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Ma X, Zhai T, Wang X, Cai C, Qiu D, Yin R, Li J, Liu G. Salinity-induced variations in bacterial composition and co-occurrence patterns within Salicornia-based constructed wetlands in mariculture. CHEMOSPHERE 2024; 363:142795. [PMID: 38986781 DOI: 10.1016/j.chemosphere.2024.142795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
Constructed wetlands use vegetation and microorganisms to remove contaminants like nitrogen and phosphorus from water. For mariculture, the impact of salinity on the efficiency of wastewater treatment of wetlands is unneglectable. However, little is known about their impact on the microbiome in constructed wetlands. Here, we set four salinity levels (15, 22, 29, and 36) in Salicornia constructed wetlands, and the experiment was conducted for a period of 72 days. The 15 group exhibited the highest removal rates of nitrogen compounds and phosphate, compared to the other salinity groups, the nosZ gene exhibited significantly higher expression in the 22 group (p < 0.05), indicated that microorganisms in 22 salinity have higher denitrification abilities. The three dominant phyla identified within the microbiomes were Proteobacteria, known for their diverse metabolic capabilities; Cyanobacteria, important for photosynthesis and nitrogen fixation; and Firmicutes, which include many fermenters. The ecological network analysis revealed a 'small world' model, characterized by high interconnectivity and short path lengths between microbial species, and had higher co-occurrence (45.13%) observed in this study comparing to the Erdös-Réyni random one (32.35%). The genus Microbulbifer emerged as the sole connector taxon, pivotal for integrating different microbial communities involved in nitrogen removal. A negative correlation was observed between salinity levels and network complexity, as assessed by the number of connections and diversity of interactions within the microbial community. Collectively, these findings underscore the critical role of microbial community interactions in optimizing nitrogen removal in constructed wetlands, with potential applications in the design and management of such systems for improved wastewater treatment in mariculture.
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Affiliation(s)
- Xiaona Ma
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China; College of Bio-systems Engineering and Food Science, Zhejiang University, Hangzhou, China; Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, China
| | - Tangfang Zhai
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China
| | - Xinyuan Wang
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China
| | - Chen Cai
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China
| | - Denggao Qiu
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Rui Yin
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China
| | - Jiayu Li
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China
| | - Gang Liu
- College of Bio-systems Engineering and Food Science, Zhejiang University, Hangzhou, China; Ocean Academy, Zhejiang University, Zhoushan, China.
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Feng Y, Duan J, Yang C, Zou Q, Chen Z, Pu J, Xiang Y, Chen M, Fan M, Zhang H. Microplastics and benthic animals reshape the geochemical characteristics of dissolved organic matter by inducing changes in keystone microbes in riparian sediments. ENVIRONMENTAL RESEARCH 2024; 262:119806. [PMID: 39151559 DOI: 10.1016/j.envres.2024.119806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 08/10/2024] [Accepted: 08/14/2024] [Indexed: 08/19/2024]
Abstract
Dissolved organic matter (DOM) in riparian sediments plays a vital role in regulating element cycling and pollutant behavior of river ecosystems. Microplastics (MPs) and benthic animals (BAs) have been frequently detected in riparian sediments, influencing the substance transformation in river ecosystems. However, there is still a lack of systematic investigation on the effects of MPs and BAs on sediment DOM. This study investigated the impact of MPs and BAs on the geochemical characteristics of DOM in riparian sediments and their microbial mechanisms. The results showed that MPs and BAs increased sediment DOC concentration by 34.24%∼232.97% and promoted the conversion of macromolecular components to small molecular components, thereby reducing the humification degree of DOM. Mathematical model verified that the changes of keystone microbes composition in sediments were direct factors affecting the characteristics of DOM in riparian sediment. Especially, MPs tolerant microbes, including Planctomicrobium, Rhodobacter, Hirschia and Lautropia, significantly increased DOC concentration and decreased humification degree (P < 0.05). In addition, MPs and BAs could also influence keystone microbes in sediments by altering the structure of microbial network, thereby indirectly affecting DOM characteristics. The study demonstrates the pollution behavior of MPs in river ecosystems and provides a basis for protecting the ecological function of riparian sediments from MPs pollution.
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Affiliation(s)
- Yuanyuan Feng
- School of Environmental Science and Engineering, Southwest Jiaotong University, Chengdu, 611756, China
| | - Jinjiang Duan
- School of Environmental Science and Engineering, Southwest Jiaotong University, Chengdu, 611756, China
| | - Cheng Yang
- School of Environmental Science and Engineering, Southwest Jiaotong University, Chengdu, 611756, China
| | - Qingping Zou
- School of Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Edinburgh, EH14 4AS, United Kingdom
| | - Ziwei Chen
- Key Laboratory of Hydraulic and Waterway Engineering, Ministry of Education, Chongqing Jiaotong University, Chongqing, 400074, China
| | - Jia Pu
- School of Environmental Science and Engineering, Southwest Jiaotong University, Chengdu, 611756, China
| | - Yu Xiang
- School of Environmental Science and Engineering, Southwest Jiaotong University, Chengdu, 611756, China
| | - Mengli Chen
- School of Environmental Science and Engineering, Southwest Jiaotong University, Chengdu, 611756, China.
| | - Meikun Fan
- School of Environmental Science and Engineering, Southwest Jiaotong University, Chengdu, 611756, China
| | - Han Zhang
- School of Environmental Science and Engineering, Southwest Jiaotong University, Chengdu, 611756, China.
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Fournier C, Fiedler A, Weidele M, Kautz H, Schleheck D. Description of a 'plankton filtration bias' in sequencing-based bacterial community analysis and of an Arduino microcontroller-based flowmeter device that can help to resolve it. PLoS One 2024; 19:e0303937. [PMID: 38805423 PMCID: PMC11132488 DOI: 10.1371/journal.pone.0303937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 05/03/2024] [Indexed: 05/30/2024] Open
Abstract
Diversity studies of aquatic picoplankton (bacterioplankton) communities using size-class filtration, DNA extraction, PCR and sequencing of phylogenetic markers, require a robust methodological pipeline, since biases have been demonstrated essentially at all levels, including DNA extraction, primer choice and PCR. Even different filtration volumes of the same plankton sample and, thus, different biomass loading of the filters, can distort the sequencing results. In this study, we designed an Arduino microcontroller-based flowmeter that records the decrease of initial (maximal) flowrate as proxy for increasing biomass loading and clogging of filters during plankton filtration. The device was tested using freshwater plankton of Lake Constance, and total DNA was extracted and an 16S rDNA amplicon was sequenced. We confirmed that different filtration volumes used for the same water sample affect the sequencing results. Differences were visible in alpha and beta diversities and across all taxonomic ranks. Taxa most affected were typical freshwater Actinobacteria and Bacteroidetes, increasing up to 38% and decreasing up to 29% in relative abundance, respectively. In another experiment, a lake water sample was filtered undiluted and three-fold diluted, and each filtration was stopped once the flowrate had reduced to 50% of initial flowrate, hence, at the same degree of filter clogging. The three-fold diluted sample required three-fold filtration volumes, while equivalent amounts of total DNA were extracted and differences across all taxonomic ranks were not statistically significant compared to the undiluted controls. In conclusion, this work confirms a volume/biomass-dependent bacterioplankton filtration bias for sequencing-based community analyses and provides an improved procedure for controlling biomass loading during filtrations and recovery of equivalent amounts of DNA from samples independent of the plankton density. The application of the device can also avoid the distorting of sequencing results as caused by the plankton filtration bias.
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Affiliation(s)
- Corentin Fournier
- Department of Biology, Microbial Ecology and Limnic Microbiology, Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Alexander Fiedler
- Department of Biology, Microbial Ecology and Limnic Microbiology, Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Maximilian Weidele
- Scientific Engineering and Manufacturing Services, University of Konstanz, Konstanz, Germany
| | - Harald Kautz
- Scientific Engineering and Manufacturing Services, University of Konstanz, Konstanz, Germany
| | - David Schleheck
- Department of Biology, Microbial Ecology and Limnic Microbiology, Limnological Institute, University of Konstanz, Konstanz, Germany
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Hidalgo-Martinez K, Giachini AJ, Schneider M, Soriano A, Baessa MP, Martins LF, de Oliveira VM. Shifts in structure and dynamics of the soil microbiome in biofuel/fuel blend-affected areas triggered by different bioremediation treatments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:33663-33684. [PMID: 38687451 DOI: 10.1007/s11356-024-33304-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
The use of biofuels has grown in the last decades as a consequence of the direct environmental impacts of fossil fuel use. Elucidating structure, diversity, species interactions, and assembly mechanisms of microbiomes is crucial for understanding the influence of environmental disturbances. However, little is known about how contamination with biofuel/petrofuel blends alters the soil microbiome. Here, we studied the dynamics in the soil microbiome structure and composition of four field areas under long-term contamination with biofuel/fossil fuel blends (ethanol 10% and gasoline 90%-E10; ethanol 25% and gasoline 75%-E25; soybean biodiesel 20% and diesel 80%-B20) submitted to different bioremediation treatments along a temporal gradient. Soil microbiomes from biodiesel-polluted areas exhibited higher richness and diversity index values and more complex microbial communities than ethanol-polluted areas. Additionally, monitored natural attenuation B20-polluted areas were less affected by perturbations caused by bioremediation treatments. As a consequence, once biostimulation was applied, the degradation was slower compared with areas previously actively treated. In soils with low diversity and richness, the impact of bioremediation treatments on the microbiomes was greater, and as a result, the hydrocarbon degradation extent was higher. The network analysis showed that all abundant keystone taxa corresponded to well-known degraders, suggesting that the abundant species are core targets for biostimulation in soil remediation processes. Altogether, these findings showed that the knowledge gained through the study of microbiomes in contaminated areas may help design and conduct optimized bioremediation approaches, paving the way for future rationalized and efficient pollutant mitigation strategies.
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Affiliation(s)
- Kelly Hidalgo-Martinez
- Divisão de Recursos Microbianos, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas E Agrícolas (CPQBA), Universidade Estadual de Campinas (UNICAMP), Paulínia, SP, CEP 13148-218, Brazil.
- Programa de Pós-Graduação de Genética E Biologia Molecular, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, CEP 13083-970, Brazil.
| | - Admir José Giachini
- Núcleo Ressacada de Pesquisas Em Meio Ambiente (REMA)-Department of Microbiology, Federal University of Santa Catarina (UFSC), Campus Universitário Sul da Ilha-Rua José Olímpio da Silva, 1326-Bairro Tapera, Florianópolis, SC, 88049-500, Brazil
| | - Marcio Schneider
- Núcleo Ressacada de Pesquisas Em Meio Ambiente (REMA)-Department of Microbiology, Federal University of Santa Catarina (UFSC), Campus Universitário Sul da Ilha-Rua José Olímpio da Silva, 1326-Bairro Tapera, Florianópolis, SC, 88049-500, Brazil
| | - Adriana Soriano
- PETROBRAS/R&D Center (CENPES), Cidade Universitária, Av. Horácio Macedo, Ilha Do Fundão, Rio de Janeiro, 950, ZIP 21941-915, Brazil
| | - Marcus Paulus Baessa
- PETROBRAS/R&D Center (CENPES), Cidade Universitária, Av. Horácio Macedo, Ilha Do Fundão, Rio de Janeiro, 950, ZIP 21941-915, Brazil
| | - Luiz Fernando Martins
- PETROBRAS/R&D Center (CENPES), Cidade Universitária, Av. Horácio Macedo, Ilha Do Fundão, Rio de Janeiro, 950, ZIP 21941-915, Brazil
| | - Valéria Maia de Oliveira
- Divisão de Recursos Microbianos, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas E Agrícolas (CPQBA), Universidade Estadual de Campinas (UNICAMP), Paulínia, SP, CEP 13148-218, Brazil
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Abuin-Denis L, Piloto-Sardiñas E, Maître A, Wu-Chuang A, Mateos-Hernández L, Obregon D, Corona-González B, Fogaça AC, Palinauskas V, Aželytė J, Rodríguez-Mallon A, Cabezas-Cruz A. Exploring the impact of Anaplasma phagocytophilum on colonization resistance of Ixodes scapularis microbiota using network node manipulation. CURRENT RESEARCH IN PARASITOLOGY & VECTOR-BORNE DISEASES 2024; 5:100177. [PMID: 38765730 PMCID: PMC11098721 DOI: 10.1016/j.crpvbd.2024.100177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 05/22/2024]
Abstract
Upon ingestion from an infected host, tick-borne pathogens (TBPs) have to overcome colonization resistance, a defense mechanism by which tick microbiota prevent microbial invasions. Previous studies have shown that the pathogen Anaplasma phagocytophilum alters the microbiota composition of the nymphs of Ixodes scapularis, but its impact on tick colonization resistance remains unclear. We analyzed tick microbiome genetic data using published Illumina 16S rRNA sequences, assessing microbial diversity within ticks (alpha diversity) through species richness, evenness, and phylogenetic diversity. We compared microbial communities in ticks with and without infection with A. phagocytophilum (beta diversity) using the Bray-Curtis index. We also built co-occurrence networks and used node manipulation to study the impact of A. phagocytophilum on microbial assembly and network robustness, crucial for colonization resistance. We examined network robustness by altering its connectivity, observing changes in the largest connected component (LCC) and the average path length (APL). Our findings revealed that infection with A. phagocytophilum does not significantly alter the overall microbial diversity in ticks. Despite a decrease in the number of nodes and connections within the microbial networks of infected ticks, certain core microbes remained consistently interconnected, suggesting a functional role. The network of infected ticks showed a heightened vulnerability to node removal, with smaller LCC and longer APL, indicating reduced resilience compared to the network of uninfected ticks. Interestingly, adding nodes to the network of infected ticks led to an increase in LCC and a decrease in APL, suggesting a recovery in network robustness, a trend not observed in networks of uninfected ticks. This improvement in network robustness upon node addition hints that infection with A. phagocytophilum might lower ticks' resistance to colonization, potentially facilitating further microbial invasions. We conclude that the compromised colonization resistance observed in tick microbiota following infection with A. phagocytophilum may facilitate co-infection in natural tick populations.
