna from an ecological perspective.
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Affiliation(s)
- Qian Xiang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, 88 Zhongke Road, NingBo 315800, China
| | - Qing-Lin Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, 88 Zhongke Road, NingBo 315800, China
| | - Xiao-Ru Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Gang Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, 88 Zhongke Road, NingBo 315800, China
| | - Dong Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, 88 Zhongke Road, NingBo 315800, China.
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Zakharova Y, Bashenkhaeva M, Galachyants Y, Petrova D, Tomberg I, Marchenkov A, Kopyrina L, Likhoshway Y. Variability of Microbial Communities in Two Long-Term Ice-Covered Freshwater Lakes in the Subarctic Region of Yakutia, Russia. MICROBIAL ECOLOGY 2022; 84:958-973. [PMID: 34741646 DOI: 10.1007/s00248-021-01912-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
Although under-ice microbial communities are subject to a cold environment, low concentrations of nutrients, and a lack of light, they nevertheless take an active part in biogeochemical cycles. However, we still lack an understanding of how high their diversity is and how these communities are distributed during the long-term ice-cover period. Here, we assessed for the first time the composition and distribution of microbial communities during the ice-cover period in two subarctic lakes (Labynkyr and Vorota) located in the area of the lowest temperature in the Northern Hemisphere. The diversity distribution and abundance of main bacterial taxa as well as the composition of microalgae varied by time and habitat. The 16S rRNA gene sequencing method revealed, in general, a high diversity of bacterial communities where Proteobacteria (~ 45%) and Actinobacteria (~ 21%) prevailed. There were significant differences between the communities of the lakes: Chthoniobacteraceae, Moraxellaceae, and Pirellulaceae were abundant in Lake Labynkyr, while Cyanobiaceae, Oligoflexales, Ilumatobacteraceae, and Methylacidiphilaceae were more abundant in Lake Vorota. The most abundant families were evenly distributed in April, May, and June their contribution was different in different habitats. In April, Moraxellaceae and Ilumatobacteraceae were the most abundant in the water column, while Sphingomonadaceae was abundant both in water column and on the ice bottom. In May, the abundance of Comamonadaceae increased and reached the maximum in June, while Cyanobiaceae, Oxalobacteraceae, and Pirellulaceae followed. We found a correlation of the structure of bacterial communities with snow thickness, pH, Nmin concentration, and conductivity. We isolated psychrophilic heterotrophic bacteria both from dominating and minor taxa of the communities studied. This allowed for specifying their ecological function in the under-ice communities. These findings will advance our knowledge of the under-ice microbial life.
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Affiliation(s)
- Yulia Zakharova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Street, Irkutsk, 664033, Russia
| | - Maria Bashenkhaeva
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Street, Irkutsk, 664033, Russia.
| | - Yuri Galachyants
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Street, Irkutsk, 664033, Russia
| | - Darya Petrova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Street, Irkutsk, 664033, Russia
| | - Irina Tomberg
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Street, Irkutsk, 664033, Russia
| | - Artyom Marchenkov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Street, Irkutsk, 664033, Russia
| | - Liubov Kopyrina
- Institute for Biological Problems of Cryolithozone, Siberian Branch of the Russian Academy of Sciences, 41 Lenin Ave, Yakutsk, 677980, Russia
| | - Yelena Likhoshway
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Street, Irkutsk, 664033, Russia
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55
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Jia X, Dini-Andreote F, Salles JF. Unravelling the interplay of ecological processes structuring the bacterial rare biosphere. ISME COMMUNICATIONS 2022; 2:96. [PMID: 37938751 PMCID: PMC9723687 DOI: 10.1038/s43705-022-00177-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 09/13/2022] [Accepted: 09/13/2022] [Indexed: 06/17/2023]
Abstract
Most ecological communities harbor many rare species (i.e., the rare biosphere), however, relatively little is known about how distinct ecological processes structure their existence. Here, we used spatiotemporal data on soil bacterial communities along a natural ecosystem gradient to model the relative influences of assembly processes structuring the rare and common biospheres. We found a greater influence of homogeneous selection (i.e., imposed by spatiotemporally constant variables) mediating the assembly of the rare biosphere, whereas the common biosphere was mostly governed by variable selection (i.e., imposed by spatial and/or temporal fluctuating variables). By partitioning the different types of rarity, we found homogeneous selection to explain the prevalence of permanently rare taxa, thus suggesting their persistence at low abundances to be restrained by physiological traits. Conversely, the dynamics of conditionally rare taxa were mostly structured by variable selection, which aligns with the ability of these taxa to switch between rarity and commonness as responses to environmental spatiotemporal variations. Taken together, our study contributes to the establishment of a link between conceptual and empirical developments in the ecology of the soil microbial rare biosphere. Besides, this study provides a framework to better understand, model, and predict the existence and dynamics of microbial rare biospheres across divergent systems and scales.
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Affiliation(s)
- Xiu Jia
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, 9747AG, The Netherlands.
| | - Francisco Dini-Andreote
- Department of Plant Science, The Pennsylvania State University, Pennsylvania, University Park, PA, 16801, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16801, USA
| | - Joana Falcão Salles
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, 9747AG, The Netherlands.
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56
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Chen W, Wei J, Su Z, Wu L, Liu M, Huang X, Yao P, Wen D. Deterministic mechanisms drive bacterial communities assembly in industrial wastewater treatment system. ENVIRONMENT INTERNATIONAL 2022; 168:107486. [PMID: 36030743 DOI: 10.1016/j.envint.2022.107486] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/18/2022] [Accepted: 08/21/2022] [Indexed: 06/15/2023]
Abstract
Microbial communities are responsible for biological treatment of many industrial wastewater, but our knowledge of their diversity, assembly patterns, and function is still poor. Here, we analyzed the bacterial communities of wastewater and activated sludge samples taken from 11 full-scale industrial wastewater treatment plants (IWWTPs) characterized by the same process design but different wastewater types and WWTP compartments. We found significantly different diversity and compositions of bacterial assemblages among distinct wastewater types and IWWTPs compartments. IWWTPs bacterial communities exhibited a clear species abundance distribution. The dispersal-driven process was weak in shaping IWWTP communities. Meanwhile, environmental and operating conditions were important factors in regulating the structure of the activated sludge community and pollutants removal, indicating that bacterial community was largely driven by deterministic mechanisms. The core microbial community in IWWTPs was different from that in municipal wastewater treatment plants (MWWTPs), and many taxa (e.g. the genus Citreitalea) rarely were detected before, indicating IWWTPs harbored unique core bacterial communities. Furthermore, we found that bacterial community compositions were strongly linked to activated sludge function. These findings are important to both microbial ecologists and environmental engineers, who may optimize the operation strategies jointly for maintaining biodiversity, which in turn may promote a more stable performance of the IWWTP. Overall, our study enhances the mechanistic understanding of the IWWTP microbial community diversity, assembly patterns, and function, and provides important implications for microbial ecology and wastewater treatment processes.
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Affiliation(s)
- Weidong Chen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Jie Wei
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Zhiguo Su
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; School of Environment, Tsinghua University, Beijing 100084, China
| | - Linwei Wu
- Institute of Ecology, Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing China
| | - Min Liu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Xiaoxuan Huang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Pengcheng Yao
- Zhejiang Institute of Hydraulics and Estuary, Hangzhou 310017, China
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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57
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Arboleda-Baena C, Pareja CB, Pla I, Logares R, De la Iglesia R, Navarrete SA. Hidden interactions in the intertidal rocky shore: variation in pedal mucus microbiota among marine grazers that feed on epilithic biofilm communities. PeerJ 2022; 10:e13642. [PMID: 36172502 PMCID: PMC9512015 DOI: 10.7717/peerj.13642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 06/07/2022] [Indexed: 01/17/2023] Open
Abstract
In marine ecosystems, most invertebrates possess diverse microbiomes on their external surfaces, such as those found in the pedal mucus of grazing gastropods and chitons that aids displacement on different surfaces. The microbes are then transported around and placed in contact with free-living microbial communities of micro and other macro-organisms, potentially exchanging species and homogenizing microbial composition and structure among grazer hosts. Here, we characterize the microbiota of the pedal mucus of five distantly related mollusk grazers, quantify differences in microbial community structure, mucus protein and carbohydrate content, and, through a simple laboratory experiment, assess their effects on integrated measures of biofilm abundance. Over 665 Amplicon Sequence Variants (ASVs) were found across grazers, with significant differences in abundance and composition among grazer species and epilithic biofilms. The pulmonate limpet Siphonaria lessonii and the periwinkle Echinolittorina peruviana shared similar microbiota. The microbiota of the chiton Chiton granosus, keyhole limpet Fissurella crassa, and scurrinid limpet Scurria araucana differed markedly from one another, and form those of the pulmonate limpet and periwinkle. Flavobacteriaceae (Bacteroidia) and Colwelliaceae (Gammaproteobacteria) were the most common among microbial taxa. Microbial strict specialists were found in only one grazer species. The pedal mucus pH was similar among grazers, but carbohydrate and protein concentrations differed significantly. Yet, differences in mucus composition were not reflected in microbial community structure. Only the pedal mucus of F. crassa and S. lessonii negatively affected the abundance of photosynthetic microorganisms in the biofilm, demonstrating the specificity of the pedal mucus effects on biofilm communities. Thus, the pedal mucus microbiota are distinct among grazer hosts and can affect and interact non-trophically with the epilithic biofilms on which grazers feed, potentially leading to microbial community coalescence mediated by grazer movement. Further studies are needed to unravel the myriad of non-trophic interactions and their reciprocal impacts between macro- and microbial communities.
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Affiliation(s)
- Clara Arboleda-Baena
- Estación Costera de Investigaciones Marinas and Center for Applied Ecology and Sustainability (CAPES), Pontificia Universidad Católica de Chile, El Tabo, Chile
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago de Chile, Región Metropolitana, Chile
| | - Claudia Belén Pareja
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago de Chile, Región Metropolitana, Chile
| | - Isadora Pla
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago de Chile, Región Metropolitana, Chile
| | - Ramiro Logares
- Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalonia, Spain
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago de Chile, Región Metropolitana, Chile
- Marine Energy Research & Innovation Center (MERIC), Santiago de Chile, Chile
| | - Sergio Andrés Navarrete
- Estación Costera de Investigaciones Marinas and Center for Applied Ecology and Sustainability (CAPES), Pontificia Universidad Católica de Chile, El Tabo, Chile
- Marine Energy Research & Innovation Center (MERIC), Santiago de Chile, Chile
- Centro Basal COPAS-COASTAL, Universidad de Concepción
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58
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Wang L, Li Y, Zhao Z, Zhu M, Hu T. Tidal flat aquaculture pollution governs sedimentary antibiotic resistance gene profiles but not bacterial community based on metagenomic data. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 833:155206. [PMID: 35421458 DOI: 10.1016/j.scitotenv.2022.155206] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 03/29/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
Coastal tidal flats are intersection zones between terrestrial and marine environments and are considered repositories of pollutants from anthropogenic activities (e.g., fishery and aquaculture). Specifically, the prevalence of antibiotics and antibiotic resistance genes (ARGs) in coastal aquaculture environments pose critical threats to estuarine ecosystems. However, the contribution of aquaculture to the occurrence and abundance of ARGs and community assemblies has not been fully explored in tidal flat zones. Thus, we investigated ARGs profiles, ARG-carrying host bacteria, and their associate microbial community in the Dongtai and Sheyang tidal flat aquaculture regions of Jiangsu, China using metagenomic assembly methods. The antibiotic concentrations in the sediment samples ranged from nd to 35.50 ng/g dw, and the antibiotic pollution in the Dongtai tidal flat was more severe than in the Sheyang tidal flats. Metagenomic assembly indicated that a total of 247 ARG subtypes associated with ARG 33 types were characterized across all samples and their abundance in the Dongtai region exceeded that in the Sheyang region. Meanwhile, 21 bacteria in the tidal flat aquaculture were identified as ARG-carrying pathogens, including Escherichia coli, Vibrio fluvialis, and Staphylococcus aureus. Using neutral and null modeling analysis to determine the community ecological processes, the results revealed bacterial and ARG communities were generally dominated by stochastic and deterministic processes, respectively. The above results suggested that aquaculture pollution was contributed to shape ARG profiles in tidal flats. The observed deterministic processes affecting the ARG community in tidal flat aquaculture also provides an effective foundation to control the risks of environmental antibiotic resistance through reducing aquaculture antibiotic usage.