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Affiliation(s)
- Lianet Abuin-Denis
- Animal Biotechnology Department, Center for Genetic Engineering and Biotechnology, Avenue 31 between 158 and 190, P.O. Box 6162, Havana, 10600, Cuba
- ANSES, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, F-94700, France
| | - Elianne Piloto-Sardiñas
- ANSES, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, F-94700, France
- Direction of Animal Health, National Center for Animal and Plant Health, Carretera de Tapaste y Autopista Nacional, Apartado Postal 10, San José de las Lajas, Mayabeque, 32700, Cuba
| | - Apolline Maître
- ANSES, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, F-94700, France
- INRAE, UR 0045 Laboratoire de Recherches sur le Développement de l'Elevage (SELMET-LRDE), 20250, Corte, France
- EA 7310, Laboratoire de Virologie, Université de Corse, Corte, France
| | - Alejandra Wu-Chuang
- ANSES, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, F-94700, France
| | - Lourdes Mateos-Hernández
- ANSES, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, F-94700, France
| | - Dasiel Obregon
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Belkis Corona-González
- Direction of Animal Health, National Center for Animal and Plant Health, Carretera de Tapaste y Autopista Nacional, Apartado Postal 10, San José de las Lajas, Mayabeque, 32700, Cuba
| | - Andréa Cristina Fogaça
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, 05508-000, SP, Brazil
| | | | - Justė Aželytė
- Nature Research Centre, Akademijos 2, Vilnius, Lithuania
| | - Alina Rodríguez-Mallon
- Animal Biotechnology Department, Center for Genetic Engineering and Biotechnology, Avenue 31 between 158 and 190, P.O. Box 6162, Havana, 10600, Cuba
| | - Alejandro Cabezas-Cruz
- ANSES, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, F-94700, France
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Zhang L, Yuan L, Xiang J, Liao Q, Zhang D, Liu J. Response of the microbial community structure to the environmental factors during the extreme flood season in Poyang Lake, the largest freshwater lake in China. Front Microbiol 2024; 15:1362968. [PMID: 38633691 PMCID: PMC11021660 DOI: 10.3389/fmicb.2024.1362968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/13/2024] [Indexed: 04/19/2024] Open
Abstract
Background Poyang Lake is the largest freshwater lake in China, and there are several studies on the composition and diversity of bacteria in Poyang Lake, while few quantitative studies were carried out on the response of the bacterial community to environmental factors during the extreme flood season in Poyang Lake. Methods The connected-lake heterogeneity of bacterial community composition (BCC) was investigated in Poyang Lake during the flood season in 2020. Illumina high-throughput sequencing technology was used in this study. Results The bacterial community structure in the water was different from that in the sediment of Poyang Lake during extreme flood seasons. The bacterial diversity in water was much lower than that in sediment. In the water column, the dominant phyla were Actinobacteriota, while the composition of bacteria in sediment was more complex than that in water, and the dominant phyla in sediment were Proteobacteria, Chloroflexi, Acidobacteriota, and Actinobacteriota. The bacterial diversity in the water of Poyang Lake showed seasonal dynamics, while no seasonal variation of bacterial communities in sediment was observed. The bacterial community structure in the sediment from the two bays and channel areas of Poyang Lake can be distinguished from each other. The microbial diversity in sediment gradually increased from the Sancha Bay to the Zhouxi Bay and then to the channel, but the total nitrogen (TN) concentration in sediment (STN) and the total phosphorus (TP) concentration in sediment (STP) showed opposite trends. This might be due to the anthropogenic disturbances from the extreme flood. The bacterial community structure in, water column was significantly correlated with WT, NH4-N, STP, SOM, Chl a, DO, TP, and Eh, while the bacterial community structure in sediment was significantly correlated with SOM and STP. Conclusion The bacterial community structure in water was greatly different from that in sediment in Poyang Lake during extreme flood seasons. The bacterial community structure in the water column was not only sensitive to the geochemical characteristics of the water but also affected by some nutrient concentrations in the sediment. During the wet seasons, bacterial diversity was only affected by SOM and STP.
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Affiliation(s)
- Li Zhang
- Institute of Quality & Safety and Standards of Agricultural Products Research, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Lijuan Yuan
- Institute of Quality & Safety and Standards of Agricultural Products Research, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Jianjun Xiang
- Institute of Quality & Safety and Standards of Agricultural Products Research, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Qiegen Liao
- Institute of Quality & Safety and Standards of Agricultural Products Research, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Dawen Zhang
- Institute of Quality & Safety and Standards of Agricultural Products Research, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Jutao Liu
- Jiangxi Provincial Institute of Water Sciences, Nanchang, Jiangxi, China
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Wang Z, Wang L, Li Y, Zou Y, Hou X, Wang L. How redox gradient potentially influences nitrate reduction coupled with sulfur cycling: A new insight into nitrogen cycling in the hyporheic zone of effluent-dominated rivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:170070. [PMID: 38218484 DOI: 10.1016/j.scitotenv.2024.170070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/21/2023] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
The coupled N and S cycling in variable redox gradients in the hyporheic zone (HZ) of the rivers receiving effluents from wastewater treatment plants is unclear. Using two representative effluent-dominated rivers as model systems, a metagenome approach was employed to explore the spatiotemporal redox zonation of the HZ and the N/S cycling processes within the system. The results manifested that nitrate reduction represented the fundamental nitrogen pathway in the HZ. Interestingly, DNRA coupled with sulfur reduction, and denitrification coupled with sulfur oxidation were respectively abundant in the oxic and anoxic zone. Lower nitrate concentration (0-2.72 mg-N/L) and more abundant genes involved in denitrification (napB, NarGHI) and sulfur oxidation (sseA, glpE) were detected in the anoxic zone. Contrarily, the nitrate concentration (0.07-4.87 mg-N/L) and the abundance of genes involved in sulfur reduction (ttrB, sudA) and DNRA (nirBD) were observed more abundant in the oxic zone. Therefore, the results verified the oxygen-limited condition did not suppress but rather facilitated the denitrification process in the presence of active S cycling. The high relative abundances of nosZ gene encoding sequence (3-5 % relative to all nitrogen-cycling processes) in both the effluent-discharging area and downstream area highly confirmed that HZ was capable of alleviating the N2O emission in the region. The functional keystone taxa were revealed through co-occurrence network analysis. The structural equation model shows that the genes of N/S cycling were positively impacted by functional keystone taxa, especially the N cycling genes. Functional keystone taxa were proven driven by the redox gradient, demonstrating their positive roles in mediating N/S cycling processes. The promoting effect on nitrate reduction coupled with sulfur cycling was clarified when redox conditions oscillated, providing a new perspective on mitigating nitrogen pollution and greenhouse gas emissions in effluent-receiving rivers.
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Affiliation(s)
- Ziyi Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, Jiangsu 210098, China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, Jiangsu 210098, China.
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, Jiangsu 210098, China.
| | - Yina Zou
- Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, China
| | - Xing Hou
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, Jiangsu 210098, China; Institute of Water Science and Technology, Hohai University, Nanjing 210098, China
| | - Linqiong Wang
- College of Oceanography, Hohai University, Nanjing 210098, China
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Gou Y, Song Y, Li P, Wei W, Luo N, Wang H. Study on the accelerated biodegradation of PAHs in subsurface soil via coupled low-temperature thermally treatment and electron acceptor stimulation based on metagenomic sequencing. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133265. [PMID: 38113745 DOI: 10.1016/j.jhazmat.2023.133265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/21/2023]
Abstract
In situ anoxic bioremediation is a sustainable technology to remediate PAHs contaminated soils. However, the limited degradation rate of PAHs under anoxic conditions has become the primary bottleneck hindering the application of this technology. In this study, coupled low-temperature thermally treatment (<50 °C) and EA biostimulation was used to enhance PAH removal. Anoxic biodegradation of PAHs in soil was explored in microcosms in the absence and presence of added EAs at 3 temperatures (15 °C, 30 °C, and 45 °C). The influence of temperature, EA, and their interaction on the removal of PAHs were identified. A PAH degradation model based on PLSR analysis identified the importance and the positive/negative role of parameters on PAH removal. Soil archaeal and bacterial communities showed similar succession patterns, the impact of temperature was greater than that of EA. Soil microbial community and function were more influenced by temperature than EAs. Close and frequent interactions were observed among soil bacteria, archaea, PAH-degrading genes and methanogenic genes. A total of 15 bacterial OTUs, 1 PAH-degrading gene and 2 methanogenic genes were identified as keystones in the network. Coupled low-temperature thermally treatment and EA stimulation resulted in higher PAH removal efficiencies than EA stimulation alone and low-temperature thermally treatment alone.
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Affiliation(s)
- Yaling Gou
- Beijing Key Laboratory of Remediation of Industrial Pollution Sites, Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing 100089, China; College of Water Sciences, Beijing Normal University, Beijing 100875, China.
| | - Yun Song
- Beijing Key Laboratory of Remediation of Industrial Pollution Sites, Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing 100089, China
| | - Peizhong Li
- Beijing Key Laboratory of Remediation of Industrial Pollution Sites, Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing 100089, China
| | - Wenxia Wei
- Beijing Key Laboratory of Remediation of Industrial Pollution Sites, Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing 100089, China
| | - Nan Luo
- Beijing Key Laboratory of Remediation of Industrial Pollution Sites, Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing 100089, China
| | - Hongqi Wang
- College of Water Sciences, Beijing Normal University, Beijing 100875, China.
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Liu C, Ma X, Xie J, Wang J, Wang H, Wang Y. Impact of waste separation on the biological nitrogen removal in a MSW incineration leachate treatment plant: Performance and microbial community shift. ENVIRONMENTAL RESEARCH 2024; 244:117876. [PMID: 38072101 DOI: 10.1016/j.envres.2023.117876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/20/2023]
Abstract
After waste separation program was launched in China in 2019, incineration leachate treatment plants are facing a challenge of effective removal of nitrogen from leachate due to lack of sufficient carbon source. In this study, the performance of a biological incineration leachate treatment process (anaerobic digestion (AD) - two-stage anoxic/aerobic (A/O) process) was evaluated after adopting the waste separation program, and the changes in the microbial community and function was analyzed using 16S rRNA amplicon sequencing technology. Results showed that after the waste separation, the influent chemical oxygen demand (COD) concentration reduced by 90% (from 19,300 to 1780 mg L-1) with the COD/N ratio decreased from 12.3 to 1.4, which led to a decreased nitrogen removal efficiency (NRE) of <65% and a high effluent NO3- accumulation (445.8-986.5 mg N·L-1). By bypassing approximately 60% of the influent to the two-stage A/O process and adding external carbon source (glucose), the mean NRE increased to 86.3 ± 7.4%. Spearman's analysis revealed that refractory compounds in the bypassed leachate were closely related to the variations in bacterial community composition and nitrogen removal function in the two-stage A/O, leading to a weakened correlation of microbial network. KEGG functional pathway predictions based on Tax4Fun also confirmed that the bypassed leachate induced xenobiotic compounds to the two-stage A/O process, the relative abundance of nitrogen metabolism was reduced by 32%, and more external carbon source was required to ensure the satisfactory nitrogen removal of >80%. The findings provide a good guide for regulation of incineration leachate treatment processes after the waste separation.
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Affiliation(s)
- Chao Liu
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai, 200092, PR China; Shanghai Youlin Zhuyuan Sewage Investment and Development Co. Ltd., Shanghai, 200125, PR China
| | - Xiaoqian Ma
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai, 200092, PR China; Xiamen Tungsten Co., Ltd, Xiamen, 361009, PR China.
| | - Junxiang Xie
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai, 200092, PR China
| | - Jialin Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai, 200092, PR China
| | - Han Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai, 200092, PR China
| | - Yayi Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai, 200092, PR China.
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10
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Chen C, Ai J, Chen L, Li Y, Tang X, Li J. Nitrogen metabolism pathways and functional microorganisms in typical karst wetlands. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:22494-22506. [PMID: 38407711 DOI: 10.1007/s11356-024-32587-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 02/18/2024] [Indexed: 02/27/2024]
Abstract
Aha Lake artificial reservoir wetland, Niangniang Mountain karst mountain wetland, and Caohai plateau lake wetland are typical karst wetlands in Guizhou Province with unique topography and geomorphic features. They were selected as research objects in this study to explore microorganisms and functional genes in nitrogen metabolism adopting macro-genome sequencing technology. It was found that Proteobacteria, Actinobacteria, and Acidobacteria were the dominant phyla in nitrogen metabolism in these three wetlands, similar to previous studies. However, at the genus level, there was a significant difference, with the dominant bacteria being Bradyrhizobium, Methylocystis, and Anaeromyxobacter. Six nitrogen metabolism pathways, including nitrogen fixation, nitrification, denitrification, dissimilatory nitrate reduction, assimilatory nitrate reduction, and complete nitrification, comammox, were revealed, but anaerobic ammonia oxidation genes were not detected. Nitrogen metabolism microorganisms and pathways were more affected by SOM, pH, NO3-, and EC in karst wetlands. This study further discussed microorganisms and functions of nitrogen metabolism in karst wetlands, which was of great significance to nitrogen cycles of karst wetland ecosystems.