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Affiliation(s)
- Linqiong Wang
- Key Laboratory of Marine Hazards Forecasting, Ministry of Natural Resources, Hohai University, Xikang Road #1, Nanjing, China; College of Oceanography, Hohai University, Xikang Road #1, Nanjing, China
| | - Yi Li
- College of Environment, Hohai University, Xikang Road #1, Nanjing, China.
| | - Zhe Zhao
- Key Laboratory of Marine Hazards Forecasting, Ministry of Natural Resources, Hohai University, Xikang Road #1, Nanjing, China; College of Oceanography, Hohai University, Xikang Road #1, Nanjing, China
| | - Mengjie Zhu
- College of Environment, Hohai University, Xikang Road #1, Nanjing, China
| | - Tong Hu
- College of Environment, Hohai University, Xikang Road #1, Nanjing, China
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59
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Biderre‐Petit C, Charvy J, Bronner G, Chauvet M, Debroas D, Gardon H, Hennequin C, Jouan‐Dufournel I, Moné A, Monjot A, Ravet V, Vellet A, Lepère C. FreshOmics
: a manually curated and standardized –omics database for investigating freshwater microbiomes. Mol Ecol Resour 2022; 23:222-232. [DOI: 10.1111/1755-0998.13692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Corinne Biderre‐Petit
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Jean‐Christophe Charvy
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Gisèle Bronner
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Marina Chauvet
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Didier Debroas
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Hélène Gardon
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Claire Hennequin
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Isabelle Jouan‐Dufournel
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Anne Moné
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Arthur Monjot
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Viviane Ravet
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Agnès Vellet
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Cécile Lepère
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
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60
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Abdullah Al M, Xue Y, Xiao P, Xu J, Chen H, Mo Y, Shimeta J, Yang J. Community assembly of microbial habitat generalists and specialists in urban aquatic ecosystems explained more by habitat type than pollution gradient. WATER RESEARCH 2022; 220:118693. [PMID: 35667165 DOI: 10.1016/j.watres.2022.118693] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/19/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
Urban freshwater ecosystems have important ecosystem functions, provide habitats for diverse microbial communities and are susceptible to multiple interconnected factors such as environmental pollution. Despite the ecological significance of bacteria and microeukaryotes, little is known about how their community assembly responds to various environmental factors across water and sediment habitats and ecological processes shaping them. Here, environmental DNA-based approaches were used to investigate the community assembly processes of bacteria and microeukaryotes (including habitat generalists and specialists) in urban water and sediment across an urban-pollution gradient in Wuhan, central China. The diversity, community composition and potential function of bacteria and microeukaryotes showed significantly stronger variation between water and sediment than across an urban pollution gradient. Although, bacterial and microeukaryotic community assemblies were dominated by strong selection processes in both water and sediment habitats, but a contrasting community assembly mechanism was identified between habitat generalists and specialists. Bacterial and microeukaryotic communities showed a greater response to physicochemical variability in water, while a strong distance-decay relationship was found in sediment. Further, cross-kingdom microbial network analysis revealed strong modular associations of bacteria and microeukaryotes, meanwhile, microeukaryotic habitat specialists might be keystone, but generalists have higher proportion of connections in the networks. This study provides significant insights into the response of bacteria and microeukaryotes to different urban pollutions between water and sediment, and the ecological processes structuring microbial community dynamics across habitat types under anthropogenic disturbances.
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Affiliation(s)
- Mamun Abdullah Al
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinses Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanyuan Xue
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinses Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Peng Xiao
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinses Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Jing Xu
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan 430072, China
| | - Huihuang Chen
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinses Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanyuan Mo
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinses Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jeff Shimeta
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Jun Yang
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinses Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China.
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Li Y, Khan FH, Wu J, Zhang Y, Jiang Y, Chen X, Yao Y, Pan Y, Han X. Drivers of Spatiotemporal Eukaryote Plankton Distribution in a Trans-Basin Water Transfer Canal in China. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.899993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Planktonic eukaryotes are important components of aquatic ecosystems, and analyses of the whole eukaryotic planktonic community composition and function have far-reaching significance for water resource management. We aimed to understand the spatiotemporal variation and drivers of eukaryotic plankton distribution in the Middle Route Project of the South-to-North Water Diversion in Henan Province, China. Specifically, we examined planktonic assemblages and water quality at five stations along the canal and another one located before the dam in March, June, September, and December 2019. High-throughput sequencing revealed that the eukaryotic plankton community was primarily composed of 53 phyla, 200 genera, and 277 species, with Cryptophyta, Ciliophora, and norank_k_Cryptophyta being the dominant phyla. Redundancy analysis of the eukaryotic community and environmental factors showed that five vital factors affecting eukaryotic plankton distribution were oxidation-reduction potential, nitrate nitrogen, pH, total phosphorus, and water flow velocity. Furthermore, the geographical distribution of eukaryotic communities was consistent with the distance decay model. Importantly, environmental selection dominantly shaped the geographical distribution of the eukaryotic community. In summary, our study elucidates the ecological response of planktonic eukaryotes by identifying the diversity and ecological distribution of planktonic eukaryotes in trans-basin diversion channels.
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Co-Occurrence Relationship and Stochastic Processes Affect Sedimentary Archaeal and Bacterial Community Assembly in Estuarine-Coastal Margins. Microorganisms 2022; 10:microorganisms10071339. [PMID: 35889058 PMCID: PMC9318014 DOI: 10.3390/microorganisms10071339] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/24/2022] Open
Abstract
Sedimentary microorganisms play crucial roles in maintaining the functional stability of aquatic ecosystems. However, their taxonomic composition and assembly processes are not well known in estuarine−coastal margins because of their complex environment. We investigated microbial communities, co-occurrence relationships, and underlying mechanisms in 33 surface sediment samples collected in the Jiulong River Estuary and the Taiwan Strait to reveal their composition dynamics. The abundance, diversity, and composition of microorganisms demonstrated obvious spatial variables. Methanobacterium and Methanosarcina, as well as Candidatus_Nitrosopumilus and Nitrososphaeraceae were the main methanogenic and ammonia-oxidizing archaea, with an average abundance of more than 5.91% and 4.27%, respectively. Along with a salinity gradient increase, the relative abundance of methanogenic archaea (from 42.9% to 16.6%) contrasted with the trend of ammonia-oxidizing archaea (from 6.04% to 18.7%). The number of methanogenic archaea gradually decreased with increasing geographic distance (p < 0.05), whereas ammonia-oxidizing archaea showed no significant change (p > 0.05). In co-occurrence patterns, closer inter-taxa connections were observed among archaea−archaea and bacteria−bacteria than in archaea−bacteria, which indicated that coexistence within the same kingdom was greater than interaction between different kingdoms in shaping the community structure along the salinity gradient. Furthermore, null model analyses of the microbial community showed that undominated was the most prominent process, explaining over 44.9% of community variation, followed by heterogeneous selection and dispersal limitation, which contributed to 27.7% and 16.3%, respectively. We demonstrated that stochasticity, rather than determinism, regulates community assembly. These results further highlight that intra-kingdom co-occurrence and stochastic processes shape the structure and assembly of microbial communities in estuarine−coastal margins.
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Hu W, Hou Q, Delgado-Baquerizo M, Stegen JC, Du Q, Dong L, Ji M, Sun Y, Yao S, Gong H, Xiong J, Xia R, Liu J, Aqeel M, Akram MA, Ran J, Deng J. Continental-scale niche differentiation of dominant topsoil archaea in drylands. Environ Microbiol 2022; 24:5483-5497. [PMID: 35706137 DOI: 10.1111/1462-2920.16099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/07/2022] [Indexed: 11/26/2022]
Abstract
Archaea represent a diverse group of microorganisms often associated with extreme environments. However, an integrated understanding of biogeographical patterns of the specialist Haloarchaea and the potential generalist ammonia-oxidizing archaea (AOA) across large-scale environmental gradients remains limited. We hypothesize that niche differentiation determines their distinct distributions along environmental gradients. To test the hypothesis, we use a continental-scale research network including 173 dryland sites across northern China. Our results demonstrate that Haloarchaea and AOA dominate topsoil archaeal communities. As hypothesized, Haloarchaea and AOA show strong niche differentiation associated with two ecosystem types mainly found in China's drylands (i.e., deserts vs. grasslands), and they differ in the degree of habitat specialization. The relative abundance and richness of Haloarchaea are higher in deserts due to specialization to relatively high soil salinity and extreme climates, while those of AOA are greater in grassland soils. Our results further indicate a divergence in ecological processes underlying the segregated distributions of Haloarchaea and AOA. Haloarchaea are governed primarily by environmental-based processes while the more generalist AOA are assembled mostly via spatial-based processes. Our findings add to existing knowledge of large-scale biogeography of topsoil archaea, advancing our predictive understanding on changes in topsoil archaeal communities in a drier world. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Weigang Hu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Qingqing Hou
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistemico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, Sevilla, Spain.,Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, Sevilla, Spain
| | - James C Stegen
- Ecosystem Science Team, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Qiajun Du
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Longwei Dong
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Mingfei Ji
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Yuan Sun
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Shuran Yao
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Haiyang Gong
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Junlan Xiong
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Rui Xia
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jiayuan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Muhammad Aqeel
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Muhammad Adnan Akram
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China.,School of Economics, Lanzhou University, Lanzhou, China
| | - Jinzhi Ran
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianming Deng
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
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Ding X, Jin F, Xu J, Zhang S, Chen D, Hu B, Hong Y. The impact of aquaculture system on the microbiome and gut metabolome of juvenile Chinese softshell turtle ( Pelodiscus sinensis). IMETA 2022; 1:e17. [PMID: 38868566 PMCID: PMC10989827 DOI: 10.1002/imt2.17] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/03/2022] [Accepted: 03/13/2022] [Indexed: 06/14/2024]
Abstract
The commercial aquatic animal microbiome may markedly affect the successful host's farming in various aquaculture systems. However, very little was known about it. Here, two different aquaculture systems, the rice-fish culture (RFC) and intensive pond culture (IPC) systems, were compared to deconstruct the skin, oral, and gut microbiome, as well as the gut metabolome of juvenile Chinese softshell turtle (Pelodiscus sinensis). Higher alpha-diversity and functional redundancy of P. sinensis microbial community were found in the RFC than those of the IPC. The aquaculture systems have the strongest influence on the gut microbiome, followed by the skin microbiome, and finally the oral microbiome. Source-tracking analysis showed that the RFC's microbial community originated from more unknown sources than that of the IPC across all body regions. Strikingly, the RFC's oral and skin microbiome exhibited a significantly higher proportion of generalists and broader habitat niche breadth than those of the IPC, but not the gut. Null model analysis revealed that the RFC's oral and skin microbial community assembly was governed by a significantly greater proportion of deterministic processes than that of the IPC, but not the gut. We further identified the key gene and microbial contribution to five significantly changed gut metabolites, 2-oxoglutarate, N-acetyl-d-mannosamine, cis-4-hydroxy-d-proline, nicotinamide, and l-alanine, which were significantly correlated with important categories of microbe-mediated processes, including the amino acid metabolism, GABAergic synapse, ABC transporters, biosynthesis of unsaturated fatty acids, as well as citrate cycle. Moreover, different aquaculture systems have a significant impact on the hepatic lipid metabolism and body shape of P. sinensis. Our results provide new insight into the influence of aquaculture systems on the microbial community structure feature and assembly mechanism in an aquatic animal, also highlighting the key microbiome and gene contributions to the metabolite variation in the gut microbiome-metabolome association.