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Affiliation(s)
- Chen Chen
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - Jia Ai
- Ecological and Environmental Monitoring Center, Guizhou, 558013, Qiannan, China
| | - Li Chen
- College of Civil Engineering, Chongqing Vocational Institute of Engineering, Chongqing, 402260, China
| | - Yancheng Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 550025, China.
- Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang, 550025, Guizhou, China.
| | - Xin Tang
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - Jiang Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 550025, China
- Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang, 550025, Guizhou, China
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11
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Wang L, Wang Z, Li Y, Cai W, Zou Y, Hui C. Deciphering solute transport, microbiota assembly patterns and metabolic functions in the hyporheic zone of an effluent-dominated river. WATER RESEARCH 2024; 251:121190. [PMID: 38281336 DOI: 10.1016/j.watres.2024.121190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/05/2023] [Accepted: 01/23/2024] [Indexed: 01/30/2024]
Abstract
We lack a clear understanding of how anthropogenic pressures, exemplified by effluent discharge from wastewater treatment plants, destabilize microbial communities in the hyporheic zone (HZ) of receiving rivers. In this study, the spatiotemporal characteristics of hydrological parameters, and the physicochemical properties of surface and subsurface water in a representative effluent-dominated river were monitored. Sequencing of 16S rRNA amplicons and metagenomes revealed the microbial community structure in the HZ of both effluent discharge area and downstream region. The keystone taxa (taxa vital in determining the composition of each microbial cluster) and the keystone functions they controlled were subsequently identified. Effluent discharge amplified the depth of the oxic/suboxic zone and the hyporheic exchange fluxes in the effluent discharge area, which was 50-120% and 40-300% higher than in the downstream region, respectively. Microbial community structure pattern analysis demonstrated an enhancement in the rate of dispersal, an increase in microbial diversity, and an improved community network complexity in the effluent discharge area. By contrast, the number of keystone taxa in the effluent discharge area was 50-70% lower than that of the downstream region, resulting in reduced community network stability and functionality. The keystone taxa controlling metabolic functions in the networks categorized to effluent discharge area were comprised of more genera related to nitrogen and sulfur cycling, e.g., Dechloromonas, Desulfobacter, Flavobacterium, Nitrosomonas, etc., highlighting a research need in monitoring species associated with nutrient element cycling in the HZ of receiving waterbodies. The results showed that the keystone taxa could contribute positively to network stability, which was negatively correlated to hyporheic exchange fluxes and redox gradients. This study provides valuable insights that will improve our understanding of how river ecosystems respond to changes in anthropogenic pressures.
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Affiliation(s)
- Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, Jiangsu, 210098, PR China
| | - Ziyi Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, Jiangsu, 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, Jiangsu, 210098, PR China.
| | - Wei Cai
- College of Environmental Science and Engineering, Yangzhou University, Huayang West Road #196, Yangzhou 225009, PR China
| | - Yina Zou
- Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, China
| | - Cizhang Hui
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, Jiangsu, 210098, PR China
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Wang W, Ye Z, Li J, Liu G, Wu Q, Wang Z, He G, Yan W, Zhang C. Intermediate irrigation with low fertilization promotes soil nutrient cycling and reduces CO 2 and CH 4 emissions via regulating fungal communities in arid agroecosystems. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 351:119688. [PMID: 38064990 DOI: 10.1016/j.jenvman.2023.119688] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/07/2023] [Accepted: 11/21/2023] [Indexed: 01/14/2024]
Abstract
The field practices, including irrigation and fertilization, strongly affect greenhouse gas emissions and soil nutrient cycling from agriculture. Understanding the underlying mechanism of greenhouse gas emissions, soil nutrient cycling, and their impact factors (fungal diversity, network characteristics, soil pH, salt, and moisture) is essential for efficiently managing global greenhouse gas mitigation and agricultural production. By considering abundant and rare taxa, we determine the identities and relative importance of ecological processes that modulate the fungal communities and identify whether they are crucial contributors to soil nutrient cycling and greenhouse gas emissions. The research is based on a 4-year field fertigation experiment with low (300 kg/ha P2O5 with 150 kg/ha urea) and high (600 kg/ha P2O5 with 300 kg/ha urea) fertilization level and three irrigation levels, that is, low (200 mm), medium (300 mm), and high (400 mm). The α-diversity (richness and Shannon index) of fungal subcommunities was significantly higher under medium irrigation (300 mm) and low fertilization (300 kg/ha P2O5 with 150 kg/ha urea) than under other treatments. Intermediate irrigation with low fertilization treatment yielded the most significant higher multinutrient cycling index and the lowest CO2 and CH4 emissions. The null model indicated that abundant taxa are mainly regulated by stochastic processes (dispersal limitation), and rare taxa are mainly regulated by environmental selection, especially by soil salinity. The co-occurrence network of rare taxa explained the changes in the entire fungal network stability. The abundant taxa played vital roles in regulating soil nutrient status, owing to the stronger association between their network and multinutrient cycling index. Furthermore, we have confirmed that soil moisture and fungal network stability are crucial factors affecting greenhouse gas emissions. Together, these results provide a deep understanding of the mechanisms that reveal fungal community assembly and soil fungal-driven variations in nutrient status and network stability, link fungal network characteristics to ecosystem functions, and reveal the factors that influence greenhouse gas emissions.
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Affiliation(s)
- Wancai Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, China
| | - Zhencheng Ye
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, China
| | - Jing Li
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, China
| | - Guobin Liu
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, 712100, China
| | - Qixiao Wu
- Bangor College China, a Joint Unit of Bangor University, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Zhaoyang Wang
- Bangor College China, a Joint Unit of Bangor University, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Guoqin He
- Bangor College China, a Joint Unit of Bangor University, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Wende Yan
- National Engineering Laboratory for Applied Technology in Forestry and Ecology in South China, Central South University of Forestry and Technology, Changsha, 410004, China.
| | - Chao Zhang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, China; Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, 712100, China.
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13
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Liu Y, Jin X, Huang S, Liu Y, Kong Z, Wu L, Ge G. Co-Occurrence Patterns of Soil Fungal and Bacterial Communities in Subtropical Forest-Transforming Areas. Curr Microbiol 2024; 81:64. [PMID: 38225342 DOI: 10.1007/s00284-023-03608-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 09/30/2021] [Indexed: 01/17/2024]
Abstract
Soil microbial communities are engineers of important biogeochemical processes and play a critical role in regulating the functions and stability of forest ecosystem. However, few studies have assessed microbial interactions during forest conversion, which is essential to the understanding of the structure and function of soil microbiome. Herein, we investigated the co-occurrence network pattern and putative functions of fungal and bacterial communities in forest-transforming areas (five sites that cover the typical forests) using high-throughput sequencing of the ITS genes and 16S rRNA. Our study showed that the bacterial network had higher average connectivity and more links than fungal network, which might indicate that the bacterial community had more complex internal interactions compared with fungal one. Alphaproteobacteria_unclassfied, Telmatobacter, 0319-6A21 and Latescibacteria_unclassfied were the keystone taxa in bacterial network. For the fungal community network, the keystone taxon was Ceratobasidium. A structural equation model indicated that the available potassium and total organic carbon were important soil environmental factors, which affected all microbial modules, including bacterial and fungi. Total nitrogen had significant effects on the bacterial module that contains a relatively rich group of nitrogen cycling functions, and pH influenced the bacterial module which have higher potential functions of carbon cycling. And, more fungal modules were directly affected by forest structure (S Tree) compared with bacterial ones. This study provides new insights into our understanding of the feedback of underground creatures to forest conversion and highlights the importance of microbial modules in the nutrient cycling process.
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Affiliation(s)
- Yajun Liu
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, 330031, China
| | - Xin Jin
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, 330031, China
| | - Shihao Huang
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, 330031, China
| | - Yizhen Liu
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, 330031, China
| | - Zhaoyu Kong
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, 330031, China
| | - Lan Wu
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, 330031, China.
| | - Gang Ge
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, 330031, China
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14
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Layoun P, López-Pérez M, Haro-Moreno JM, Haber M, Thrash JC, Henson MW, Kavagutti VS, Ghai R, Salcher MM. Flexible genomic island conservation across freshwater and marine Methylophilaceae. THE ISME JOURNAL 2024; 18:wrad036. [PMID: 38365254 PMCID: PMC10872708 DOI: 10.1093/ismejo/wrad036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 02/18/2024]
Abstract
The evolutionary trajectory of Methylophilaceae includes habitat transitions from freshwater sediments to freshwater and marine pelagial that resulted in genome reduction (genome-streamlining) of the pelagic taxa. However, the extent of genetic similarities in the genomic structure and microdiversity of the two genome-streamlined pelagic lineages (freshwater "Ca. Methylopumilus" and the marine OM43 lineage) has so far never been compared. Here, we analyzed complete genomes of 91 "Ca. Methylopumilus" strains isolated from 14 lakes in Central Europe and 12 coastal marine OM43 strains. The two lineages showed a remarkable niche differentiation with clear species-specific differences in habitat preference and seasonal distribution. On the other hand, we observed a synteny preservation in their genomes by having similar locations and types of flexible genomic islands (fGIs). Three main fGIs were identified: a replacement fGI acting as phage defense, an additive fGI harboring metabolic and resistance-related functions, and a tycheposon containing nitrogen-, thiamine-, and heme-related functions. The fGIs differed in relative abundances in metagenomic datasets suggesting different levels of variability ranging from strain-specific to population-level adaptations. Moreover, variations in one gene seemed to be responsible for different growth at low substrate concentrations and a potential biogeographic separation within one species. Our study provides a first insight into genomic microdiversity of closely related taxa within the family Methylophilaceae and revealed remarkably similar dynamics involving mobile genetic elements and recombination between freshwater and marine family members.
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Affiliation(s)
- Paul Layoun
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 Ceske Budejovice, Czech Republic
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, 03550 San Juan de Alicante, Spain
| | - Jose M Haro-Moreno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, 03550 San Juan de Alicante, Spain
| | - Markus Haber
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
| | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Michael W Henson
- Department of Geophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Vinicius Silva Kavagutti
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 Ceske Budejovice, Czech Republic
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
| | - Michaela M Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
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15
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Qiu X, Ma S, Pan J, Cui Q, Zheng W, Ding L, Liang X, Xu B, Guo X, Rillig MC. Microbial metabolism influences microplastic perturbation of dissolved organic matter in agricultural soils. THE ISME JOURNAL 2024; 18:wrad017. [PMID: 38365242 PMCID: PMC10811734 DOI: 10.1093/ismejo/wrad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 11/22/2023] [Accepted: 12/11/2023] [Indexed: 02/18/2024]
Abstract
An estimated 258 million tons of plastic enter the soil annually. Joining persistent types of microplastic (MP), there will be an increasing demand for biodegradable plastics. There are still many unknowns about plastic pollution by either type, and one large gap is the fate and composition of dissolved organic matter (DOM) released from MPs as well as how they interact with soil microbiomes in agricultural systems. In this study, polyethylene MPs, photoaged to different degrees, and virgin polylactic acid MPs were added to agricultural soil at different levels and incubated for 100 days to address this knowledge gap. We find that, upon MP addition, labile components of low aromaticity were degraded and transformed, resulting in increased aromaticity and oxidation degree, reduced molecular diversity, and changed nitrogen and sulfur contents of soil DOM. Terephthalate, acetate, oxalate, and L-lactate in DOM released by polylactic acid MPs and 4-nitrophenol, propanoate, and nitrate in DOM released by polyethylene MPs were the major molecules available to the soil microbiomes. The bacteria involved in the metabolism of DOM released by MPs are mainly concentrated in Proteobacteria, Actinobacteriota, and Bacteroidota, and fungi are mainly in Ascomycota and Basidiomycota. Our study provides an in-depth understanding of the microbial transformation of DOM released by MPs and its effects of DOM evolution in agricultural soils.
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Affiliation(s)
- Xinran Qiu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Sirui Ma
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Jianrui Pan
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Qian Cui
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Wei Zheng
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Ling Ding
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Xujun Liang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Baile Xu
- Institut für Biologie, Freie Universität Berlin, Berlin 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin 14195, Germany
| | - Xuetao Guo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Matthias C Rillig
- Institut für Biologie, Freie Universität Berlin, Berlin 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin 14195, Germany
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16
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Wang K, Huang Y, Zhang M, Xiao H, Zhang G, Zhang T, Wang X. Pressure of different level PFOS on aerobic granule sludge: Insights on performance, AGS structure, community succession, and microbial interaction responses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167682. [PMID: 37820810 DOI: 10.1016/j.scitotenv.2023.167682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 10/13/2023]
Abstract
Perfluorooctane sulfonic acid (PFOS) has received much attention due to its potential environmental risks. However, the response of aerobic granular sludge (AGS) to PFOS exposure, particularly the microbial interactions, remains unclear. In this study, we investigated the particle structure of AGS, pollutant removal performance, community succession, and microbial interaction in the AGS system under different PFOS concentrations (0.1 and 1 mg/L). The mass balance showed that PFOS was mainly removed by adsorption with a removal rate of >85 %. PFOS caused some particles to break up and decreased the average particle size from 3.37 mm to 2.64 mm. It also significantly decreased the total nitrogen and total phosphorus removal rates, which was consistent with the deterioration of microbial activity, such as denitrification rate (25 % inhibition), phosphorus uptake rate (73.19 % inhibition), and phosphorus release rate (73.33 % inhibition). PFOS promoted the secretion of extracellular polymer (EPS) in AGS, especially proteins, leading to poor particle hydrophobicity. The network analysis illustrated that PFOS slowed down the information transfer between microorganisms, and increased the competition between them, which may be responsible for the deterioration of the system performance. Connections related to rare species accounted for >75 % of the network, suggesting that rare species have an indispensable role in community information exchange. In addition, rare species acted as seed banks for microorganisms, and under PFOS stress, they transformed into keystone species, which could contribute to system stabilization. This study provides new insights into the effects of PFOS on microbial interactions in AGS systems and the roles of rare species in the AGS microbial community.
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Affiliation(s)
- Kening Wang
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yan Huang
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Minglu Zhang
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Haihe Xiao
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Gengyi Zhang
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Tingting Zhang
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Xiaohui Wang
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
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17
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Tóth AG, Farkas R, Papp M, Kilim O, Yun H, Makrai L, Maróti G, Gyurkovszky M, Krikó E, Solymosi N. Ixodes ricinus tick bacteriome alterations based on a climatically representative survey in Hungary. Microbiol Spectr 2023; 11:e0124323. [PMID: 37966205 PMCID: PMC10715062 DOI: 10.1128/spectrum.01243-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 10/10/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE Climate-sensitive disease vectors, such as ticks, respond to the environment with changes in their microbiome. These changes can affect the emergence or re-emergence of various vector-borne pathogens, such as the causative agent of Lyme borreliosis (LB) or tick-borne encephalitis. This aspect is particularly emphasized in light of climate change. The climatically representative assessment of microbiome differences in various developmental stages of the most common Central European tick species, Ixodes ricinus, deepens our understanding of the potential climatic factors behind microbial relative abundance and interaction changes. This knowledge can support the development of novel disease vector control strategies.
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Affiliation(s)
- Adrienn Gréta Tóth
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Hungary
| | - Róbert Farkas
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary
| | - Márton Papp
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Hungary
| | - Oz Kilim
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Haeun Yun
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Hungary
| | | | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, HUN-REN, Szeged, Hungary
- Faculty of Water Sciences, University of Public Service, Baja, Hungary
| | - Mónika Gyurkovszky
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary
| | - Eszter Krikó
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Hungary
| | - Norbert Solymosi
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Hungary
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
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18
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Wu K, Lu X, Chen L, Qin J, Li C, Zhao Q, Ye Z. Evaluating the inhibitory effects of Nitrobenzene short-term stress on denitrification performance: Electron behaviors, bacterial and fungal community. CHEMOSPHERE 2023; 343:140014. [PMID: 37678599 DOI: 10.1016/j.chemosphere.2023.140014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 09/09/2023]
Abstract
Denitrifying system is a feasible way to remove nitro-aromatic compounds (NACs) in wastewater. However, the toxicity and mechanisms of NACs to denitrification remain unknown. This study investigated effects of nitrobenzene (NB, a typical NAC) on denitrification in short term. Results showed that NB in 10-50 mg/L groups decreased NO3--N removal efficiency by 9%-24%, but increased nitrous oxide (N2O) generation by 6-17fold. Mechanistic research indicated that NB could deteriorate electron behaviors and disturbed enzyme activities of microbial metabolism and denitrification, leading to a decline in denitrification performance. Structural equation modeling revealed that N2O reductase activity was the core factor in predicting denitrification performance at exposure of NB, with the indirect effects of NADH and electron transport system activity. High-throughput sequencing analysis demonstrated that NB had made an alteration on both bacterial and fungal community structure, as well as their interactions.
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Affiliation(s)
- Kun Wu
- Department of Environmental Engineering, Peking University, Beijing, 100871, China.
| | - Xinyue Lu
- Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Liuzhou Chen
- Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Jiangzhou Qin
- Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Chenxi Li
- Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Quanlin Zhao
- Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Zhengfang Ye
- Department of Environmental Engineering, Peking University, Beijing, 100871, China.
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19
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Yang Q, Yan Y, Huang J, Wang Z, Feng M, Cheng H, Zhang P, Zhang H, Xu J, Zhang M. The Impact of Warming on Assembly Processes and Diversity Patterns of Bacterial Communities in Mesocosms. Microorganisms 2023; 11:2807. [PMID: 38004818 PMCID: PMC10672829 DOI: 10.3390/microorganisms11112807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Bacteria in lake water bodies and sediments play crucial roles in various biogeochemical processes. In this study, we conducted a comprehensive analysis of bacterioplankton and sedimentary bacteria community composition and assembly processes across multiple seasons in 18 outdoor mesocosms exposed to three temperature scenarios. Our findings reveal that warming and seasonal changes play a vital role in shaping microbial diversity, species interactions, and community assembly disparities in water and sediment ecosystems. We observed that the bacterioplankton networks were more fragile, potentially making them susceptible to disturbances, whereas sedimentary bacteria exhibited increased stability. Constant warming and heatwaves had contrasting effects: heatwaves increased stability in both planktonic and sedimentary bacteria communities, but planktonic bacterial networks became more fragile under constant warming. Regarding bacterial assembly, stochastic processes primarily influenced the composition of planktonic and sedimentary bacteria. Constant warming intensified the stochasticity of bacterioplankton year-round, while heatwaves caused a slight shift from stochastic to deterministic in spring and autumn. In contrast, sedimentary bacteria assembly is mainly dominated by drift and remained unaffected by warming. Our study enhances our understanding of how bacterioplankton and sedimentary bacteria communities respond to global warming across multiple seasons, shedding light on the complex dynamics of microbial ecosystems in lakes.
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Affiliation(s)
- Qian Yang
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Yifeng Yan
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Jinhe Huang
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Zhaolei Wang
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Mingjun Feng
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Haowu Cheng
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Peiyu Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (P.Z.); (H.Z.); (J.X.)
| | - Huan Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (P.Z.); (H.Z.); (J.X.)
| | - Jun Xu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (P.Z.); (H.Z.); (J.X.)
| | - Min Zhang
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
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20
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Rodríguez-Gijón A, Hampel JJ, Dharamshi J, Bertilsson S, Garcia SL. Shotgun metagenomes from productive lakes in an urban region of Sweden. Sci Data 2023; 10:810. [PMID: 37978200 PMCID: PMC10656542 DOI: 10.1038/s41597-023-02722-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
Urban lakes provide multiple benefits to society while influencing life quality. Moreover, lakes and their microbiomes are sentinels of anthropogenic impact and can be used for natural resource management and planning. Here, we release original metagenomic data from several well-characterized and anthropogenically impacted eutrophic lakes in the vicinity of Stockholm (Sweden). Our goal was to collect representative microbial community samples and use shotgun sequencing to provide a broad view on microbial diversity of productive urban lakes. Our dataset has an emphasis on Lake Mälaren as a major drinking water reservoir under anthropogenic impact. This dataset includes short-read sequence data and metagenome assemblies from each of 17 samples collected from eutrophic lakes near the greater Stockholm area. We used genome-resolved metagenomics and obtained 2378 metagenome assembled genomes that de-replicated into 514 species representative genomes. This dataset adds new datapoints to previously sequenced lakes and it includes the first sequenced set of metagenomes from Lake Mälaren. Our dataset serves as a baseline for future monitoring of drinking water reservoirs and urban lakes.
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Affiliation(s)
- Alejandro Rodríguez-Gijón
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, 10691, Stockholm, Sweden.
| | - Justyna J Hampel
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, 10691, Stockholm, Sweden
| | - Jennah Dharamshi
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, 10691, Stockholm, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75651, Uppsala, Sweden
| | - Sarahi L Garcia
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, 10691, Stockholm, Sweden.
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, 26129, Oldenburg, Germany.
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21
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Basili M, Perini L, Zaggia L, Luna GM, Quero GM. Integrating culture-based and molecular methods provides an improved assessment of microbial quality in a coastal lagoon. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 334:122140. [PMID: 37414126 DOI: 10.1016/j.envpol.2023.122140] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/07/2023] [Accepted: 07/02/2023] [Indexed: 07/08/2023]
Abstract
Faecal pollution in aquatic environments is a worldwide public health concern, yet the reliability and comprehensiveness of the methods used to assess faecal contamination are still debated. We compared three approaches, namely a culture-based method to enumerate Faecal Indicator Bacteria (FIB), a FIB-targeting qPCR assay, and High-Throughput Sequencing (HTS) to detect faeces- and sewage-associated taxa in water and sediment samples of an impacted model lagoon and its adjacent sea across one year. Despite at different levels, all approaches agreed in showing a higher contamination in the lagoon than in the sea, and higher in sediments than water. FIB significantly correlated when considering separately sediment and water, and when using both cultivation and qPCR. Similarly, FIB correlated between cultivation and qPCR, but qPCR provided consistently higher estimates of FIB. Faeces-associated bacteria positively correlated with cultivated FIB in both compartments, whereas sewage-associated bacteria did only in water. Considering their benefits and limitations, we conclude that, in our study site, improved quali-quantitative information on contamination is provided when at least two approaches are combined (e.g., cultivation and qPCR or HTS data). Our results provide insights to move beyond the use of FIB to improve faecal pollution management in aquatic environments and to incorporate HTS analysis into routine monitoring.
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Affiliation(s)
- Marco Basili
- CNR IRBIM, National Research Council - Institute of Marine Biological Resources and Biotechnologies, Largo Fiera della Pesca, 60125, Ancona, Italy
| | - Laura Perini
- Department of Environmental Science, Aarhus University, 4000, Roskilde, Denmark
| | - Luca Zaggia
- CNR IGG, National Research Council - Institute of Geosciences and Earth Resources, Via G. Gradenigo 6, 35131, Padova, Italy
| | - Gian Marco Luna
- CNR IRBIM, National Research Council - Institute of Marine Biological Resources and Biotechnologies, Largo Fiera della Pesca, 60125, Ancona, Italy
| | - Grazia Marina Quero
- CNR IRBIM, National Research Council - Institute of Marine Biological Resources and Biotechnologies, Largo Fiera della Pesca, 60125, Ancona, Italy.
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22
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Pernthaler J, Krempaska N, le Moigne A. Small-scale spatial beta diversity of bacteria in the mixed upper layer of a lake. Environ Microbiol 2023; 25:1847-1859. [PMID: 37173811 DOI: 10.1111/1462-2920.16399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/27/2023] [Indexed: 05/15/2023]
Abstract
Bacterial community composition among individual, experimentally generated 'lake snow' particles may be highly variable. Since such aggregates are seasonally abundant in the mixed upper layer of lakes, we hypothesized that particle-attached (PA) bacteria disproportionally contribute to the small-scale spatial beta diversity of pelagic communities. Community composition was analysed in sets of small (10 mL) samples collected from a pre-alpine lake in May, July and October 2018. Bacteria were classified as free-living (FL) or PA depending on their presence in large, 5-μm pre-filtered reference samples. FL exhibited clear seasonal differences in community composition and assembly. They were spatially uniform in May and July, and only a few FL taxa exhibited significant spatial variability. Spatial heterogeneity of FL in October was caused by high alpha and beta diversity of rare taxa, many with a presumably 'tychoplanktic' (alternating attached and free-living) lifestyle. The spatial beta diversity of PA was always high, and only about 10% of their seasonal richness was present in any single sample. Thus, most compositional variability of pelagic bacteria at spatial scales of cm to m either directly or indirectly originated from PA. On a functional level, this genotypic heterogeneity might affect the spatial distribution of rare metabolic traits.
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Affiliation(s)
- Jakob Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Natalia Krempaska
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Alizée le Moigne
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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23
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Sushmitha TJ, Rajeev M, Murthy PS, Rao TS, Pandian SK. Planktonic and early-stage biofilm microbiota respond contrastingly to thermal discharge-created seawater warming. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 264:115433. [PMID: 37696079 DOI: 10.1016/j.ecoenv.2023.115433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 07/21/2023] [Accepted: 08/30/2023] [Indexed: 09/13/2023]
Abstract
Thermal-discharges from power plants highly disturb the biological communities of the receiving water body and understanding their influence is critical, given the relevance to global warming. We employed 16 S rRNA gene sequencing to examine the response of two dominant marine bacterial lifestyles (planktonic and biofilm) against elevated seawater temperature (+5 ℃). Obtained results demonstrated that warming prompted high heterogeneity in diversity and composition of planktonic and biofilm microbiota, albeit both communities responded contrastingly. Alpha diversity revealed that temperature exhibited positive effect on biofilm microbiota and negative effect on planktonic microbiota. The community composition of planktonic microbiota shifted significantly in warming area, with decreased abundances of Bacteroidetes, Cyanobacteria, and Actinobacteria. Contrastingly, these bacterial groups exhibited opposite trend in biofilm microbiota. Co-occurrence networks of biofilm microbiota displayed higher node diversity and co-presence in warming area. The study concludes that with increasing ocean warming, marine biofilms and biofouling management strategies will be more challenging.
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Affiliation(s)
- T J Sushmitha
- Department of Biotechnology, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Meora Rajeev
- Department of Biotechnology, Alagappa University, Karaikudi, Tamil Nadu, India
| | - P Sriyutha Murthy
- Water & Steam Chemistry Division, Bhabha Atomic Research Centre Facilities, Kalpakkam, Tamil Nadu, India
| | - Toleti Subba Rao
- School of Arts & Sciences, Sai University, OMR, Paiyanur, 603105 Tamil Nadu, India
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24
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Li Z, Sun L, Liu S, Lei P, Wang R, Li S, Gu Y. Interkingdom network analyses reveal microalgae and protostomes as keystone taxa involved in nutrient cycling in large freshwater lake sediment. FEMS Microbiol Ecol 2023; 99:fiad111. [PMID: 37715306 DOI: 10.1093/femsec/fiad111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/26/2023] [Accepted: 09/14/2023] [Indexed: 09/17/2023] Open
Abstract
Few studies have explored the role of interkingdom interactions between bacteria and microeukaryotes in nutrient cycling in lake ecosystems. We conducted sediment sampling from 40 locations covering Hongze Lake and analyzed their chemical properties. Intra- and interkingdom networks were constructed using 16S and 18S rRNA gene amplicon sequencing. Microeukaryotic intranetworks were more complex in spring than in autumn, while no clear variation in the complexity of bacterial intranetworks was found between autumn and spring. Larger and more complex bacterial-microeukaryotic bipartite networks emerged in spring than in autumn, correlated with lower carbon, nitrogen, and phosphorus levels in spring, likely resulting in intense microbial competition. Bacteria and microeukaryotes played different topological roles in interkingdom networks, with microeukaryotes contributing to the networks' greater complexity. Seven keystone modules were identified in spring and autumn nutrient cycling. Importantly, keystone taxa in these modules belonged to photoautotrophic microalgae or predatory protostomes, indicating that these organisms are key drivers in lake sediment nutrient cycling. Our results suggested that nutrient content variation in autumn and spring changes interkingdom networks' topological structure between bacteria and microeukaryotes. Microalgae and protostomes are essential in freshwater lake nutrient cycling and may be targeted to modulate nutrient cycling in large freshwater ecosystems.