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Affiliation(s)
- Xia Ding
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Feng Jin
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Jiawang Xu
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Shulei Zhang
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Dongxu Chen
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Beijuan Hu
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Yijiang Hong
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
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65
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Zhu X, Ji L, Cheng M, Wei H, Wang Z, Ning K. Sustainability of the rice-crayfish co-culture aquaculture model: microbiome profiles based on multi-kingdom analyses. ENVIRONMENTAL MICROBIOME 2022; 17:27. [PMID: 35599327 PMCID: PMC9124410 DOI: 10.1186/s40793-022-00422-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/13/2022] [Indexed: 05/31/2023]
Abstract
While the rice-crayfish culture (RCFP) model, an important aquaculture model in Asia, is generally considered a sustainable model, its sustainability in terms of microbial community profiles has not been evaluated. In this study, multi-kingdom analyses of microbiome profiles (i.e., bacteria, archaea, viruses, and eukaryotes) were performed using environmental (i.e., water and sediment) and animal gut (i.e., crayfish and crab gut) microbial samples from the RCFP and other aquaculture models, including the crab-crayfish co-culture, crayfish culture, and crab culture models, to evaluate the sustainability of the RCFP systematically. Results showed that RCFP samples are enriched with a distinct set of microbes, including Shewanella, Ferroplasma, Leishmania, and Siphoviridae, when compared with other aquaculture models. Additionally, most microbes in the RCFP samples, especially microbes from different kingdoms, were densely and positively connected, which indicates their robustness against environmental stress. Whereas microbes in different aquaculture models demonstrated moderate levels of horizontal gene transfer (HGT) across kingdoms, the RCFP showed relatively lower frequencies of HGT events, especially those involving antibiotic resistance genes. Finally, environmental factors, including pH, oxidation-reduction potential, temperature, and total nitrogen, contributed profoundly to shaping the microbial communities in these aquaculture models. Interestingly, compared with other models, the microbial communities of the RCFP model were less influenced by these environmental factors, which suggests that microbes in the latter have stronger ability to resist environmental stress. The findings collectively reflect the unique multi-kingdom microbial patterns of the RCFP model and suggest that this model is a sustainable model from the perspective of microbiome profiles.
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Affiliation(s)
- Xue Zhu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Lei Ji
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Mingyue Cheng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Huimin Wei
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430077, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi Wang
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430077, China.
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
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66
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Zhang L, Ji L, Liu X, Zhu X, Ning K, Wang Z. Linkage and driving mechanisms of antibiotic resistome in surface and ground water: Their responses to land use and seasonal variation. WATER RESEARCH 2022; 215:118279. [PMID: 35305488 DOI: 10.1016/j.watres.2022.118279] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/24/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Antibiotic resistance in the environment, mostly mediated by antibiotic resistance genes (ARGs), has posed a threat to ecological and human health. Contamination of surface water and groundwater with ARGs has become a serious environmental concern. However, the distinctions and similarities across ARG profiles, the various ecological processes associated with ARGs, the driving mechanisms for ARG profiles in surface water and groundwater, and how they respond to land use and seasonal variation remain unknown. To tackle these issues, the contamination of ARGs in surface water and groundwater in central China was investigated using metagenomic technology. The results indicated that seasonal changes in ARG abundance and diversity were inconsistent across surface water and groundwater, and that the relationship between ARGs in surface water and groundwater was stronger during the rainy season. Land use had a greater effect on ARGs in surface water than in groundwater and was stronger during the dry season than during the rainy season. More interestingly, the ideal buffer zones with the greatest impact of land use on the ARGs of surface water and groundwater had distinct radii: 1500 m for both dry and rainy seasons in surface water, and 1000 m for dry season and 500 m for rainy season in groundwater. Furthermore, stochastic mechanisms mediated by mobile gene elements (MGEs) contribute significantly more to ARG assemblages than deterministic processes, particularly in groundwater. Furthermore, our results also showed that ARG enrichment in microbial communities was host- dependent, and the risk of ARGs in groundwater was greater both during the rainy season and dry season. In conclusion, the findings have improved our understanding of the relationship and driving mechanisms of ARGs in surface and ground water, as well as their responses to land use and seasonal variation, which may be beneficial for limiting ARG pollution in a watershed with high levels of anthropogenic activity.
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Affiliation(s)
- Lu Zhang
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Ji
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xi Liu
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China; Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological Environment, Wuhan 430010, China
| | - Xue Zhu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
| | - Zhi Wang
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China.
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67
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Wang Y, Xie R, Shen Y, Cai R, He C, Chen Q, Guo W, Shi Q, Jiao N, Zheng Q. Linking Microbial Population Succession and DOM Molecular Changes in Synechococcus-Derived Organic Matter Addition Incubation. Microbiol Spectr 2022; 10:e0230821. [PMID: 35380472 PMCID: PMC9045170 DOI: 10.1128/spectrum.02308-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/10/2022] [Indexed: 12/04/2022] Open
Abstract
The molecular-level interactions between phytoplankton-derived dissolved organic matter (DOM) and heterotrophic prokaryotes represent a fundamental and yet poorly understood component of the marine elemental cycle. Here, we investigated the degradation of Synechococcus-derived organic matter (SynOM) by coastal microorganisms using spectroscopic and ultrahigh-resolution mass spectrometry analyses coupled with high-throughput sequencing. The added SynOM showed a spectrum of reactivity during a 180-day dark incubation experiment. Along with the decrease in DOM bioavailability, the chemical properties of DOM molecules overall showed increases in oxidation state and aromaticity. Both the microbial community and DOM molecular compositions became more homogeneous toward the end of the incubation. The experiment was partitioned into three phases (I, II, and III) based on the total organic carbon consumption rates from 7.0 ± 1.0 to 1.0 ± 0.1 and to 0.1 ± 0.0 μmol C L-1 day-1, respectively. Diverse generalists with low abundance were present in all three phases of the experiment, while a few abundant specialists dominated specific phases, suggesting their diverse roles in the transformation of DOM molecules from labile and semilabile to recalcitrant. The changes of organic molecules belonging to CHO, CHNO, and CHOS containing formulas were closely associated with specific microbial populations, suggesting close interactions between the different bacterial metabolic potential for substrates and DOM molecular compositional characteristics. This study sheds light on the interactions between microbial population succession and DOM molecular changes processes and collectively advances our understanding of microbial processing of the marine elemental cycle. IMPORTANCE Phytoplankton are a major contributor of labile dissolved organic matter (DOM) in the upper ocean, fueling tremendous marine prokaryotic activity. Interactions between microorganisms and algae-derived DOM regulate biogeochemical cycles in the ocean, but key aspects of their interactions remain poorly understood. Under global warming and eutrophication scenarios, Synechococcus blooms are commonly observed in coastal seawaters, and they significantly influence the elemental biogeochemistry cycling in eutrophic ecosystems. To understand the interactions between Synechococcus-derived DOM and heterotrophic prokaryotes as well as their influence on the coastal environment, we investigated the degradation of DOM by coastal microbes during a 180-day dark incubation. We showed substantial DOM compositional changes that were closely linked to the developments of microbial specialists and generalists. Our study provides information on the interactions between microbial population succession and DOM molecular changes, thereby advancing our understanding of microbial processing of the marine DOM pool under the influence of climate change.
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Affiliation(s)
- Yu Wang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Rui Xie
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Yuan Shen
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Ruanhong Cai
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China
| | - Qi Chen
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Weidong Guo
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Key Laboratory of Coastal and Wetland Ecosystems, Ministry of Education, Xiamen University, Xiamen, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Qiang Zheng
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
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68
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Li Y, Wei J, Yang H, Zhang D, Hu C. Biogeographic, Driving Factors, Assembly, and Co-occurrence Patterns of Archaeal Community in Biocrusts. Front Microbiol 2022; 13:848908. [PMID: 35495652 PMCID: PMC9042396 DOI: 10.3389/fmicb.2022.848908] [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: 01/05/2022] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Archaea exhibit strong community heterogeneity with microhabitat gradients and are a non-negligible part of biocrust's microorganisms. The study on archaeal biogeography in biocrusts could provide new insights for its application in environmental restoration. However, only a few studies on assembly processes and co-occurrence patterns of the archaeal community in patchy biocrusts have been reported, especially considering the number of species pools (SPs). Here, we comprehensively collected biocrusts across 3,500 km of northern China. Different successional biocrusts from various regions contain information of local climate and microenvironments, which can shape multiple unique archaeal SPs. The archaeal community differences in the same successional stage exceeded the variations between successional stages, which was due to the fact that the heterogeneous taxa tended to exchange between unknown patches driven by drift. We also comparatively studied the driving forces of community heterogeneity across three to ten SPs, and assembly and co-occurrence patterns were systematically analyzed. The results revealed that the impact of spatial factors on biogeographic patterns was greater than that of environmental and successional factors and that impact decreased with the number of SPs considered. Meanwhile, community heterogeneity at the phylogenetic facet was more sensitive to these driving factors than the taxonomic facet. Subgroups 1 (SG1) and 2 (SG2) of the archaeal communities in biocrusts were dominated by Nitrososphaeraceae and Haloarchaea, respectively. The former distribution pattern was associated with non-salinity-related variables and primarily assembled by drift, whereas the latter was associated with salinity-related variables and primarily assembled by homogeneous selection. Finally, network analysis indicated that the SG1 network had a higher proportion of competition and key taxa than the SG2 network, but the network of SG2 was more complex. Our study suggested that the development of the archaeal community was not consistent with biocrusts succession. The dominant taxa may determine the patterns of community biogeography, assembly, and co-occurrence.
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Affiliation(s)
- Yuanlong Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingyi Wei
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haijian Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Delu Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chunxiang Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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69
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Chung TH, Zakaria BS, Meshref MNA, Dhar BR. Enhancing quorum sensing in biofilm anode to improve biosensing of naphthenic acids. Biosens Bioelectron 2022; 210:114275. [PMID: 35447397 DOI: 10.1016/j.bios.2022.114275] [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: 02/13/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 11/18/2022]
Abstract
The feasibility of enhancing quorum sensing (QS) in anode biofilm to improve the quantifications of commercial naphthenic acid concentrations (9.4-94 mg/L) in a microbial electrochemical cell (MXC) based biosensor was demonstrated in this study. First, three calibration methods were systematically compared, and the charging-discharging operation was selected for further experiments due to its 71-227 folds higher electrical signal outputs than the continuous closed-circuit operation and cyclic voltammetry modes. Then, the addition of acylase (5 μg/L) as an exogenous QS autoinducer (acylase) was investigated, which further improved the biosensor's electrical signal output by ∼70%, as compared to the control (without acylase). The addition of acylase increased the relative expression of QS-associated genes (lasR, lasI, rhlR, rhlI, lasA, and luxR) by 7-100%, along with increased abundances of known electroactive bacterial genera, such as Geobacter (from 42% to 47%) and Desulfovibrio (from 6% to 11%). Furthermore, toxicities of different NAs concentrations measured with the Microtox bioassay test were correlated with corresponding electrical signals, indicating that MXC-biosensor can provide a dual platform for rapid assessment of both NA concentrations and NA-associated toxicity.
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Affiliation(s)
- Tae Hyun Chung
- Civil and Environmental Engineering, University of Alberta, 9211-116, Street NW, Edmonton, AB, T6G 1H9, Canada
| | - Basem S Zakaria
- Civil and Environmental Engineering, University of Alberta, 9211-116, Street NW, Edmonton, AB, T6G 1H9, Canada
| | - Mohamed N A Meshref
- Civil and Environmental Engineering, University of Alberta, 9211-116, Street NW, Edmonton, AB, T6G 1H9, Canada; Public Works Department, Faculty of Engineering, Ain Shams University, 1 El Sarayat St., Abbassia, Cairo, 11517, Egypt
| | - Bipro Ranjan Dhar
- Civil and Environmental Engineering, University of Alberta, 9211-116, Street NW, Edmonton, AB, T6G 1H9, Canada.