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Affiliation(s)
- Zhidan Li
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Liang Sun
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Sijie Liu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Peng Lei
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Rui Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Sha Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Yian Gu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, P.R. China
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25
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Márton Z, Csitári B, Felföldi T, Hidas A, Jordán F, Szabó A, Székely AJ. Contrasting response of microeukaryotic and bacterial communities to the interplay of seasonality and local stressors in shallow soda lakes. FEMS Microbiol Ecol 2023; 99:fiad095. [PMID: 37586889 PMCID: PMC10449373 DOI: 10.1093/femsec/fiad095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/08/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023] Open
Abstract
Seasonal environmental variation is a leading driver of microbial planktonic community assembly and interactions. However, departures from usual seasonal trends are often reported. To understand the role of local stressors in modifying seasonal succession, we sampled fortnightly, throughout three seasons, five nearby shallow soda lakes exposed to identical seasonal and meteorological changes. We characterised their microeukaryotic and bacterial communities by amplicon sequencing of the 16S and 18S rRNA gene, respectively. Biological interactions were inferred by analyses of synchronous and time-shifted interaction networks, and the keystone taxa of the communities were topologically identified. The lakes showed similar succession patterns during the study period with spring being characterised by the relevance of trophic interactions and a certain level of community stability followed by a more dynamic and variable summer-autumn period. Adaptation to general seasonal changes happened through shared core microbiome of the lakes. Stochastic events such as desiccation disrupted common network attributes and introduced shifts from the prevalent seasonal trajectory. Our results demonstrated that, despite being extreme and highly variable habitats, shallow soda lakes exhibit certain similarities in the seasonality of their planktonic communities, yet local stressors such as droughts instigate deviations from prevalent trends to a greater extent for microeukaryotic than for bacterial communities.
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Affiliation(s)
- Zsuzsanna Márton
- Institute of Aquatic Ecology, Centre for Ecological Research, H-1113 Budapest, Hungary
- National Multidisciplinary Laboratory for Climate Change, Centre for Ecological Research, H-1113 Budapest, Hungary
- Doctoral School of Environmental Sciences, Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Bianka Csitári
- Doctoral School of Environmental Sciences, Eötvös Loránd University, H-1117 Budapest, Hungary
- Karolinska Institutet, 171 65 Stockholm, Sweden
- Uppsala University, 752 36 Uppsala, Sweden
| | - Tamás Felföldi
- Institute of Aquatic Ecology, Centre for Ecological Research, H-1113 Budapest, Hungary
- Department of Microbiology, Eötvös Loránd University, H-1117 Budapest, Hungary
| | - András Hidas
- Institute of Aquatic Ecology, Centre for Ecological Research, H-1113 Budapest, Hungary
- Doctoral School of Environmental Sciences, Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Ferenc Jordán
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Attila Szabó
- Institute of Aquatic Ecology, Centre for Ecological Research, H-1113 Budapest, Hungary
- Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Anna J Székely
- Uppsala University, 752 36 Uppsala, Sweden
- Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
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26
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Feng J, Li X, Lu Z, Yang Y, Zhou Z, Liang H. Enhanced permeation performance of biofiltration-facilitated gravity-driven membrane (GDM) systems by in-situ application of UV and VUV: Comprehensive insights from thermodynamic and multi-omics perspectives. WATER RESEARCH 2023; 242:120254. [PMID: 37354843 DOI: 10.1016/j.watres.2023.120254] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 05/22/2023] [Accepted: 06/19/2023] [Indexed: 06/26/2023]
Abstract
Biofouling is a major challenge limiting the practical application of biofiltration-facilitated gravity-driven membrane (GDM) systems in drinking water treatment. In this study, ultraviolet irradiation, including ultraviolet (UV) and vacuum ultraviolet (VUV) irradiation, was used for in-situ purification of membrane tanks to control membrane biofouling. After using UV and VUV, the permeate flux increased significantly by 26.1% and 78.3%, respectively, which was mainly due to the decreased cake layer resistance (Rc). The permeability of the biofouling layer improved after UV and VUV application, as evidenced by the increased surface porosity and decreased thickness. The contents of loosely bound extracellular proteins (LB-PN) and tightly bound extracellular proteins (TB-PN) in the biofouling layer were reduced after UV and VUV irradiation. The decreased LB-PN and TB-PN improved the interfacial free energy between the fouling itself and between the fouling and the membrane, which contributed to the reduction of interfacial cohesion and adhesion, resulting in a looser and thinner biofouling layer and a cleaner membrane. The concentration of protein-like material in the membrane tank decreased after UV and VUV irradiation, significantly altering the bacterial community structure on the membrane surface (Mantel's r > 0.7, p < 0.05). The changes in the metabolic state were responsible for the differences in the LB-PN and TB-PN contents. The inhibition of "Alanine, aspartate and glutamate metabolism" and "Glycine, serine and threonine metabolism" reduced amino acid biosynthesis, which restricted the secretion of LB-PN and TB-PN. Critical genera in the Proteobacteria phylum, such as Hirschia, Rhodobacter, Nordella, Candidatus_Berkiella, and Limnohabitans, were involved in metabolite transformation. Overall, the in-situ application of UV and VUV can be an effective alternative strategy to mitigate membrane biofouling, which would facilitate the practical application of biofiltration-facilitated GDM systems in drinking water treatment.
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Affiliation(s)
- Jianyong Feng
- College of Architecture and Civil Engineering, Faculty of Urban Construction, Beijing University of Technology, Beijing 100124, China
| | - Xing Li
- College of Architecture and Civil Engineering, Faculty of Urban Construction, Beijing University of Technology, Beijing 100124, China
| | - Zedong Lu
- College of Architecture and Civil Engineering, Faculty of Urban Construction, Beijing University of Technology, Beijing 100124, China
| | - Yanling Yang
- College of Architecture and Civil Engineering, Faculty of Urban Construction, Beijing University of Technology, Beijing 100124, China
| | - Zhiwei Zhou
- College of Architecture and Civil Engineering, Faculty of Urban Construction, Beijing University of Technology, Beijing 100124, China.
| | - Heng Liang
- State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), Harbin Institute of Technology, Harbin 150090, China
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27
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Romano F, Pitta P, John U. Community dynamics and co-occurrence relationships of pelagic ciliates and their potential prey at a coastal and an offshore station in the ultra-oligotrophic Eastern Mediterranean Sea. Front Genet 2023; 14:1219085. [PMID: 37547468 PMCID: PMC10400710 DOI: 10.3389/fgene.2023.1219085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/05/2023] [Indexed: 08/08/2023] Open
Abstract
Ciliates have been recognized as one of the major components of the microbial food web, especially in ultra-oligotrophic waters, such as the Eastern Mediterranean Sea, where nutrients are scarce and the microbial community is dominated by pico- and nano-sized organisms. For this reason, ciliates play an important role in these ecosystems since they are the main planktonic grazers. Regardless the importance of these organisms, little is known about the community structure of heterotrophic and mixotrophic ciliates and how they are associated to their potential prey. In this study, we used 18S V4 rRNA gene metabarcoding to analyze ciliate community dynamics and how the relationship with potential prey changes according to different seasons and depths. Samples were collected seasonally at two stations of the Eastern Mediterranean Sea (HCB: coastal, M3A: offshore) from the surface and deep chlorophyll maximum (DCM) layers. The ciliate community structure varied across depths in HCB and across seasons in M3A, and the network analysis showed that in both stations, mixotrophic oligotrichs were positively associated with diatoms and showed few negative associations with ASVs annotated as marine Stramenopiles (MAST). On the other hand, heterotrophic tintinnids showed negative relationships in both HCB and M3A stations, mostly with Ochrophyta and Chlorophyta. These results showed, in first place that, although the two stations are close to each other, the ciliate dynamics differed between them. Moreover, mixotrophic and heterotrophic ciliates may have different ecological niches since mixotrophic ciliates may be more selective compared to heterotrophic species regarding their prey. These findings are the first glimpse into an understanding of the dynamics between heterotrophic and mixotrophic ciliates and their role in microbial assemblages and dynamics of ultra-oligotrophic environments.
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Affiliation(s)
- Filomena Romano
- Marine Biological Section, University of Copenhagen, Helsingør, Denmark
- Hellenic Centre for Marine Research, Institute of Oceanography, Heraklion, Greece
| | - Paraskevi Pitta
- Marine Biological Section, University of Copenhagen, Helsingør, Denmark
| | - Uwe John
- Ecological Chemistry, Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany
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28
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Lin W, Fan F, Xu G, Gong K, Cheng X, Yuan X, Zhang C, Gao Y, Wang S, Ng HY, Dong Y. Microbial community assembly responses to polycyclic aromatic hydrocarbon contamination across water and sediment habitats in the Pearl River Estuary. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131762. [PMID: 37285790 DOI: 10.1016/j.jhazmat.2023.131762] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/26/2023] [Accepted: 06/01/2023] [Indexed: 06/09/2023]
Abstract
Along with rapid urbanization and intensive human activities, polycyclic aromatic hydrocarbon (PAH) pollution in the Pearl River Estuary (PRE) and its effects on the microbial community have attracted extensive attention. However, the potential and mechanism of microbial degradation of PAHs across water and sediment habitats remain obscure. Herein, the estuarine microbial community structure, function, assembly process and co-occurrence patterns impacted by PAHs were comprehensively analyzed using environmental DNA-based approaches. The contamination and distribution of PAHs were jointly affected by anthropogenic and natural factors. Some of the keystone taxa were identified as PAH-degrading bacteria (i.e., genera Defluviimonas, Mycobacterium, families 67-14, Rhodobacteraceae, Microbacteriaceae and order Gaiellales in water) or biomarkers (i.e., Gaiellales in sediment) that were significantly correlated with PAH levels. The proportion of deterministic process in the high PAH-polluted water (76%) was much higher than that in the low pollution area (7%), confirming the significant effect of PAHs on the microbial community assembly. In sediment, the communities with high phylogenetic diversity demonstrated a great extent of niche differentiation, exhibited a stronger response to environmental variables and were strongly influenced by deterministic processes (40%). Overall, deterministic and stochastic processes are closely related to the distribution and mass transfer of pollutants, and substantially affect the biological aggregation and interspecies interaction within communities in the habitats.
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Affiliation(s)
- Wei Lin
- Guangdong-Hong Kong Joint Laboratory for Water Security, Beijing Normal University, Zhuhai 519087, China; Center for Water Research, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, China
| | - Fuqiang Fan
- Guangdong-Hong Kong Joint Laboratory for Water Security, Beijing Normal University, Zhuhai 519087, China; Center for Water Research, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, China
| | - Guangming Xu
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Kaiyuan Gong
- Guangdong-Hong Kong Joint Laboratory for Water Security, Beijing Normal University, Zhuhai 519087, China; Center for Water Research, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, China
| | - Xiang Cheng
- Guangdong-Hong Kong Joint Laboratory for Water Security, Beijing Normal University, Zhuhai 519087, China; Center for Water Research, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, China
| | - Xingyu Yuan
- Guangdong-Hong Kong Joint Laboratory for Water Security, Beijing Normal University, Zhuhai 519087, China; Center for Water Research, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, China
| | - Cheng Zhang
- Instrumentation and Service Center for Science and Technology, Beijing Normal University, Zhuhai 519087, China; School of Engineering Technology, Beijing Normal University, Zhuhai 519087, China
| | - Yuan Gao
- Instrumentation and Service Center for Science and Technology, Beijing Normal University, Zhuhai 519087, China
| | - Shengrui Wang
- Guangdong-Hong Kong Joint Laboratory for Water Security, Beijing Normal University, Zhuhai 519087, China; Center for Water Research, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, China
| | - How Yong Ng
- Guangdong-Hong Kong Joint Laboratory for Water Security, Beijing Normal University, Zhuhai 519087, China; Center for Water Research, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, China
| | - Yue Dong
- Guangdong-Hong Kong Joint Laboratory for Water Security, Beijing Normal University, Zhuhai 519087, China; Center for Water Research, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, China.
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Zhao X, Zhang T, Chen X, Guo M, Meng X, Wang X, Bai S. Exploring the resilience of constructed wetlands to harmful algal blooms disturbances: A study on microbial response mechanisms. BIORESOURCE TECHNOLOGY 2023; 383:129251. [PMID: 37268089 DOI: 10.1016/j.biortech.2023.129251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/21/2023] [Accepted: 05/26/2023] [Indexed: 06/04/2023]
Abstract
Constructed wetlands (CWs) have emerged as a promising environmentally sustainable technique for wastewater treatment. However, the susceptibility of CWs to disturbances caused by harmful algal blooms (HABs) raises concerns. This study aimed to investigate the impact of HABs on the pollutants' removal performance of CWs and the response of rhizosphere microbial community. Results revealed that CWs possessed an adaptive capacity that enabled them to recover caused by HABs. The rhizosphere was found to stimulate the occurrence of Acinetobacter, which played a critical role to help resist HABs disturbance. This study also observed an increased dissimilatory nitrate reduction metabolic pathway which promoted denitrification and enhanced the nitrogen removal efficiency of CWs. Additionally, the structural equation model further suggested that dissolved oxygen exerted a significant influence on the microbial activities and then affected the pollutants removal performance. Overall, our findings shed light on the mechanism for CW stability maintenance during HABs disturbance.
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Affiliation(s)
- Xinyue Zhao
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Tuoshi Zhang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Xi Chen
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Mengran Guo
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Xiangwei Meng
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Xiaohui Wang
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Shunwen Bai
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
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Mioduchowska M, Konecka E, Gołdyn B, Pinceel T, Brendonck L, Lukić D, Kaczmarek Ł, Namiotko T, Zając K, Zając T, Jastrzębski JP, Bartoszek K. Playing Peekaboo with a Master Manipulator: Metagenetic Detection and Phylogenetic Analysis of Wolbachia Supergroups in Freshwater Invertebrates. Int J Mol Sci 2023; 24:ijms24119400. [PMID: 37298356 DOI: 10.3390/ijms24119400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/21/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
The infamous "master manipulators"-intracellular bacteria of the genus Wolbachia-infect a broad range of phylogenetically diverse invertebrate hosts in terrestrial ecosystems. Wolbachia has an important impact on the ecology and evolution of their host with documented effects including induced parthenogenesis, male killing, feminization, and cytoplasmic incompatibility. Nonetheless, data on Wolbachia infections in non-terrestrial invertebrates are scarce. Sampling bias and methodological limitations are some of the reasons limiting the detection of these bacteria in aquatic organisms. In this study, we present a new metagenetic method for detecting the co-occurrence of different Wolbachia strains in freshwater invertebrates host species, i.e., freshwater Arthropoda (Crustacea), Mollusca (Bivalvia), and water bears (Tardigrada) by applying NGS primers designed by us and a Python script that allows the identification of Wolbachia target sequences from the microbiome communities. We also compare the results obtained using the commonly applied NGS primers and the Sanger sequencing approach. Finally, we describe three supergroups of Wolbachia: (i) a new supergroup V identified in Crustacea and Bivalvia hosts; (ii) supergroup A identified in Crustacea, Bivalvia, and Eutardigrada hosts, and (iii) supergroup E infection in the Crustacea host microbiome community.
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Affiliation(s)
- Monika Mioduchowska
- Department of Evolutionary Genetics and Biosystematics, Faculty of Biology, University of Gdansk, 80-308 Gdańsk, Poland
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Łódź, Poland
- Department of Marine Plankton Research, Institute of Oceanography, University of Gdansk, 81-378 Gdynia, Poland
| | - Edyta Konecka
- Department of Microbiology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614 Poznań, Poland
| | - Bartłomiej Gołdyn
- Department of General Zoology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614 Poznań, Poland
| | - Tom Pinceel
- Animal Ecology, Global Change and Sustainable Development, KU Leuven, 3000 Leuven, Belgium
- Centre for Environmental Management, University of the Free State, Potchefstroom 2520, South Africa
- Community Ecology Laboratory, Department of Biology, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
| | - Luc Brendonck
- Animal Ecology, Global Change and Sustainable Development, KU Leuven, 3000 Leuven, Belgium
- Water Research Group, Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2531, South Africa
| | - Dunja Lukić
- Department of Wetland Ecology, Estación Biológica de Doñana-CSIC, 41092 Sevilla, Spain
| | - Łukasz Kaczmarek
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614 Poznań, Poland
| | - Tadeusz Namiotko
- Department of Evolutionary Genetics and Biosystematics, Faculty of Biology, University of Gdansk, 80-308 Gdańsk, Poland
| | - Katarzyna Zając
- Institute of Nature Conservation, Polish Academy of Sciences, 31-120 Kraków, Poland
| | - Tadeusz Zając
- Institute of Nature Conservation, Polish Academy of Sciences, 31-120 Kraków, Poland
| | - Jan P Jastrzębski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland
- Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland
| | - Krzysztof Bartoszek
- Department of Computer and Information Science, Division of Statistics and Machine Learning, Linköping University, SE-581 83 Linköping, Sweden
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Park H, Shabarova T, Salcher MM, Kosová L, Rychtecký P, Mukherjee I, Šimek K, Porcal P, Seďa J, Znachor P, Kasalický V. In the right place, at the right time: the integration of bacteria into the Plankton Ecology Group model. MICROBIOME 2023; 11:112. [PMID: 37210505 DOI: 10.1186/s40168-023-01522-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 03/17/2023] [Indexed: 05/22/2023]
Abstract
BACKGROUND Planktonic microbial communities have critical impacts on the pelagic food web and water quality status in freshwater ecosystems, yet no general model of bacterial community assembly linked to higher trophic levels and hydrodynamics has been assessed. In this study, we utilized a 2-year survey of planktonic communities from bacteria to zooplankton in three freshwater reservoirs to investigate their spatiotemporal dynamics. RESULTS We observed site-specific occurrence and microdiversification of bacteria in lacustrine and riverine environments, as well as in deep hypolimnia. Moreover, we determined recurrent bacterial seasonal patterns driven by both biotic and abiotic conditions, which could be integrated into the well-known Plankton Ecology Group (PEG) model describing primarily the seasonalities of larger plankton groups. Importantly, bacteria with different ecological potentials showed finely coordinated successions affiliated with four seasonal phases, including the spring bloom dominated by fast-growing opportunists, the clear-water phase associated with oligotrophic ultramicrobacteria, the summer phase characterized by phytoplankton bloom-associated bacteria, and the fall/winter phase driven by decay-specialists. CONCLUSIONS Our findings elucidate the major principles driving the spatiotemporal microbial community distribution in freshwater ecosystems. We suggest an extension to the original PEG model by integrating new findings on recurrent bacterial seasonal trends. Video Abstract.
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Grants
- CZ.02.1.01/0.0/0.0/16_025/0007417 Ministerstvo Školství, Mládeže a Tělovýchovy
- CZ.02.1.01/0.0/0.0/16_025/0007417 Ministerstvo Školství, Mládeže a Tělovýchovy
- CZ.02.1.01/0.0/0.0/16_025/0007417 Ministerstvo Školství, Mládeže a Tělovýchovy
- CZ.02.1.01/0.0/0.0/16_025/0007417 Ministerstvo Školství, Mládeže a Tělovýchovy
- CZ.02.1.01/0.0/0.0/16_025/0007417 Ministerstvo Školství, Mládeže a Tělovýchovy
- CZ.02.1.01/0.0/0.0/16_025/0007417 Ministerstvo Školství, Mládeže a Tělovýchovy
- CZ.02.1.01/0.0/0.0/16_025/0007417 Ministerstvo Školství, Mládeže a Tělovýchovy
- CZ.02.1.01/0.0/0.0/16_025/0007417 Ministerstvo Školství, Mládeže a Tělovýchovy
- CZ.02.1.01/0.0/0.0/16_025/0007417 Ministerstvo Školství, Mládeže a Tělovýchovy
- CZ.02.1.01/0.0/0.0/16_025/0007417 Ministerstvo Školství, Mládeže a Tělovýchovy
- 20-12496X Grantová Agentura České Republiky
- 19-00113S Grantová Agentura České Republiky
- 19-23469S Grantová Agentura České Republiky
- 19-00113S Grantová Agentura České Republiky
- 22-33245S Grantová Agentura České Republiky
- 20-12496X Grantová Agentura České Republiky
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Affiliation(s)
- Hongjae Park
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic.
| | - Tanja Shabarova
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Michaela M Salcher
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Lenka Kosová
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Pavel Rychtecký
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Indranil Mukherjee
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Karel Šimek
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Petr Porcal
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Jaromír Seďa
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Petr Znachor
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Vojtěch Kasalický
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
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Xu R, Zhang W, Fu Y, Fan F, Zhou Z, Chen J, Liu W, Meng F. The positive roles of influent species immigration in mitigating membrane fouling in membrane bioreactors treating municipal wastewater. WATER RESEARCH 2023; 235:119907. [PMID: 37001232 DOI: 10.1016/j.watres.2023.119907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
The influence of influent species immigration (ISI) on membrane fouling behaviors of membrane bioreactors (MBRs) treating municipal wastewater remains elusive, leading to an incomprehensive understanding of fouling ecology in MBRs. To address this issue, two anoxic/aerobic MBRs, which were fed with raw (named MBR-C) and sterilized (MBR-E) municipal wastewater, were operated. Compared with the MBR-E, the average fouling rate of the MBR-C was lowered by 30% over the long-term operation. In addition, the MBR-E sludge had significantly higher unified membrane fouling index and biofilm formation potential than the MBR-C sludge. Considerably larger flocs size and lower soluble microbial products (SMP) concentrations were observed in the MBR-C than in the MBR-E. Moreover, the 16S rRNA gene sequencing results showed that highly diverse and abundant populations responsible for floc-forming, hydrolysis/fermentation and SMP degradation readily inhabited the influent, shaping a unique microbial niche. Based on species mass balance-based assessment, most of these populations were nongrowing and their relative abundances were higher in the MBR-C than in the MBR-E. This suggested an important contribution of the ISI on the assemblage of these bacteria, thus supporting the increased flocs size and lowered SMP concentrations in the MBR-C. Moreover, the SMP-degrading related bacteria and functional pathways played a more crucial role in the MBR-C ecosystem as revealed by the bacterial co-occurrence network and Picrust2 analysis. Taken together, this study reveals the positive role of ISI in fouling mitigation and highlights the necessity for incorporating influent wastewater communities for fouling control in MBR plants.
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Affiliation(s)
- Ronghua Xu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, 510275, China
| | - Wentian Zhang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, 510275, China
| | - Yue Fu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, 510275, China
| | - Fuqiang Fan
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China; Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, 519087, China.
| | - Zanmin Zhou
- Zhuhai Urban Drainage Co., Ltd., Zhuhai, 519000, China
| | - Jincan Chen
- Zhuhai Urban Drainage Co., Ltd., Zhuhai, 519000, China
| | - Wanli Liu
- Zhuhai Water Environment Holdings Group Ltd., Zhuhai, 519000, China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, 510275, China.
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Liu J, Sun X, Zuo Y, Hu Q, He X. Plant species shape the bacterial communities on the phyllosphere in a hyper-arid desert. Microbiol Res 2023; 269:127314. [PMID: 36724560 DOI: 10.1016/j.micres.2023.127314] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 01/14/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023]
Abstract
Microorganisms are an important component of global biodiversity. However, they are vulnerable to hyper-arid climates in desert regions. Xerophytes are desert vegetation with unique biodiversity. However, little is known about the identities and communities of phyllosphere epiphytic microorganisms inhabiting the xerophyte leaf surface in the hot and dry environment. The diversity and community composition of phyllosphere epiphytes on different desert plants in Gansu, China, was investigated using the next-generation sequencing technique, revealing the diversity and community composition of the phyllosphere epiphytic bacteria associated with desert xerophytes. In addition, the ecological functions of the bacterial communities were investigated by combining the sequence classification information and prokaryotic taxonomic function annotation (FAPROTAX). This study determined the phyllosphere bacterial community composition, microbial interactions, and their functions. Despite harsh environments in the arid desert, we found that there are still diverse epiphytic bacteria on the leaves of desert plants. The bacterial communities mainly included Actinobacteria (52.79%), Firmicutes (31.62%), and Proteobacteria (12.20%). Further comparisons revealed different microbial communities, including Firmicutes at the phylum and Paenibacillaceae at the family level, in the phyllosphere among different plants, suggesting that the host plants had strong filter effects on bacteria. Co-occurrence network analysis revealed positive relationships were dominant among different bacterial taxa. The abundance of Actinobacteria and Proteobacteria was positively correlated, demonstrating their mutual relationship. On the other hand, the abundance of Firmicutes was negatively correlated, which suggested that they inhibit the growth of other bacterial taxa. FAPROTAX prediction revealed that chemoheterotrophy (accounting for 39.02% of the community) and aerobic chemoheterotrophy (37.01%) were the main functions of the leaf epiphytic bacteria on desert plants. This study improves our understanding of the community composition and ecological functions of plant-associated microbial communities inhabiting scattered niches in the desert ecosystem. In addition, the study provides insight into the biodiversity assessment in the desert region.
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Affiliation(s)
- Jiaqiang Liu
- School of Life Sciences, Hebei University, Baoding 071002, China.
| | - Xiang Sun
- School of Life Sciences, Hebei University, Baoding 071002, China.
| | - Yiling Zuo
- School of Life Sciences, Hebei University, Baoding 071002, China.
| | - Qiannan Hu
- School of Life Sciences, Hebei University, Baoding 071002, China.
| | - Xueli He
- School of Life Sciences, Hebei University, Baoding 071002, China.