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70
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Schiro G, Chen Y, Blankinship JC, Barberán A. Ride the dust: Linking dust dispersal and spatial distribution of microorganisms across an arid landscape. Environ Microbiol 2022; 24:4094-4107. [PMID: 35384241 DOI: 10.1111/1462-2920.15998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/01/2022] [Accepted: 04/03/2022] [Indexed: 11/30/2022]
Abstract
In arid ecosystems, where the soil is directly exposed to the action of the wind due to sparse vegetation, dust aerosolization is a consequence of soil degradation and concomitantly, a major vector of microbial dispersal. Disturbances such as livestock grazing or fire can exacerbate wind erosion and dust production. Here, we sampled surface soils in 29 locations across an arid landscape in southwestern USA and characterized their prokaryotic and fungal communities. At four of these locations, we also sampled potential fugitive dust. By comparing the composition of soil and dust samples, we determined the role of dust dispersal in structuring the biogeography of soil microorganisms across the landscape. For Bacteria/Archaea, we found dust associated taxa to have on average, higher regional occupancies compared to soil associated taxa. Complementarily, we found dust samples to harbor a higher amount of widely distributed taxa compared to soil samples. Overall, our study shows how dust dispersal plays a role in the spatial distribution of soil Bacteria/Archaea, but not soil Fungi, and might inform indicators of soil health and stability in arid ecosystems. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Gabriele Schiro
- Department of Environmental Science, University of Arizona, Tucson, Arizona, 85721, USA
| | - Yongjian Chen
- Department of Environmental Science, University of Arizona, Tucson, Arizona, 85721, USA
| | - Joseph C Blankinship
- Department of Environmental Science, University of Arizona, Tucson, Arizona, 85721, USA
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, Tucson, Arizona, 85721, USA
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71
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Microbial Community Structure and Bacterial Lineages Associated with Sulfonamides Resistance in Anthropogenic Impacted Larut River. WATER 2022. [DOI: 10.3390/w14071018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Anthropogenic activities often contribute to antibiotic resistance in aquatic environments. Larut River Malaysia is polluted with both organic and inorganic pollutants from domestic and industrial wastewater that are probably treated inadequately. The river is characterized by high biochemical oxygen demand, chemical oxygen demand, total suspended solids, ammonia, and heavy metals. In our previous study, sulfonamides (SAs) and sulfonamide resistance genes (sul) were detected in the Larut River. Hence, in this study, we further examined the microbial community structure, diversity of sulfonamide-resistant bacteria (SARB), and their resistance genes. The study also aimed at identifying cultivable bacteria potential carriers of sul genes in the aquatic environment. Proteobacteria (22.4–66.0%), Firmicutes (0.8–41.6%), Bacteroidetes (2.0–29.4%), and Actinobacteria (5.5–27.9%) were the most dominant phyla in both the effluents and river waters. SARB isolated consisted only 4.7% of the total genera identified, with SAR Klebsiella as the most dominant (38.0–61.3%) followed by SAR Escherichia (0–22.2%) and Acinetobacter (3.2–16.0%). The majority of the SAR Klebsiella isolated from the effluents and middle downstream were positive for sul genes. Sul genes-negative SAR Escherichia and Acinetobacter were low (<20%). Canonical-correlation analysis (CCA) showed that SAs residues and inorganic nutrients exerted significant impacts on microbial community and total sul genes. Network analysis identified 11 SARB as potential sul genes bacterial carriers. These findings indicated that anthropogenic activities exerted impacts on the microbial community structure and SAs resistance in the Larut River.
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72
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Wang L, Li J, Zhang S. A Comprehensive Network Integrating Signature Microbes and Crucial Soil Properties During Early Biological Soil Crust Formation on Tropical Reef Islands. Front Microbiol 2022; 13:831710. [PMID: 35369528 PMCID: PMC8969229 DOI: 10.3389/fmicb.2022.831710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/15/2022] [Indexed: 11/26/2022] Open
Abstract
Biological soil crusts (BSCs/biocrusts), which are distributed across various climatic zones and well-studied in terrestrial drylands, harbor polyextremotolerant microbial topsoil communities and provide ecological service for local and global ecosystem. Here, we evaluated BSCs in the tropical reef islands of the South China Sea. Specifically, we collected 41 BSCs, subsurface, and bare soil samples from the Xisha and Nansha Archipelagos. High-throughput amplicon sequencing was performed to analyze the bacterial, fungal, and archaeal compositions of these samples. Physicochemical measurement and enzyme activity assays were conducted to characterize the soil properties. Advanced computational analysis revealed 47 biocrust-specific microbes and 10 biocrust-specific soil properties, as well as their correlations in BSC microbial community. We highlighted the previously underestimated impact of manganese on fungal community regulation and BSC formation. We provide comprehensive insight into BSC formation networks on tropical reef islands and established a foundation for BSC-directed environmental restoration.
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Affiliation(s)
- Lin Wang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- *Correspondence: Jie Li,
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Si Zhang,
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73
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Mai Y, Peng S, Lai Z, Wang X. Seasonal and inter-annual variability of bacterioplankton communities in the subtropical Pearl River Estuary, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:21981-21997. [PMID: 34775557 DOI: 10.1007/s11356-021-17449-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
It is widely recognized that environmental factors substantially influence on the seasonal and inter-annual variability of bacterioplankton communities, yet little is known about the seasonality of bacterioplankton communities in subtropical estuaries at longer-term time scales. Here, the bacterioplankton communities from the eight major outlets of the subtropical Pearl River Estuary were investigated across 3 years (2017-2019) using full-length 16S rRNA gene sequencing. Significant seasonal and inter-annual variation was observed in bacterioplankton community compositions across the 3 years (p < 0.05). In addition, the inferred functional composition of the communities varied with seasons, although not significantly, suggesting that functional redundancy existed among communities and across seasons that could help to cope with environmental changes. Five evaluated environmental parameters (temperature, salinity, pH, total dissolved solids (TDS), total phosphorus (TP)) were significantly correlated with community composition variation, while only three environmental parameters (temperature, pH, and TDS) were correlated with variation in inferred functional composition. Moreover, community composition tracked the seasonal temperature gradients, indicating that temperature was a key environmental factor that affected bacterioplankton community's variation along with seasonal succession patterns. Gammaproteobacteria and Alphaproteobacteria were the most dominant classes in the surface waters of Pearl River Estuary, and their members exhibited divergent responses to temperature changes, while several taxa within these group could be indicators of low and high temperatures that are associated with seasonal changes. These results strengthen our understanding of bacterioplankton community variation in association with temperature-dependent seasonal changes in subtropical estuarine ecosystems.
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Affiliation(s)
- Yongzhan Mai
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Songyao Peng
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Zini Lai
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
- Guangdong Provincial Key Laboratory of Aquatic Animal Immune Technology, Guangzhou, 510070, China.
| | - Xuesong Wang
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou), Guangzhou, 100 Xianlie Middle Road, 510070, China.
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74
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Zhang T, Xu S, Yan R, Wang R, Gao Y, Kong M, Yi Q, Zhang Y. Similar geographic patterns but distinct assembly processes of abundant and rare bacterioplankton communities in river networks of the Taihu Basin. WATER RESEARCH 2022; 211:118057. [PMID: 35066261 DOI: 10.1016/j.watres.2022.118057] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/16/2021] [Accepted: 01/09/2022] [Indexed: 06/14/2023]
Abstract
Bacterioplankton play an important role in the biogeochemical cycling in rivers. The dynamics of hydrologic conditions in rivers were believed to affect geographic pattern and assembly process of these microorganisms, which have not been widely investigated. In this study, the geographic pattern and assembly process of bacterioplankton community in river networks of the Taihu Basin were systematically explored using amplicon sequencing of the 16S rRNA gene. The results showed that the diversity, structure, and taxonomic composition of bacterioplankton community all exhibited significant temporal variation during wet, normal, and dry seasons (p<0.01). The neutral community model and null model were applied to reveal the assembly process of bacterioplankton community. The stochastic process and deterministic process both shaped the bacterioplankton community with greater influence of deterministic process. In addition, the abundant and rare bacterioplankton communities were comparatively analyzed. The abundant and rare bacterioplankton communities exhibited similar temporal dynamics (principal coordinates analysis) and spatial variations (distance-decay relationship), indicating similar geographic patterns. Meanwhile, distinct assembly processes were observed for the abundant and rare bacterioplankton communities. Stochastic process (dispersal limitation) shaped the abundant bacterioplankton community while deterministic process (heterogeneous selection) dominated the assembly process of rare bacterioplankton community. Mantel test, redundancy analysis, and correlation analysis together indicated that pH and dissolved oxygen were the major environmental attributes that affected thestructure and assembly process of bacterioplankton community. These results expanded our understanding of the geographic pattern, assembly process, and driving factors of bacterioplankton community in river networks and provided clues for the underlying mechanisms.
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Affiliation(s)
- Tao Zhang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Sai Xu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China; Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Ruomeng Yan
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Ruyue Wang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Yuexiang Gao
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Ming Kong
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Qitao Yi
- School of Civil Engineering, Yantai University, Yantai 264005, China
| | - Yimin Zhang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China.
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75
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Gill JG, Hill-Spanik KM, Whittaker KA, Jones ML, Plante C. Sargasso Sea bacterioplankton community structure and drivers of variance as revealed by DNA metabarcoding analysis. PeerJ 2022; 10:e12835. [PMID: 35251777 PMCID: PMC8893026 DOI: 10.7717/peerj.12835] [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: 08/17/2021] [Accepted: 01/04/2022] [Indexed: 01/10/2023] Open
Abstract
Marine microbes provide the backbone for pelagic ecosystems by cycling and fixing nutrients and establishing the base of food webs. Microbial communities are often assumed to be highly connected and genetically mixed, with localized environmental filters driving minor changes in structure. Our study applied high-throughput Illumina 16S ribosomal RNA gene amplicon sequencing on whole-community bacterial samples to characterize geographic, environmental, and stochastic drivers of community diversity. DNA was extracted from seawater collected from the surface (N = 18) and at depth just below the deep chlorophyll-a maximum (DCM mean depth = 115.4 m; N = 22) in the Sargasso Sea and adjacent oceanographic regions. Discrete bacterioplankton assemblages were observed at varying depths in the North Sargasso Sea, with a signal for distance-decay of bacterioplankton community similarity found only in surface waters. Bacterial communities from different oceanic regions could be distinguished statistically but exhibited a low magnitude of divergence. Redundancy analysis identified temperature as the key environmental variable correlated with community structuring. The effect of dispersal limitation was weak, while variation partitioning and neutral community modeling demonstrated stochastic processes influencing the communities. This study advances understanding of microbial biogeography in the pelagic ocean and highlights the use of high-throughput sequencing methods in studying microbial community structure.
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Affiliation(s)
- John Geoffrey Gill
- Grice Marine Laboratory, College of Charleston, Charleston, SC, United States
| | | | - Kerry A. Whittaker
- Sea Education Association, Woods Hole, MA, United States,Maine Maritime Academy, Castine, Maine, United States
| | - Martin L. Jones
- Department of Mathematics, College of Charleston, Charleston, SC, United States
| | - Craig Plante
- Grice Marine Laboratory, College of Charleston, Charleston, SC, United States
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76
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Potts L, Douglas A, Perez Calderon LJ, Anderson JA, Witte U, Prosser JI, Gubry-Rangin C. Chronic Environmental Perturbation Influences Microbial Community Assembly Patterns. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:2300-2311. [PMID: 35103467 PMCID: PMC9007448 DOI: 10.1021/acs.est.1c05106] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 05/11/2023]
Abstract
Acute environmental perturbations are reported to induce deterministic microbial community assembly, while it is hypothesized that chronic perturbations promote development of alternative stable states. Such acute or chronic perturbations strongly impact on the pre-adaptation capacity to the perturbation. To determine the importance of the level of microbial pre-adaptation and the community assembly processes following acute or chronic perturbations in the context of hydrocarbon contamination, a model system of pristine and polluted (hydrocarbon-contaminated) sediments was incubated in the absence or presence (discrete or repeated) of hydrocarbon amendment. The community structure of the pristine sediments changed significantly following acute perturbation, with selection of different phylotypes not initially detectable. Conversely, historically polluted sediments maintained the initial community structure, and the historical legacy effect of chronic pollution likely facilitated community stability. An alternative stable state was also reached in the pristine sediments following chronic perturbation, further demonstrating the existence of a legacy effect. Finally, ecosystem functional resilience was demonstrated through occurrence of hydrocarbon degradation by different communities in the tested sites, but the legacy effect of perturbation also strongly influenced the biotic response. This study therefore demonstrates the importance of perturbation chronicity on microbial community assembly processes and reveals ecosystem functional resilience following environmental perturbation.
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Affiliation(s)
- Lloyd
D. Potts
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Alex Douglas
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Luis J. Perez Calderon
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - James A. Anderson
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Ursula Witte
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - James I. Prosser
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Cécile Gubry-Rangin
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
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77
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Yu Q, Yang J, Su W, Li T, Feng T, Li H. Heavy metals and microbiome are negligible drivers than mobile genetic elements in determining particle-attached and free-living resistomes in the Yellow River. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127564. [PMID: 34736202 DOI: 10.1016/j.jhazmat.2021.127564] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/27/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
Suspended particles in water can shelter both microorganisms and contaminants. However, the emerging pollutants antibiotic resistance genes (ARGs) in free-living (FL) or particle-attached (PA) bacteria in aquatic environments are less explored. In this study, we compared the free-living and particle-attached ARGs during four seasons in the Yellow River using high-throughput quantitative PCR techniques and 16S rRNA gene sequencing. Our results demonstrated that both the free-living water and particles were dominated by tetracycline and beta-lactamase resistance genes. The PA-ARGs had a higher absolute abundance than FL-ARGs in the Yellow River, regardless of the season. Both PA-ARGs and FL-ARGs had the highest absolute abundance and diversity during winter. Mobile genetic elements (MGEs) were the dominant driver for both size-fractionated ARGs. However, the microbiome had less influence on PA-ARG profiles than the FL-ARG profiles, while the effects of the heavy metals on ARGs were negligible. The community assembly of both FL-ARG and PA-ARG can be explained by neutral processes. Several opportunistic pathogens (e.g., Escherichia coli) associated with human health exhibited a higher relative abundance in the particles than during a free-living lifestyle. Parts of these pathogens were potential ARG hosts. As such, it is important to monitor the ARGs and opportunistic pathogens from size-fractionated bacteria and develop targeted strategies to manage ARG dissemination and opportunistic pathogens to ensure public health.
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Affiliation(s)
- Qiaoling Yu
- 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
| | - Tongtong Li
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Tianshu Feng
- School of Public Health, Lanzhou University, Lanzhou 730000, 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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78
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Zhang J, Ling J, Zhou W, Zhang W, Yang F, Wei Z, Yang Q, Zhang Y, Dong J. Biochar Addition Altered Bacterial Community and Improved Photosynthetic Rate of Seagrass: A Mesocosm Study of Seagrass Thalassia hemprichii. Front Microbiol 2021; 12:783334. [PMID: 34925287 PMCID: PMC8678274 DOI: 10.3389/fmicb.2021.783334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Seagrass meadows, as typical “blue carbon” ecosystems, play critical ecological roles in the marine ecosystem and decline every year. The application of biochar in soil has been proposed as a potential soil amendment to improve soil quality and mitigate global climate change. The effects of biochar on soil bacterial activities are integrally linked to the potential of biochar in achieving these benefits. However, biochar has been rarely applied in marine ecosystems. Whether the application of biochar could work on the seagrass ecosystem remained unknown. In this study, we investigated the responses of sediment and rhizosphere bacterial communities of seagrass Thalassia hemprichii to the biochar addition derived from maize at ratios of 5% by dry weight in the soil during a one-month incubation. Results indicated that the biochar addition significantly changed the sedimental environment with increasing pH, total phosphorus, and total kalium while total nitrogen decreased. Biochar addition significantly altered both the rhizosphere and sediment bacterial community compositions. The significant changes in rhizosphere bacterial community composition occurred after 30days of incubation, while the significant variations in sediment bacterial community composition distinctly delayed than in sediment occurred on the 14th day. Biochar application improved nitrification and denitrification, which may accelerate nitrogen cycling. As a stabilizer to communities, biochar addition decreased the importance of deterministic selection in sediment and changed the bacterial co-occurrence pattern. The biochar addition may promote seagrass photosynthesis and growth by altering the bacterial community compositions and improving nutrient circulation in the seagrass ecosystem, contributing to the seagrass health improvement. This study provided a theoretical basis for applying biochar to the seagrass ecosystem and shed light on the feasible application of biochar in the marine ecosystem. ![]()
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Affiliation(s)
- Jian Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China.,College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
| | - Juan Ling
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China.,Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China
| | - Weiguo Zhou
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Wenqian Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China.,College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
| | - Fangfang Yang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Zhangliang Wei
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Qingsong Yang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China.,Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China
| | - Ying Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Junde Dong
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China.,Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China
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Voskuhl L, Akbari A, Müller H, Pannekens M, Brusilova D, Dyksma S, Haque S, Graupner N, Dunthorn M, Meckenstock RU, Brauer VS. Indigenous microbial communities in heavy oil show a threshold response to salinity. FEMS Microbiol Ecol 2021; 97:6447536. [PMID: 34864985 PMCID: PMC8684454 DOI: 10.1093/femsec/fiab157] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/29/2021] [Indexed: 11/14/2022] Open
Abstract
Microbial degradation influences the quality of oil resources. The environmental factors that shape the composition of oil microbial communities are largely unknown because most samples from oil fields are impacted by anthropogenic oil production, perturbing the native ecosystem with exogenous fluids and microorganisms. We investigated the relationship between formation water geochemistry and microbial community composition in undisturbed oil samples. We isolated 43 microliter-sized water droplets naturally enclosed in the heavy oil of the Pitch Lake, Trinidad and Tobago. The water chemistry and microbial community composition within the same water droplet were determined by ion chromatography and 16S rRNA gene amplicon sequencing, respectively. The results revealed a high variability in ion concentrations and community composition between water droplets. Microbial community composition was mostly affected by the chloride concentration, which ranged from freshwater to brackish-sea water. Remarkably, microbial communities did not respond gradually to increasing chloride concentration but showed a sudden change to less diverse and uneven communities when exceeding a chloride concentration of 57.3 mM. The results reveal a threshold-regulated response of microbial communities to salinity, offering new insights into the microbial ecology of oil reservoirs.
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Affiliation(s)
- Lisa Voskuhl
- Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Ali Akbari
- Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Hubert Müller
- Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Mark Pannekens
- Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Darya Brusilova
- Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Stefan Dyksma
- Faculty of Technology, Microbiology - Biotechnology, University of Applied Sciences Emden/Leer, Emden, Germany.,German Collection of Microorganisms and Cell Cultures, Leibniz Institute DSMZ, Inhoffenstr. 7B, D-38124 Braunschweig, Germany
| | - Shirin Haque
- Faculty of Science and Technology, Department of Physics, The University of The West Indies, St. Augustine, Trinidad and Tobago
| | - Nadine Graupner
- Eukaryotic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Micah Dunthorn
- Eukaryotic Microbiology, Natural History Museum of Oslo, P.O. Box 1172, Blindern, Oslo 0318, Norway
| | - Rainer U Meckenstock
- Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Verena S Brauer
- Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
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80
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Hussain S, Liu H, Liu S, Yin Y, Yuan Z, Zhao Y, Cao H. Distribution and Assembly Processes of Soil Fungal Communities along an Altitudinal Gradient in Tibetan Plateau. J Fungi (Basel) 2021; 7:jof7121082. [PMID: 34947064 PMCID: PMC8706254 DOI: 10.3390/jof7121082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 12/25/2022] Open
Abstract
In soil ecosystems, fungi exhibit diverse biodiversity and play an essential role in soil biogeochemical cycling. Fungal diversity and assembly processes across soil strata along altitudinal gradients are still unclear. In this study, we investigated the structure and abundance of soil fungal communities among soil strata and elevational gradients on the Tibetan Plateau using Illumina MiSeq sequencing of internal transcribed spacer1 (ITS1). The contribution of neutral and niche ecological processes were quantified using a neutral community model and a null model-based methodology. Our results showed that fungal gene abundance increased along altitudinal gradients, while decreasing across soil strata. Along with altitudinal gradients, fungal α-diversity (richness) decreased from surface to deeper soil layers, while β-diversity showed weak correlations with elevations. The neutral community model showed an excellent fit for neutral processes and the lowest migration rate (R2 = 0.75). The null model showed that stochastic processes dominate in all samples (95.55%), dispersal limitations were dominated at the surface layer and decreased significantly with soil strata, while undominated processes (ecological drift) show a contrary trend. The log-normal model and the null model (βNTI) correlation analysis also neglect the role of niche-based processes. We conclude that stochastic dispersal limitations, together with ecological drifts, drive fungal communities.
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Affiliation(s)
- Sarfraz Hussain
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
| | - Hao Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
| | - Senlin Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
| | - Yifan Yin
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
| | - Zhongyuan Yuan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
| | - Yuguo Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China;
| | - Hui Cao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
- Correspondence:
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81
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Diversity Distribution, Driving Factors and Assembly Mechanisms of Free-Living and Particle-Associated Bacterial Communities at a Subtropical Marginal Sea. Microorganisms 2021; 9:microorganisms9122445. [PMID: 34946047 PMCID: PMC8704526 DOI: 10.3390/microorganisms9122445] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/21/2021] [Accepted: 11/24/2021] [Indexed: 01/04/2023] Open
Abstract
Free-living (FL) and particle-associated (PA) bacterioplankton communities play critical roles in biogeochemical cycles in the ocean. However, their community composition, assembly process and functions in the continental shelf and slope regions are poorly understood. Based on 16S rRNA gene amplicon sequencing, we investigated bacterial communities’ driving factors, assembly processes and functional potentials at a subtropical marginal sea. The bacterioplankton community showed specific distribution patterns with respect to lifestyle (free living vs. particle associated), habitat (slope vs. shelf) and depth (surface vs. DCM and Bottom). Salinity and water temperature were the key factors modulating turnover in the FL community, whereas nitrite, silicate and phosphate were the key factors for the PA community. Model analyses revealed that stochastic processes outweighed deterministic processes and had stronger influences on PA than FL. Homogeneous selection (Hos) was more responsible for the assembly and turnover of FL, while drift and dispersal limitation contributed more to the assembly of PA. Importantly, the primary contributor to Hos in PA was Gammaproteobacteria:Others, whereas that in FL was Cyanobacteria:Bin6. Finally, the PICRUSt2 analysis indicated that the potential metabolisms of carbohydrates, cofactors, amino acids, terpenoids, polyketides, lipids and antibiotic resistance were markedly enriched in PA than FL.
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82
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Lan S, Wu L, Adessi A, Hu C. Cyanobacterial persistence and influence on microbial community dynamics over 15 years in induced biocrusts. Environ Microbiol 2021; 24:66-81. [PMID: 34816560 DOI: 10.1111/1462-2920.15853] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/13/2021] [Indexed: 11/29/2022]
Abstract
Biocrusts provide numerous ecological functions in drylands. Recovering biocrusts via cyanobacterial inoculation recently gathered interest for ecological restoration, yet it still lacks long-term experiments to unravel biocrust community dynamics. To examine how cyanobacterial inoculants influenced local microbial community and biocrust development, we observed a 2 km2 (Qubqi Desert, China) inoculation experiment after 10 and 15 years, following biocrust formation. Our results revealed that biocrust development was in line with ecological regime shift, providing evidence for biocrust community succession, from cyanobacteria- to moss-dominated types. Associated with biocrust development, microbial communities differed significantly with less specialists compared to shifting sands. Cyanobacterial community analysis showed that Microcoleus vaginatus and Scytonema javanicum are an ideal inoculating model, as they were still dominating the community after 15 years since inoculation, while other nitrogen-fixing cyanobacteria occurred profusely with biocrust development. Biocrust community composition combined with thickness, Chl-a and exopolysaccharide measurements revealed the large variation of cyanobacterial ecological functions along biocrust development, suggesting a main function shift: from carbon fixation associated with exopolysaccharide secretion in bare sandy soils to nitrogen fixation in developed biocrusts. This large-scale field study verifies that cyanobacterial inoculation accelerates biocrust development and forwards succession, shaping the biocrust community composition over a long time.