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Lan G, Wei Y, Li Y, Wu Z. Diversity and assembly of root-associated microbiomes of rubber trees. FRONTIERS IN PLANT SCIENCE 2023; 14:1136418. [PMID: 37063173 PMCID: PMC10102524 DOI: 10.3389/fpls.2023.1136418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION Understanding the diversity and assembly of the microbiomes of plant roots is crucial to manipulate them for sustainable ecosystem functioning. However, there are few reports about microbial communities at a continuous fine-scale of roots for rubber trees. METHODS We investigate the structure, diversity, and assembly of bacterial and fungal communities for the soil (non-rhizosphere), rhizosphere, and rhizoplane as well as root endosphere of rubber trees using the amplicon sequencing of 16S ribosomal ribonucleic acid (rRNA) and Internally Transcribed Spacer (ITS) genes. RESULTS We show that 18.69% of bacterial and 20.20% of fungal operational taxonomic units (OTUs) in the rhizoplane derived from the endosphere and 20.64% of bacterial and 20.60% of fungal OTUs from the soil. This suggests that the rhizoplane microbial community was a mixed community of soil and endosphere microbial communities and that microorganisms can disperse bidirectionally across different compartments of the plant root. On the other hand, in the absence of an enrichment or depletion of core bacterial and fungal OTUs in the rhizosphere, little differences in microbial composition as well as a more shared microbial network structure between the soil and the rhizosphere support the theory that the rhizosphere microbial community is a subset of the soil community. A large number of functional genes (such as nitrogen fixation and nitrite reduction) and more enriched core OTUs as well as a less stable but more complex network structure were observed in the rhizoplane of rubber tree roots. This demonstrated that the rhizoplane is the most active root compartment and a hotspot for plant-soil-environment interactions. In addition, bacterial and fungal communities in the rhizoplane were more stochastic compared to the rhizosphere and soil. DISCUSSION Our study expands our understanding of root-associated microbial community structure and function, which may provide the scientific basis for sustainable agriculture through biological process management.
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Affiliation(s)
- Guoyu Lan
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Tropical Forestry Ecology Group, Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou, Hainan, China
| | - Yaqing Wei
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- College of Ecology and Environment, Hainan University, Haikou, Hainan, China
| | - Yuwu Li
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Zhixiang Wu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Tropical Forestry Ecology Group, Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou, Hainan, China
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Ji L, Xin Y, Guo D. Soil Fungal Community Structure and Its Effect on CO 2 Emissions in the Yellow River Delta. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:4190. [PMID: 36901198 PMCID: PMC10001496 DOI: 10.3390/ijerph20054190] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Soil salinization is one of the most compelling environmental problems on a global scale. Fungi play a crucial role in promoting plant growth, enhancing salt tolerance, and inducing disease resistance. Moreover, microorganisms decompose organic matter to release carbon dioxide, and soil fungi also use plant carbon as a nutrient and participate in the soil carbon cycle. Therefore, we used high-throughput sequencing technology to explore the characteristics of the structures of soil fungal communities under different salinity gradients and whether the fungal communities influence CO2 emissions in the Yellow River Delta; we then combined this with molecular ecological networks to reveal the mechanisms by which fungi adapt to salt stress. In the Yellow River Delta, a total of 192 fungal genera belonging to eight phyla were identified, with Ascomycota dominating the fungal community. Soil salinity was the dominant factor affecting the number of OTUs, Chao1 index, and ACE index of the fungal communities, with correlation coefficients of -0.66, 0.61, and -0.60, respectively (p < 0.05). Moreover, the fungal richness indices (Chao1 and ACE) and OTUs increased with the increase in soil salinity. Chaetomium, Fusarium, Mortierella, Alternaria, and Malassezia were the dominant fungal groups, leading to the differences in the structures of fungal communities under different salinity gradients. Electrical conductivity, temperature, available phosphorus, available nitrogen, total nitrogen, and clay had a significant impact on the fungal community structure (p < 0.05). Electrical conductivity had the greatest influence and was the dominant factor that led to the difference in the distribution patterns of fungal communities under different salinity gradients (p < 0.05). The node quantity, edge quantity, and modularity coefficients of the networks increased with the salinity gradient. The Ascomycota occupied an important position in the saline soil environment and played a key role in maintaining the stability of the fungal community. Soil salinity decreases soil fungal diversity (estimate: -0.58, p < 0.05), and soil environmental factors also affect CO2 emissions by influencing fungal communities. These results highlight soil salinity as a key environmental factor influencing fungal communities. Furthermore, the significant role of fungi in influencing CO2 cycling in the Yellow River Delta, especially in the environmental context of salinization, should be further investigated in the future.
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Cheng J, Liu M, Su X, Rittmann BE, Lu Z, Xu J, He Y. Conductive Materials on Biocathodes Altered the Electron-Transfer Paths and Modulated γ-HCH Dechlorination and CH 4 Production in Microbial Electrochemical Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:2739-2748. [PMID: 36724064 DOI: 10.1021/acs.est.2c06097] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Adding conductive materials to the cathode of a microbial electrochemical system (MES) can alter the route of interspecies electron transfer and the kinetics of reduction reactions. We tested reductive dechlorination of γ-hexachlorocyclohexane (γ-HCH), along with CH4 production, in MES systems whose cathodes were coated with conductive magnetite nanoparticles (NaFe), biochar (BC), magnetic biochar (FeBC), or anti-conductive silica biochar (SiBC). Coating with NaFe enriched electroactive microorganisms, boosted electro-bioreduction, and accelerated γ-HCH dechlorination and CH4 production. In contrast, BC only accelerated dechlorination, while FeBC only accelerated methanogenesis, because of their assemblies of functional taxa that selectively transferred electrons to those electron sinks. SiBC, which decreased electro-bioreduction, yielded the highest CH4 production and increased methanogens and the mcrA gene. This study provides a strategy to selectively control the distribution of electrons between reductive dechlorination and methanogenesis by adding conductive or anti-conductive materials to the MES's cathode. If the goal is to maximize dechlorination and minimize methane generation, then BC is the optimal conductive material. If the goal is to accelerate electro-bioreduction, then the best addition is NaFe. If the goal is to increase the rate of methanogenesis, adding anti-conductive SiBC is the best.
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Affiliation(s)
- Jie Cheng
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou310058, China
| | - Meng Liu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou310058, China
| | - Xin Su
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou310058, China
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona85287-5701, United States
| | - Zhijiang Lu
- Department of Environmental Science and Geology, Wayne State University, Detroit, Michigan48201, United States
| | - Jianming Xu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou310058, China
| | - Yan He
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou310058, China
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Hangzhou310058, China
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Kavagutti VS, Bulzu PA, Chiriac CM, Salcher MM, Mukherjee I, Shabarova T, Grujčić V, Mehrshad M, Kasalický V, Andrei AS, Jezberová J, Seďa J, Rychtecký P, Znachor P, Šimek K, Ghai R. High-resolution metagenomic reconstruction of the freshwater spring bloom. MICROBIOME 2023; 11:15. [PMID: 36698172 PMCID: PMC9878933 DOI: 10.1186/s40168-022-01451-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 12/16/2022] [Indexed: 05/16/2023]
Abstract
BACKGROUND The phytoplankton spring bloom in freshwater habitats is a complex, recurring, and dynamic ecological spectacle that unfolds at multiple biological scales. Although enormous taxonomic shifts in microbial assemblages during and after the bloom have been reported, genomic information on the microbial community of the spring bloom remains scarce. RESULTS We performed a high-resolution spatio-temporal sampling of the spring bloom in a freshwater reservoir and describe a multitude of previously unknown taxa using metagenome-assembled genomes of eukaryotes, prokaryotes, and viruses in combination with a broad array of methodologies. The recovered genomes reveal multiple distributional dynamics for several bacterial groups with progressively increasing stratification. Analyses of abundances of metagenome-assembled genomes in concert with CARD-FISH revealed remarkably similar in situ doubling time estimates for dominant genome-streamlined microbial lineages. Discordance between quantitations of cryptophytes arising from sequence data and microscopic identification suggested the presence of hidden, yet extremely abundant aplastidic cryptophytes that were confirmed by CARD-FISH analyses. Aplastidic cryptophytes are prevalent throughout the water column but have never been considered in prior models of plankton dynamics. We also recovered the first metagenomic-assembled genomes of freshwater protists (a diatom and a haptophyte) along with thousands of giant viral genomic contigs, some of which appeared similar to viruses infecting haptophytes but owing to lack of known representatives, most remained without any indication of their hosts. The contrasting distribution of giant viruses that are present in the entire water column to that of parasitic perkinsids residing largely in deeper waters allows us to propose giant viruses as the biological agents of top-down control and bloom collapse, likely in combination with bottom-up factors like a nutrient limitation. CONCLUSION We reconstructed thousands of genomes of microbes and viruses from a freshwater spring bloom and show that such large-scale genome recovery allows tracking of planktonic succession in great detail. However, integration of metagenomic information with other methodologies (e.g., microscopy, CARD-FISH) remains critical to reveal diverse phenomena (e.g., distributional patterns, in situ doubling times) and novel participants (e.g., aplastidic cryptophytes) and to further refine existing ecological models (e.g., factors affecting bloom collapse). This work provides a genomic foundation for future approaches towards a fine-scale characterization of the organisms in relation to the rapidly changing environment during the course of the freshwater spring bloom. Video Abstract.
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Affiliation(s)
- Vinicius S Kavagutti
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic.
| | - Paul-Adrian Bulzu
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Cecilia M Chiriac
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Michaela M Salcher
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Indranil Mukherjee
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Tanja Shabarova
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Vesna Grujčić
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
- Present address: Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Maliheh Mehrshad
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
- Present address: Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Vojtěch Kasalický
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Adrian-Stefan Andrei
- Limnological Station, Microbial Evogenomics Lab (MiEL), University of Zurich, Kilchberg, Switzerland
| | - Jitka Jezberová
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Jaromir Seďa
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Pavel Rychtecký
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Petr Znachor
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Karel Šimek
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Rohit Ghai
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic.
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Liu Y, Chu G, Stirling E, Zhang H, Chen S, Xu C, Zhang X, Ge T, Wang D. Nitrogen fertilization modulates rice seed endophytic microbiomes and grain quality. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159181. [PMID: 36191720 DOI: 10.1016/j.scitotenv.2022.159181] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
The intensive use of chemical fertilizer, particularly nitrogen (N) has resulted in not only markedly increased crop yields but also detrimental effects on ecosystems. Plant microbiomes represent an eco-friendly alternative for plant nutrition and productivity, and the effect of N fertilization on plant and soil microbes has been well studied. However, if and how N fertilization modulates seed endophytic microbiomes and grain quality remains largely unknown. Here, we investigated the effect of different N fertilization rates on rice seed endophytic bacterial and fungal communities as well as on grain quality. Higher bacterial and fungal community diversity and richness, but lower grain protein and amino acid contents were found in seeds of rice treated moderate N fertilization than those treated insufficient or excessive N input. There were also more complex co-occurrence networks, and an enrichment of putative beneficial bacterial taxa in seeds under moderate N application, while there was an opposite trend under the excessive N treatment. In addition, the grain amylose and amylopectin contents were positively correlated with the relative abundance of bacterial and fungal dominant genera, while the grain amino acid contents were negatively correlated with the bacterial dominant genera but positively associated with fungal dominant genera. Together, we demonstrate that moderate N fertilization can enhance bacterial and fungal community colonization in seeds and improve grain eating and cooking qualities. This study extends our knowledge regarding the significant role of rational fertilization on seed-microbe interactions in sustainable agriculture.
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Affiliation(s)
- Yuanhui Liu
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, Zhejiang, China
| | - Guang Chu
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, Zhejiang, China
| | - Erinne Stirling
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Adelaide 5064, Australia; School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia
| | - Haoqing Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
| | - Song Chen
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, Zhejiang, China
| | - Chunmei Xu
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, Zhejiang, China
| | - Xiufu Zhang
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, Zhejiang, China
| | - Tida Ge
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
| | - Danying Wang
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, Zhejiang, China.
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Zhou J, Liao Z, Liu Z, Guo X, Zhang W, Chen Y. Urbanization increases stochasticity and reduces the ecological stability of microbial communities in amphibian hosts. Front Microbiol 2023; 13:1108662. [PMID: 36713161 PMCID: PMC9878570 DOI: 10.3389/fmicb.2022.1108662] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023] Open
Abstract
Urbanization not only profoundly alters landscape profiles, ecosystems and vertebrate faunal diversity but also disturbs microbial communities by increasing stochasticity, vulnerability, biotic homogenization, etc. However, because of the buffering effect of host species, microbial communities are expected to be influenced by both host species and urbanization stresses. Therefore, the impacts of urbanization on animals' microbial symbionts could be more complex and uncertain. In this study, we quantified the urbanization degree of sampling sites and surveyed the gut and skin microbes of three amphibian host species in different sites in urban parks and nearby villages of Chengdu, Southwest China. Furthermore, a co-occurrence network analysis, the phylogenetic normalized stochasticity ratio and Sloan neutral community models were applied to infer the impact of urbanization on symbiotic microbial communities. For the three host species, urbanization increased the diversity of symbiotic microbes and the number of keystone microbial taxa. However, the negative effects of such increased diversification were evident, as the community stochasticity and co-occurrence network structure vulnerability also increased, while the network structure complexity and stability were reduced. Finally, the community stochasticity had positive associations with the network vulnerability, implying that the existence of many transient symbiotic rare microbial taxa in urban parks makes the symbiotic microbial community structure more fragile. Conclusively, urbanization increased the symbiotic microbial diversity at the cost of community stability; the results provide a new perspective for better understanding the complex triangulated environment-host-microbe relationship.