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Affiliation(s)
- Shubin Lan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Li Wu
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, 430070, China
| | - Alessandra Adessi
- Department of Agriculture, Food, Environment and Forestry, University of Florence, Florence, 50144, Italy
| | - Chunxiang Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
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83
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Liu S, Wang P, Wang C, Chen J, Wang X, Hu B, Yuan Q. Ecological insights into the disturbances in bacterioplankton communities due to emerging organic pollutants from different anthropogenic activities along an urban river. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 796:148973. [PMID: 34274679 DOI: 10.1016/j.scitotenv.2021.148973] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Emerging organic pollutants (EOPs) in urban rivers have raised concerns regarding their eco-toxicological effects. However, the bacterioplankton community disturbances caused by EOPs in urban rivers and the associated ecological mechanisms remain unclear. This study provided profiles of the spatial distribution of a bacterioplankton community disturbed by human activity along an urban river. The results showed that EOP concentration and composition were differently distributed in residential and industrial areas, which significantly influenced bacterioplankton community structure. Based on redundancy analysis, parabens (methylparaben and propylparaben) were the major factors driving bacterioplankton community changes. Parabens inhibited gram-positive bacteria and promoted oxidative stress-tolerant bacteria in the river ecosystem. Parabens also disturbed ecological processes of bacterioplankton community assembly, shifting from a homogeneous selection (consistent selection pressure under similar environmental condition) to stochastic processes (random changes due to birth, death, immigration, and emigration) with changing in paraben concentrations. Heterogeneous selection was predicted to dominate microbial community assembly with paraben concentration changes exceeding 61.6 ng/L, which could deteriorate the river ecosystem. Furthermore, specific bacterial genera were identified as potential bioindicators to assess the condition of EOP contaminants in the river. Overall, this study highlights significant disturbances in bacterioplankton communities by EOPs at environmental concentrations, and our results could facilitate generation of appropriate management strategies aimed at EOPs in urban rivers.
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Affiliation(s)
- Sheng Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China.
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Xun Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Bin Hu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Qiusheng Yuan
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
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84
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Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean. Nat Microbiol 2021; 6:1561-1574. [PMID: 34782724 DOI: 10.1038/s41564-021-00979-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/13/2021] [Indexed: 11/08/2022]
Abstract
The role of the Arctic Ocean ecosystem in climate regulation may depend on the responses of marine microorganisms to environmental change. We applied genome-resolved metagenomics to 41 Arctic seawater samples, collected at various depths in different seasons during the Tara Oceans Polar Circle expedition, to evaluate the ecology, metabolic potential and activity of resident bacteria and archaea. We assembled 530 metagenome-assembled genomes (MAGs) to form the Arctic MAGs catalogue comprising 526 species. A total of 441 MAGs belonged to species that have not previously been reported and 299 genomes showed an exclusively polar distribution. Most Arctic MAGs have large genomes and the potential for fast generation times, both of which may enable adaptation to a copiotrophic lifestyle in nutrient-rich waters. We identified 38 habitat generalists and 111 specialists in the Arctic Ocean. We also found a general prevalence of 14 mixotrophs, while chemolithoautotrophs were mostly present in the mesopelagic layer during spring and autumn. We revealed 62 MAGs classified as key Arctic species, found only in the Arctic Ocean, showing the highest gene expression values and predicted to have habitat-specific traits. The Artic MAGs catalogue will inform our understanding of polar microorganisms that drive global biogeochemical cycles.
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85
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Yan Q, Deng J, Wang F, Liu Y, Liu K. Community Assembly and Co-occurrence Patterns Underlying the Core and Satellite Bacterial Sub-communities in the Tibetan Lakes. Front Microbiol 2021; 12:695465. [PMID: 34745022 PMCID: PMC8567192 DOI: 10.3389/fmicb.2021.695465] [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: 04/15/2021] [Accepted: 08/09/2021] [Indexed: 11/13/2022] Open
Abstract
Microbial communities normally comprise a few core species and large numbers of satellite species. These two sub-communities have different ecological and functional roles in natural environments, but knowledge on the assembly processes and co-occurrence patterns of the core and satellite species in Tibetan lakes is still sparse. Here, we investigated the ecological processes and co-occurrence relationships of the core and satellite bacterial sub-communities in the Tibetan lakes via 454 sequencing of 16S rRNA gene. Our studies indicated that the core and satellite bacterial sub-communities have similar dominant phyla (Proteobacteria, Bacteroidetes, and Actinobacteria). But the core sub-communities were less diverse and exhibited a stronger distance-decay relationship than the satellite sub-communities. In addition, topological properties of nodes in the network demonstrated that the core sub-communities had more complex and stable co-occurrence associations and were primarily driven by stochastic processes (58.19%). By contrast, the satellite sub-communities were mainly governed by deterministic processes (62.17%). Overall, this study demonstrated the differences in the core and satellite sub-community assembly and network stability, suggesting the importance of considering species traits to understand the biogeographic distribution of bacterial communities in high-altitude lakes.
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Affiliation(s)
- Qi Yan
- School of Life Sciences, Lanzhou University, Lanzhou, China.,Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
| | - Jianming Deng
- School of Life Sciences, Lanzhou University, Lanzhou, China.,State Key Laboratory of Grassland and Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Feng Wang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yongqin Liu
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China.,State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
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86
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Tong Q, Cui LY, Bie J, Han XY, Hu ZF, Wang HB, Zhang JT. Changes in the gut microbiota diversity of brown frogs (Rana dybowskii) after an antibiotic bath. BMC Vet Res 2021; 17:333. [PMID: 34674716 PMCID: PMC8529755 DOI: 10.1186/s12917-021-03044-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 10/04/2021] [Indexed: 12/17/2022] Open
Abstract
Background Captive amphibians frequently receive antibiotic baths to control bacterial diseases. The potential collateral effect of these antibiotics on the microbiota of frogs is largely unknown. To date, studies have mainly relied on oral administration to examine the effects of antibiotics on the gut microbiota; in contrast, little is known regarding the effects of bath-applied antibiotics on the gut microbiota. The gut microbiota compositions of the gentamicin, recovery, and control groups were compared by Illumina high-throughput sequencing, and the functional profiles were analysed using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Furthermore, the relationship between the structure and predicted functional composition of the gut microbiota was determined. Results The alpha diversity indices were significantly reduced by the gentamicin bath, illustrating that this treatment significantly changed the composition of the gut microbiota. After 7 days, the gut microbiota of the recovery group was not significantly different from that of the gentamicin group. Forty-four indicator taxa were selected at the genus level, comprising 42 indicators representing the control group and 2 indicators representing the gentamicin and recovery groups. Potential pathogenic bacteria of the genera Aeromonas, Citrobacter, and Chryseobacterium were significantly depleted after the gentamicin bath. There was no significant positive association between the community composition and functional composition of the gut microbiota in the gentamicin or control frogs, indicating that the functional redundancy of the gut bacterial community was high. Conclusions Gentamicin significantly changed the structure of the gut microbiota of R. dybowskii, and the gut microbiota exhibited weak resilience. However, the gentamicin bath did not change the functional composition of the gut microbiota of R. dybowskii, and there was no significant correlation between the structural composition and the functional composition of the gut microbiota. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-021-03044-z.
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Affiliation(s)
- Qing Tong
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China.,Jiamusi Branch of Heilongjiang Academy of Forestry Sciences, Jiamusi, 154002, China.,College of Life Science, Jiamusi University, Jiamusi, 154007, China
| | - Li-Yong Cui
- Jiamusi Branch of Heilongjiang Academy of Forestry Sciences, Jiamusi, 154002, China
| | - Jia Bie
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Xiao-Yun Han
- College of Life Science, Jiamusi University, Jiamusi, 154007, China
| | - Zong-Fu Hu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Hong-Bin Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Jian-Tao Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China.
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87
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Wang B, Liu N, Yang M, Wang L, Liang X, Liu CQ. Co-occurrence of planktonic bacteria and archaea affects their biogeographic patterns in China's coastal wetlands. ENVIRONMENTAL MICROBIOME 2021; 16:19. [PMID: 34666825 PMCID: PMC8527667 DOI: 10.1186/s40793-021-00388-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/01/2021] [Indexed: 05/26/2023]
Abstract
Planktonic bacteria and archaea play a key role in maintaining ecological functions in aquatic ecosystems; however, their biogeographic patterns and underlying mechanisms have not been well known in coastal wetlands including multiple types and at a large space scale. Therefore, planktonic bacteria and archaea and related environmental factors were investigated in twenty-one wetlands along China's coast to understand the above concerns. The results indicated that planktonic bacteria had different biogeographic pattern from planktonic archaea, and both patterns were not dependent on the wetland's types. Deterministic selection shapes the former's community structure, whereas stochastic processes regulate the latter's, being consistent with the fact that planktonic archaea have a larger niche breadth than planktonic bacteria. Planktonic bacteria and archaea co-occur, and their co-occurrence rather than salinity is more important in shaping their community structure although salinity is found to be a main environmental deterministic factor in the coastal wetland waters. This study highlights the role of planktonic bacteria-archaea co-occurrence on their biogeographic patterns, and thus provides a new insight into studying underlying mechanisms of microbial biogeography in coastal wetlands.
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Affiliation(s)
- Baoli Wang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China.
- Critical Zone Observatory of Bohai Coastal Region, Tianjin University, Tianjin, 300072, China.
| | - Na Liu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Meiling Yang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China.
| | - Lijia Wang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200244, China
| | - Cong-Qiang Liu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
- Critical Zone Observatory of Bohai Coastal Region, Tianjin University, Tianjin, 300072, China
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88
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Bhattarai B, Bhattacharjee AS, Coutinho FH, Goel RK. Viruses and Their Interactions With Bacteria and Archaea of Hypersaline Great Salt Lake. Front Microbiol 2021; 12:701414. [PMID: 34650523 PMCID: PMC8506154 DOI: 10.3389/fmicb.2021.701414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/06/2021] [Indexed: 01/15/2023] Open
Abstract
Viruses play vital biogeochemical and ecological roles by (a) expressing auxiliary metabolic genes during infection, (b) enhancing the lateral transfer of host genes, and (c) inducing host mortality. Even in harsh and extreme environments, viruses are major players in carbon and nutrient recycling from organic matter. However, there is much that we do not yet understand about viruses and the processes mediated by them in the extreme environments such as hypersaline habitats. The Great Salt Lake (GSL) in Utah, United States is a hypersaline ecosystem where the biogeochemical role of viruses is poorly understood. This study elucidates the diversity of viruses and describes virus–host interactions in GSL sediments along a salinity gradient. The GSL sediment virosphere consisted of Haloviruses (32.07 ± 19.33%) and members of families Siphoviridae (39.12 ± 19.8%), Myoviridae (13.7 ± 6.6%), and Podoviridae (5.43 ± 0.64%). Our results demonstrate that salinity alongside the concentration of organic carbon and inorganic nutrients (nitrogen and phosphorus) governs the viral, bacteria, and archaeal diversity in this habitat. Computational host predictions for the GSL viruses revealed a wide host range with a dominance of viruses that infect Proteobacteria, Actinobacteria, and Firmicutes. Identification of auxiliary metabolic genes for photosynthesis (psbA), carbon fixation (rbcL, cbbL), formaldehyde assimilation (SHMT), and nitric oxide reduction (NorQ) shed light on the roles played by GSL viruses in biogeochemical cycles of global relevance.
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Affiliation(s)
- Bishav Bhattarai
- Department of Civil and Environmental Engineering, The University of Utah, Salt Lake City, UT, United States
| | - Ananda S Bhattacharjee
- Carl R. Woese Institute for Genomic Biology, The University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Felipe H Coutinho
- Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Ramesh K Goel
- Department of Civil and Environmental Engineering, The University of Utah, Salt Lake City, UT, United States
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89
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Banda JF, Zhang Q, Ma L, Pei L, Du Z, Hao C, Dong H. Both pH and salinity shape the microbial communities of the lakes in Badain Jaran Desert, NW China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 791:148108. [PMID: 34126487 DOI: 10.1016/j.scitotenv.2021.148108] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/19/2021] [Accepted: 05/24/2021] [Indexed: 05/27/2023]
Abstract
Badain Jaran Desert (BJD), characterized by extremely arid climate and tallest sand dunes in the world, is the second largest desert in China. Surprisingly, there are a large number of permanent lakes in this desert. At present, little is known about the composition and distribution of microbial communities in these desert lakes, which are an important bioresource and play a fundamental role in the elemental cycles of the lakes. In this study, the physicochemical characteristics and microbial communities of water samples from 15 lakes in BJD were comparatively investigated. The results showed that the lakes were rich in Na+, Cl-, CO32- and HCO3- while Ca2+ and Mg2+ were scarce, with pH 8.52-10.27 and salinity 1.05-478.70 g/L. Bacteria dominated exclusively in low saline lakes (salinity < 50 g/L) while archaea were predominant in hypersaline lakes (salinity > 250 g/L), which abundance increased along salinity gradient linearly. Genera Flavobacterium, Synechocystis and Roseobacter from phyla Bacteroidetes, Cyanobacteria, Alphaproteobacteria were the major members in low saline lakes whereas Halomonas, Aliidiomarina and Halopelagius from Gammaproteobacteria and Euryarchaeota were abundant in moderately saline lakes (salinity 50-250 g/L). The hypersaline lakes were predominated by extreme halophiles such as Halorubrum, Halohasta and Natronomonas from Euryarchaeota. The correlation among the microbes in the lakes was mainly positive, suggesting they can survive in the harsh environments through synergistic interactions. Statistical analyses indicated that physicochemical characteristics rather than spatial factors shaped the microbial communities in the desert lakes. The pH was the most important environmental factor controlling alpha diversity, while salinity was the major driver determining microbial community structure in BJD lakes. In contrast, geographic factors had no significant impact on the microbial community compositions.
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Affiliation(s)
- Joseph Frazer Banda
- School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China; Geomicrobiology Laboratory, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Qin Zhang
- School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China; Geomicrobiology Laboratory, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Linqiang Ma
- School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China; Geomicrobiology Laboratory, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Lixin Pei
- School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China; Geomicrobiology Laboratory, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Zerui Du
- School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China; Geomicrobiology Laboratory, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Chunbo Hao
- School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China; Geomicrobiology Laboratory, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China.
| | - Hailiang Dong
- School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China; Department of Geology and Environmental Earth Science, Miami University, Oxford, OH 45056, USA
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90
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Liu L, Wang S, Chen J. Transformations from specialists to generalists cause bacterial communities are more stable than micro-eukaryotic communities under anthropogenic activity disturbance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 790:148141. [PMID: 34090161 DOI: 10.1016/j.scitotenv.2021.148141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/07/2021] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
Different microbial components have different responses to environmental disturbances. Here, we found that the planktonic bacterial and micro-eukaryotic communities had different responses to anthropogenic activity disturbance in a subtropical river, because they had different survival strategies (generalist and specialist). We used nutrients (nitrogen and phosphorus) as indicators of anthropogenic activities. We found that river stretch 1 showed low nutrient concentrations from October 2018 to September 2019. However, a nutrient disturbance was observed in river stretch 2. The nutrient concentrations increased largely in December and January but recovered to low values in June. Bacterial communities had higher resilience under this disturbance than micro-eukaryotic communities in river stretch 2. The bacterial community composition were quite different between the two river stretches in December and January but were similar in June and July. However, the differences of micro-eukaryotic community composition between the two river stretches were always high during the study period. The bacterial communities in river stretch 2 contained more generalists and nutrient tolerant specialists. The bacterial nutrient tolerant specialists rapidly decreased in the low nutrient months and were replaced by the generalists. Bacteria which were involved in this shifts accounted for 29.3% of the total abundance. However, the micro-eukaryotic communities in river stretch 2 contained more moderate generalists. These moderate generalists were insensitive to the variation of nutrients and only 19.56% of the micro-eukaryotes had significant responses to the disturbance. The survival strategies caused bacterial communities had higher adaptability than eukaryotes to environmental fluctuation.
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Affiliation(s)
- Lemian Liu
- Technical Innovation Service Platform for High Value and High Quality Utilization of Marine Organism, Fuzhou University, Fuzhou 350108, China; Fujian Engineering and Technology Research Center for Comprehensive Utilization of Marine Products Waste, Fuzhou University, Fuzhou 350108, China; Fuzhou Industrial Technology Innovation Center for High Value Utilization of Marine Products, Fuzhou University, Fuzhou 350108, China.
| | - Shanshan Wang
- Technical Innovation Service Platform for High Value and High Quality Utilization of Marine Organism, Fuzhou University, Fuzhou 350108, China; Fujian Engineering and Technology Research Center for Comprehensive Utilization of Marine Products Waste, Fuzhou University, Fuzhou 350108, China; Fuzhou Industrial Technology Innovation Center for High Value Utilization of Marine Products, Fuzhou University, Fuzhou 350108, China
| | - Jianfeng Chen
- Technical Innovation Service Platform for High Value and High Quality Utilization of Marine Organism, Fuzhou University, Fuzhou 350108, China; Fujian Engineering and Technology Research Center for Comprehensive Utilization of Marine Products Waste, Fuzhou University, Fuzhou 350108, China; Fuzhou Industrial Technology Innovation Center for High Value Utilization of Marine Products, Fuzhou University, Fuzhou 350108, China.
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91
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Xu Q, Luo G, Guo J, Xiao Y, Zhang F, Guo S, Ling N, Shen Q. Microbial generalist or specialist: Intraspecific variation and dormancy potential matter. Mol Ecol 2021; 31:161-173. [PMID: 34626522 DOI: 10.1111/mec.16217] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/10/2021] [Accepted: 10/05/2021] [Indexed: 12/27/2022]
Abstract
Microbial generalists and specialists coexist in the soil environment while having distinctive impacts on microbial community dynamics. In microbial ecology, the underlying mechanisms as to why a species is a generalist or a specialist remain ambiguous. Herein, we collected soils across a national scale and identified bacterial generalists and specialists according to niche breadth at the species level (OTU level), and the single-nucleotide differences in each species were measured to investigate intraspecific variation (at zero-radius OTU level). Compared with that of the specialists, the intraspecific variation of the generalists was much higher, which ensured their wider niche breadth and lower variability. The higher asynchrony and different niche preferences of conspecific individuals and the higher dormancy potential within the generalists further contributed to their stability in varying environments. Besides, generalists were less controlled by environmental filtering, which was indicated by the stronger signature of stochastic processes in their assembly, and had higher diversification and transition rates that allowed them to adapt to environmental changes to a greater extent than specialists. Overall, this study provides a new comprehensive understanding of the rules of assembly and the evolutionary roles of bacterial generalists and specialists. It also highlights the importance of intraspecific variation and the dormancy potential in the stability of species.
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Affiliation(s)
- Qicheng Xu
- Jiangsu Provincial Key Laboratory for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Gongwen Luo
- Jiangsu Provincial Key Laboratory for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Junjie Guo
- Jiangsu Provincial Key Laboratory for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Yan Xiao
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Fengge Zhang
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Shiwei Guo
- Jiangsu Provincial Key Laboratory for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Ning Ling
- Jiangsu Provincial Key Laboratory for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Qirong Shen
- Jiangsu Provincial Key Laboratory for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
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92
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Dal Bello M, Lee H, Goyal A, Gore J. Resource-diversity relationships in bacterial communities reflect the network structure of microbial metabolism. Nat Ecol Evol 2021; 5:1424-1434. [PMID: 34413507 DOI: 10.1038/s41559-021-01535-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 07/14/2021] [Indexed: 02/06/2023]
Abstract
The relationship between the number of available nutrients and community diversity is a central question in ecological research that remains unanswered. Here we studied the assembly of hundreds of soil-derived microbial communities on a wide range of well-defined resource environments, from single carbon sources to combinations of up to 16. We found that, while single resources supported multispecies communities varying from 8 to 40 taxa, mean community richness increased only one-by-one with additional resources. Cross-feeding could reconcile these seemingly contrasting observations, with the metabolic network seeded by the supplied resources explaining the changes in richness due to both the identity and the number of resources, as well as the distribution of taxa across different communities. By using a consumer-resource model incorporating the inferred cross-feeding network, we provide further theoretical support to our observations and a framework to link the type and number of environmental resources to microbial community diversity.
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Affiliation(s)
- Martina Dal Bello
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Hyunseok Lee
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Akshit Goyal
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeff Gore
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
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93
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Doering M, Freimann R, Antenen N, Roschi A, Robinson CT, Rezzonico F, Smits THM, Tonolla D. Microbial communities in floodplain ecosystems in relation to altered flow regimes and experimental flooding. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 788:147497. [PMID: 34134395 DOI: 10.1016/j.scitotenv.2021.147497] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 04/10/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
River floodplains are spatially diverse ecosystems that respond quickly to flow variations and disturbance. However, it remains unclear how flow alteration and hydrological disturbance impacts the structure and biodiversity of complex microbial communities in these ecosystems. Here, we examined the spatial and seasonal dynamics of microbial communities in aquatic (benthic) and terrestrial habitats of three hydrologically contrasting (natural flow, residual flow, hydropeaking flow) floodplain systems. Microbial communities (alpha and beta diversity) differed more among floodplain habitats than between riverine floodplains. Microbial communities in all systems displayed congruent seasonal effects. In the residual and hydropeaking systems, an experimental flood was released from a reservoir to mimic a natural high flow event causing hydromorphological disturbance. The experimental flood caused a temporary shift in microbial communities by releasing microbes from the reservoir as well as redistributing communities among floodplain habitats. The flood-mediated shift in community structures had only a transient impact as pelagic bacteria did not persist within floodplain habitats over time after the flood. More frequent pulse disturbances might lead to an alternate structure of bacterial communities in floodplains over time.
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Affiliation(s)
- Michael Doering
- Ecohydrology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland; eQcharta GmbH, Wädenswil, Switzerland.
| | - Remo Freimann
- Institute of Molecular Health Science, ETH Zürich, Switzerland
| | - Nadine Antenen
- Ecohydrology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Alexia Roschi
- Ecohydrology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland; Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Christopher T Robinson
- Swiss Federal Institute of Aquatic Science and Technology (EAWAG), 8600 Dübendorf, Switzerland; Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
| | - Fabio Rezzonico
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Diego Tonolla
- Ecohydrology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland; eQcharta GmbH, Wädenswil, Switzerland
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94
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Huang WC, Liu Y, Zhang X, Zhang CJ, Zou D, Zheng S, Xu W, Luo Z, Liu F, Li M. Comparative genomic analysis reveals metabolic flexibility of Woesearchaeota. Nat Commun 2021; 12:5281. [PMID: 34489402 PMCID: PMC8421398 DOI: 10.1038/s41467-021-25565-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 08/12/2021] [Indexed: 02/08/2023] Open
Abstract
The archaeal phylum Woesearchaeota, within the DPANN superphylum, includes phylogenetically diverse microorganisms that inhabit various environments. Their biology is poorly understood due to the lack of cultured isolates. Here, we analyze datasets of Woesearchaeota 16S rRNA gene sequences and metagenome-assembled genomes to infer global distribution patterns, ecological preferences and metabolic capabilities. Phylogenomic analyses indicate that the phylum can be classified into ten subgroups, termed A-J. While a symbiotic lifestyle is predicted for most, some members of subgroup J might be host-independent. The genomes of several Woesearchaeota, including subgroup J, encode putative [FeFe] hydrogenases (known to be important for fermentation in other organisms), suggesting that these archaea might be anaerobic fermentative heterotrophs.
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Affiliation(s)
- Wen-Cong Huang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yang Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Xinxu Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Cui-Jing Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Dayu Zou
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Shiling Zheng
- Key Laboratory of Coastal Biology and Biological Resources Utilization, CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- School of Marine Sciences, Nanjing University of Information Science & Technology, Nanjing, China
| | - Fanghua Liu
- Key Laboratory of Coastal Biology and Biological Resources Utilization, CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
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95
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Zhu C, Liu W, Li X, Xu Y, El-Serehy HA, Al-Farraj SA, Ma H, Stoeck T, Yi Z. High salinity gradients and intermediate spatial scales shaped similar biogeographical and co-occurrence patterns of microeukaryotes in a tropical freshwater-saltwater ecosystem. Environ Microbiol 2021; 23:4778-4796. [PMID: 34258839 DOI: 10.1111/1462-2920.15668] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 06/12/2021] [Accepted: 07/09/2021] [Indexed: 11/26/2022]
Abstract
Microeukaryotes play key ecological roles in the microbial web of aquatic ecosystems. However, large knowledge gaps urgently need to be filled regarding the biogeography with associated shaping mechanisms and co-occurrence patterns of microeukaryotes under freshwater-saltwater gradients, especially true in tropical regions. Here, we investigated microeukaryotes of six mixed freshwater-saltwater regions in the Pearl River Estuary and surrounding coasts in southern China, with salinity ranging 0.1-32.0% and distances spanned up to 500 km, using molecular ecological methods. Results indicate that the biogeography of abundant and rare microeukaryotic communities was similar, both their co-occurrence patterns and biogeographical patterns were driven by deterministic and stochastic processes. The environmental factors with higher selective pressure than dispersal limitation meant that the role of deterministic process in structuring communities was more significant than that of stochastic process, and salinity played important role in structuring both microeukaryotic communities and networks. The abundant communities had stronger influence on entire microeukaryotic communities and seemed to be more sensitive to environmental changes than their rare counterparts, while rare ones had stronger interspecific relationships. Finally, the geographic scale and environmental gradients of study regions should firstly be clarified in future research on the ecological processes of microeukaryotes before conclusions are drawn.
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Affiliation(s)
- Changyu Zhu
- Institute of Evolution & Marine Biodiversity, and College of Fisheries, Ocean University of China, Qingdao, 266003, China.,Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Weiwei Liu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.,Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
| | - Xinghao Li
- Key Laboratory of Regional Development and Environmental Response, and Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan, 430062, China
| | - Yusen Xu
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Hamed A El-Serehy
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.,Department of Oceanography, College of Science, Port Said University, Port Said, 42511, Egypt
| | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Honggang Ma
- Institute of Evolution & Marine Biodiversity, and College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Thorsten Stoeck
- Department of Ecology, University of Technology Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Zhenzhen Yi
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
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96
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Wang JT, Shen JP, Zhang LM, Singh BK, Delgado-Baquerizo M, Hu HW, Han LL, Wei WX, Fang YT, He JZ. Generalist Taxa Shape Fungal Community Structure in Cropping Ecosystems. Front Microbiol 2021; 12:678290. [PMID: 34305842 PMCID: PMC8299105 DOI: 10.3389/fmicb.2021.678290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/17/2021] [Indexed: 12/05/2022] Open
Abstract
Fungi regulate nutrient cycling, decomposition, symbiosis, and pathogenicity in cropland soils. However, the relative importance of generalist and specialist taxa in structuring soil fungal community remains largely unresolved. We hypothesized that generalist fungi, which are adaptable to various environmental conditions, could potentially dominate the community and become the basis for fungal coexisting networks in cropping systems. In this study, we identified the generalist and habitat specialist fungi in cropland soils across a 2,200 kms environmental gradient, including three bioclimatic regions (subtropical, warm temperate, and temperate). A few fungal taxa in our database were classified as generalist taxa (~1%). These generalists accounted for >35% of the relative abundance of all fungal populations, and most of them are Ascomycota and potentially pathotrophic. Compared to the specialist taxa (5–17% of all phylotypes in three regions), generalists had a higher degree of connectivity and were often identified as hub within the network. Structural equation modeling provided further evidence that after accounting for spatial and climatic/edaphic factors, generalists had larger contributions to the fungal coexistence pattern than habitat specialists. Taken together, our study provided evidence that generalist taxa are crucial components for fungal community structure. The knowledge of generalists can provide important implication for understanding the ecological preference of fungal groups in cropland systems.
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Affiliation(s)
- Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Ju-Pei Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Manuel Delgado-Baquerizo
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, United States
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.,Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Wen-Xue Wei
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Yun-Ting Fang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.,Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
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97
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Zhang ZF, Pan J, Pan YP, Li M. Biogeography, Assembly Patterns, Driving Factors, and Interactions of Archaeal Community in Mangrove Sediments. mSystems 2021; 6:e0138120. [PMID: 34128692 PMCID: PMC8269266 DOI: 10.1128/msystems.01381-20] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 05/20/2021] [Indexed: 02/06/2023] Open
Abstract
Archaea are a major part of Earth's life. They are believed to play important roles in nutrient biogeochemical cycling in the mangrove. However, only a few studies on the archaeal community in mangroves have been reported. In particular, the assembly processes and interaction patterns that impact the archaeal communities in mangroves have not been investigated to date. Here, the biogeography, assembly patterns, and driving factors of archaeal communities in seven representative mangroves across southeastern China were systematically analyzed. The analysis revealed that the archaeal community is more diverse in surface sediments than in subsurface sediments, and more diverse in mangroves at low latitudes than at high latitudes, with Woesearchaeota and Bathyarchaeota as the most diverse and most abundant phyla, respectively. Beta nearest-taxon index analysis suggested a determinant role of homogeneous selection on the overall archaeon community in all mangroves and in each individual mangrove. In addition, the conditionally rare taxon community was strongly shaped by homogeneous selection, while stochastic processes shaped the dominant taxon and always-rare taxon communities. Further, a moderate effect of environmental selection on the archaeal community was noted, with the smallest effect on the always-rare taxon community. Mangrove location, mean annual temperature, and salinity were the major factors that greatly affected the community composition. Finally, network analysis revealed comprehensive cooccurrence relationships in the archaeal community, with a crucial role of Bathyarchaeota. This study expands the understanding of the biogeography, assembly patterns, driving factors, and cooccurrence relationships of the mangrove archaeal community and inspires functional exploration of archaeal resources in mangrove sediments. IMPORTANCE As a key microbial community component with important ecological roles, archaea merit the attention of biologists and ecologists. The mechanisms controlling microbial community diversity, composition, and biogeography are central to microbial ecology but poorly understood. Mangroves are located at the land-ocean interface and are an ideal environment for examining the above questions. We here provided the first-ever overview of archaeal community structure and biogeography in mangroves located along an over-9,000-km coastline of southeastern China. We observed that archaeal diversity in low-latitude mangroves was higher than that in high-latitude mangroves. Furthermore, our data indicated that homogeneous selection strongly controlled the assembly of the overall and conditionally rare taxon communities in mangrove sediments, while the dominant taxon and always-rare taxon communities were mainly controlled by dispersal limitation.
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Affiliation(s)
- Zhi-Feng Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Jie Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yue-Ping Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
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98
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Izabel-Shen D, Höger AL, Jürgens K. Abundance-Occupancy Relationships Along Taxonomic Ranks Reveal a Consistency of Niche Differentiation in Marine Bacterioplankton With Distinct Lifestyles. Front Microbiol 2021; 12:690712. [PMID: 34262550 PMCID: PMC8273345 DOI: 10.3389/fmicb.2021.690712] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 05/25/2021] [Indexed: 01/23/2023] Open
Abstract
Abundance-occupancy relationships (AORs) are an important determinant of biotic community dynamics and habitat suitability. However, little is known about their role in complex bacterial communities, either within a phylogenetic framework or as a function of niche breadth. Based on data obtained in a field study in the St. Lawrence Estuary, we used 16S rRNA gene sequencing to examine the vertical patterns, strength, and character of AORs for particle-attached and free-living bacterial assemblages. Free-living communities were phylogenetically more diverse than particle-attached communities. The dominant taxa were consistent in terms of their presence/absence but population abundances differed in surface water vs. the cold intermediate layer. Significant, positive AORs characterized all of the surveyed communities across all taxonomic ranks of bacteria, thus demonstrating an ecologically conserved trend for both free-living and particle-attached bacteria. The strength of the AORs was low at the species level but higher at and above the genus level. These results demonstrate that an assessment of the distributions and population densities of finely resolved taxa does not necessarily improve determinations of apparent niche differences in marine bacterioplankton communities at regional scales compared with the information inferred from a broad taxonomic classification.
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Affiliation(s)
- Dandan Izabel-Shen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Department of Biological Oceanography Leibniz Institute for Baltic Sea Research, Rostock, Germany
| | - Anna-Lena Höger
- Department of Biological Oceanography Leibniz Institute for Baltic Sea Research, Rostock, Germany
- Department of Applied Biosciences and Process Engineering, Anhalt University of Applied Sciences, Köthen, Germany
| | - Klaus Jürgens
- Department of Biological Oceanography Leibniz Institute for Baltic Sea Research, Rostock, Germany
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99
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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] [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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Sun M, Li T, Li D, Zhao Y, Gao F, Sun L, Li X. Conversion of Land Use from Upland to Paddy Field Changes Soil Bacterial Community Structure in Mollisols of Northeast China. MICROBIAL ECOLOGY 2021; 81:1018-1028. [PMID: 33219851 DOI: 10.1007/s00248-020-01632-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 10/21/2020] [Indexed: 06/11/2023]
Abstract
Mollisols are extremely important soil resource for crop and forage production. In northeast China, it is a major land use management practice from dry land crops to irrigated rice. However, there is few data regarding soil quality and microbial composition in Mollisols during land use transition. Here, we analyzed the upper 30 cm of soil from land with more than 30 years of paddy use and from adjacent areas with upland crops. Our results showed that land use and soil depth had a significant effect on soil properties and enzyme activities. Soil moisture (SM) and soil organic carbon (SOC) contents were substantially higher in paddy fields than in upland crop lands, while nitrogen-related enzyme activities were lower. Following the land use change, bacterial diversity was increased and bacterial community composition changed. Taxonomic analyses showed that Proteobacteria, Chloroflexi, Firmicutes, and Bacteroidetes were the dominant phyla present. At family level, Gemmatimonadaceae decreased with land use change, while Syntrophorhabdaceae and Syntrophacea that play a part in methane cycling and nitrifying bacteria such as Nitrospiraceae increased, indicating that the structure and composition of the bacterial community might be a promising indicator of Mollisol health. Redundancy analysis indicated that land use type had a stronger effect on the soil bacterial community composition than soil depth. Additionally, bacterial community composition was closely associated with soil parameters such as soil moisture, pH, SOC, NO3--N, and NH4+-N. Overall, land use change affects the physical and chemical properties of the soil, resulting in changes in the composition of the soil bacterial community and flora. These changes could provide a view of the bacterial community assembly and functional shifts following land use change.
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Affiliation(s)
- Minglong Sun
- Institute of Crop Breeding, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Tie Li
- Institute of Crop Breeding, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Dongmei Li
- Institute of Crop Breeding, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yuanling Zhao
- Institute of Crop Breeding, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Fengmei Gao
- Institute of Crop Breeding, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Lianfa Sun
- Institute of Crop Breeding, Heilongjiang Academy of Agricultural Sciences, Harbin, China.
| | - Xin Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, China.
- School of Forestry, Northeast Forestry University, Harbin, China.
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