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Affiliation(s)
- Jin Zhou
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China,Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China,University of Chinese Academy of Sciences, Beijing, China
| | - Ziyan Liao
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zhidong Liu
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China,University of Chinese Academy of Sciences, Beijing, China
| | - Xuecheng Guo
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China,University of Chinese Academy of Sciences, Beijing, China
| | - Wenyan Zhang
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China,University of Chinese Academy of Sciences, Beijing, China
| | - Youhua Chen
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China,*Correspondence: Youhua Chen,
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Tian L, Zhang Y, Zhang L, Zhang L, Gao X, Feng B. Biogeographic Pattern and Network of Rhizosphere Fungal and Bacterial Communities in Panicum miliaceum Fields: Roles of Abundant and Rare Taxa. Microorganisms 2023; 11:microorganisms11010134. [PMID: 36677426 PMCID: PMC9863577 DOI: 10.3390/microorganisms11010134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/24/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Unraveling how microbial interactions and assembly process regulate the rhizosphere abundant and rare taxa is crucial for determining how species diversity affects rhizosphere microbiological functions. We assessed the rare and abundant taxa of rhizosphere fungal and bacterial communities in proso millet agroecosystems to explore their biogeographic patterns and co-occurrence patterns based on a regional scale. The taxonomic composition was significantly distinct between the fungal and bacterial abundant and rare taxa. Additionally, the rare taxa of bacteria and fungi exhibited higher diversity and stronger phylogenetic clustering than those of the abundant ones. The phylogenetic turnover rate of abundant taxa of bacteria was smaller than that of rare ones, whereas that of fungi had the opposite trend. Environmental variables, particularly mean annual temperature (MAT) and soil pH, were the crucial factors of community structure in the rare and abundant taxa. Furthermore, a deterministic process was relatively more important in governing the assembly of abundant and rare taxa. Our network analysis suggested that rare taxa of fungi and bacteria were located at the core of maintaining ecosystem functions. Interestingly, MAT and pH were also the important drivers controlling the main modules of abundant and rare taxa. Altogether, these observations revealed that rare and abundant taxa of fungal and bacterial communities showed obvious differences in biogeographic distribution, which were based on the dynamic interactions between assembly processes and co-occurrence networks.
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Affiliation(s)
- Lixin Tian
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Ministry of Agriculture, Northwest A&F University, Xianyang 712100, China
| | - Yuchuan Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Ministry of Agriculture, Northwest A&F University, Xianyang 712100, China
| | - Liyuan Zhang
- Chifeng Academy of Agricultural and Animal Husbandry Sciences, Chifeng 024031, China
| | - Lei Zhang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Xiaoli Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Ministry of Agriculture, Northwest A&F University, Xianyang 712100, China
- Correspondence: (X.G.); (B.F.)
| | - Baili Feng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Ministry of Agriculture, Northwest A&F University, Xianyang 712100, China
- Correspondence: (X.G.); (B.F.)
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She Y, Qi X, Xin X, He Y, Wang W, Li Z. Insights into microbial interactive mechanism regulating dissimilatory nitrate reduction processes in riparian freshwater aquaculture sediments. ENVIRONMENTAL RESEARCH 2023; 216:114593. [PMID: 36252838 DOI: 10.1016/j.envres.2022.114593] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/28/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Aquaculture can substantially alter the accumulation and cycling of nutrients in sediments. However, the microbial mechanisms mediating sediment dissimilatory nitrate (NO3-) reduction in freshwater aquaculture ponds are still unclear, which rule the removal and retention of N element. In the present study, three microbial NO3- reduction processes in riparian aquaculture pond sediments (i.e., crab, shrimp and fish ponds) and natural freshwater sediments (i.e., lakes and rivers) were investigated via isotopic tracing and molecular analyses. The potential rates of denitrification, anaerobic ammonium oxidation (anammox) and dissimilatory nitrate reduction to ammonium (DNRA) significantly increased in the aquaculture ponds compared with the natural freshwaters. Denitrification contributed 90.40-94.22% to the total NO3- reduction (product as N2), followed by 2.49-5.82% of anammox (product as N2) and 2.09-5.18% of DRNA (product as NH4+). The availability of C and N substrates, rather than functional gene abundance, regulated the activities of NO3- reductions and microbiome composition. Microbial mechanism based on network analysis indicated that heterotrophic denitrifiers and DNRA bacteria (e.g., Bacillus, Micromonospora, Mycobacterium and Brachybacterium) determined the community structure and function for N conversions in aquaculture ponds, whereas the such microbial network in natural freshwater sediments was manipulated by autotrophic denitrifiers (e.g., Desulfuromonas, Polaromonas, Solitalea). Collectively, this study provides an in-depth exploration of microbial nitrogen removal in freshwater aquaculture areas and supports management strategies for N pollution caused by reclamation for aquaculture in riparian zones.
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Affiliation(s)
- Yuecheng She
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing, 210023, China; School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Xin Qi
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing, 210023, China; School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Xiaodong Xin
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin, 150090, China
| | - Yanqing He
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing, 210023, China; School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Wei Wang
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing, 210023, China; School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Zhengkui Li
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing, 210023, China; School of the Environment, Nanjing University, Nanjing, 210023, China.
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Microbiota Community Structure and Interaction Networks within Dermacentor silvarum, Ixodes persulcatus, and Haemaphysalis concinna. Animals (Basel) 2022; 12:ani12233237. [PMID: 36496758 PMCID: PMC9735619 DOI: 10.3390/ani12233237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/16/2022] [Accepted: 11/20/2022] [Indexed: 11/24/2022] Open
Abstract
Ticks carry and transmit a variety of pathogens, which are very harmful to humans and animals. To characterize the microbial interactions in ticks, we analysed the microbiota of the hard ticks, Dermacentor silvarum, Ixodes persulcatus, and Haemaphysalis concinna, using 16S rRNA, showing that microbial interactions are underappreciated in terms of shaping arthropod microbiomes. The results show that the bacterial richness and microbiota structures of these three tick species had significant differences. Interestingly, the bacterial richness (Chao1 index) of all ticks decreased significantly after they became engorged. All the operational taxonomic units (OTUs) were assigned to 26 phyla, 67 classes, 159 orders, 279 families, and 627 genera. Microbial interactions in D. silvarum demonstrated more connections than in I. persulcatus and H. concinna. Bacteria with a high abundance were not important families in microbial interactions. Positive interactions of Bacteroidaceae and F_Solibacteraceae Subgroup 3 with other bacterial families were detected in all nine groups of ticks. This study provides an overview of the microbiota structure and interactions of three tick species and improves our understanding of the role of the microbiota in tick physiology and vector capacity, thus being conducive to providing basic data for the prevention of ticks and tick-borne diseases.
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Adegoke A, Kumar D, Budachetri K, Karim S. Hematophagy and tick-borne Rickettsial pathogen shape the microbial community structure and predicted functions within the tick vector, Amblyomma maculatum. Front Cell Infect Microbiol 2022; 12:1037387. [PMID: 36478675 PMCID: PMC9719966 DOI: 10.3389/fcimb.2022.1037387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/03/2022] [Indexed: 11/22/2022] Open
Abstract
Background Ticks are the primary vectors of emerging and resurging pathogens of public health significance worldwide. Analyzing tick bacterial composition, diversity, and functionality across developmental stages and tissues is crucial for designing new strategies to control ticks and prevent tick-borne diseases. Materials and methods Here, we explored the microbial communities across the developmental timeline and in different tissues of the Gulf-Coast ticks (Amblyomma maculatum). Using a high-throughput sequencing approach, the influence of blood meal and Rickettsia parkeri, a spotted fever group rickettsiae infection in driving changes in microbiome composition, diversity, and functionality was determined. Results This study shows that the core microbiome of Am. maculatum comprises ten core bacterial genera. The genus Rickettsia, Francisella, and Candidatus_Midichloria are the key players, with positive interactions within each developmental stage and adult tick organ tested. Blood meal and Rickettsia parkeri led to an increase in the bacterial abundance in the tissues. According to functional analysis, the increase in bacterial numbers is positively correlated to highly abundant energy metabolism orthologs with blood meal. Correlation analysis identified an increase in OTUs identified as Candidatus Midichloria and a subsequent decrease in Francisella OTUs in Rickettsia parkeri infected tick stages and tissues. Results demonstrate the abundance of Rickettsia and Francisella predominate in the core microbiome of Am. maculatum, whereas Candidatus_Midichloria and Cutibacterium prevalence increase with R. parkeri-infection. Network analysis and functional annotation suggest that R. parkeri interacts positively with Candidatus_Midichloria and negatively with Francisella. Conclusion We conclude that tick-transmitted pathogens, such as R. parkeri establishes infection by interacting with the core microbiome of the tick vector.
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Affiliation(s)
- Abdulsalam Adegoke
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS, United States
| | - Deepak Kumar
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS, United States
| | - Khemraj Budachetri
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS, United States
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, United States
| | - Shahid Karim
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS, United States
- Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, MS, United States
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Zhang J, Shen H, Wang H, Zhang W, Deng X, Gao Q, Yang X, Chen J, Xie P. Salinity and seasonality shaping free-living and particle-associated bacterioplankton community assembly in lakeshores of the northeastern Qinghai-Tibet Plateau. ENVIRONMENTAL RESEARCH 2022; 214:113717. [PMID: 35760113 DOI: 10.1016/j.envres.2022.113717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 05/30/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Microorganisms in lakeshore zones are essential for pollution interception and biodiversity maintenance. However, the biogeographic patterns of bacterioplankton communities in lakeshore zones and the mechanisms that driving them are poorly understood. We analyzed the 16 S rRNA gene sequences of particle-associated (PA) and free-living (FL) bacterioplankton communities in the lakeshore zones of 14 alpine lakes in two seasons on Qinghai-Tibet Plateau to investigate the bacterial diversity, composition and assembly processes. Our results revealed that PA and FL bacterioplankton communities were driven by both seasonality and salinity in the lakeshores on Qinghai-Tibet Plateau. Compared to FL bacterioplankton, PA bacterioplankton communities were more susceptible to seasonality than spatial salinity. FL bacterioplankton communities were more salinity constrained than the PA counterpart. Besides, the Stegen null model analyses have validated a quantitative bias on stochastic processes at different spatial scales. At a regional scale, stochasticity was the predominant assembly process in both PA and FL bacterioplankton. While at a subregional scale, dispersal limitation was the main contributor of stochastic processes for PA bacterioplankton in summer and heterogeneous selection was the dominant deterministic processes in winter, whereas the community assembly of FL bacterioplankton was more stochastic processes (i.e., dispersal limitation) dominated in the freshwater type but deterministic process (i.e., heterogeneous selection) increased with increasing salinity. Our study provides new insights into both significant spatiotemporal patterns and distinct assembly processes of PA and FL bacterioplankton in alpine lakeshores on the northeastern Qinghai-Tibet Plateau.
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Affiliation(s)
- Jia Zhang
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Shen
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Huan Wang
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan 570228, China
| | - Weizhen Zhang
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China
| | - Xuwei Deng
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Qiang Gao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, Qinghai, China
| | - Xi Yang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, Qinghai, China
| | - Jun Chen
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Ping Xie
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, Qinghai, China; Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
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45
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A sparse Bayesian hierarchical vector autoregressive model for microbial dynamics in a wastewater treatment plant. Comput Stat Data Anal 2022. [DOI: 10.1016/j.csda.2022.107659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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46
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Costas-Selas C, Martínez-García S, Logares R, Hernández-Ruiz M, Teira E. Role of Bacterial Community Composition as a Driver of the Small-Sized Phytoplankton Community Structure in a Productive Coastal System. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02125-2. [PMID: 36305941 DOI: 10.1007/s00248-022-02125-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
We present here the first detailed description of the seasonal patterns in bacterial community composition (BCC) in shelf waters off the Ría de Vigo (Spain), based on monthly samplings during 2 years. Moreover, we studied the relationship between bacterial and small-sized eukaryotic community composition to identify potential biotic interactions among components of these two communities. Bacterial operational taxonomic unit (OTU) richness and diversity systematically peaked in autumn-winter, likely related to low resource availability during this period. BCC showed seasonal and vertical patterns, with Rhodobacteraceae and Flavobacteriaceae families dominating in surface waters, and SAR11 clade dominating at the base of the photic zone (30 m depth). BCC variability was significantly explained by environmental variables (e.g., temperature of water, solar radiation, or dissolved organic matter). Interestingly, a strong and significant correlation was found between BCC and small-sized eukaryotic community composition (ECC), which suggests that biotic interactions may play a major role as structuring factors of the microbial plankton in this productive area. In addition, co-occurrence network analyses revealed strong and significant, mostly positive, associations between bacteria and small-sized phytoplankton. Positive associations likely result from mutualistic relationships (e.g., between Dinophyceae and Rhodobacteraceae), while some negative correlations suggest antagonistic interactions (e.g., between Pseudo-nitzchia sp. and SAR11). These results support the key role of biotic interactions as structuring factors of the small-sized eukaryotic community, mostly driven by positive associations between small-sized phytoplankton and bacteria.
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Affiliation(s)
- Cecilia Costas-Selas
- Centro de Investigación Mariña, Universidade de Vigo, Departamento de Ecoloxía e Bioloxía Animal, 36310, Vigo, Spain.
| | - Sandra Martínez-García
- Centro de Investigación Mariña, Universidade de Vigo, Departamento de Ecoloxía e Bioloxía Animal, 36310, Vigo, Spain
| | - Ramiro Logares
- Departament de Biologia Marina I Oceanografia, Institut de Ciéncies del Mar (ICM), CSIC, Catalonia, Barcelona, Spain
| | - Marta Hernández-Ruiz
- Centro de Investigación Mariña, Universidade de Vigo, Departamento de Ecoloxía e Bioloxía Animal, 36310, Vigo, Spain
| | - Eva Teira
- Centro de Investigación Mariña, Universidade de Vigo, Departamento de Ecoloxía e Bioloxía Animal, 36310, Vigo, Spain
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Wu T, Ding J, Yang SS, Zhong L, Liu BF, Xie GJ, Yang F, Pang JW, Ren NQ. A novel cross-flow honeycomb bionic carrier promotes simultaneous nitrification, denitrification and phosphorus removal in IFAS system: Performance, mechanism and keystone species. WATER RESEARCH 2022; 225:119132. [PMID: 36155005 DOI: 10.1016/j.watres.2022.119132] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/13/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Simultaneously achieving efficient nitrogen (N) and phosphorus (P) removal without adding external carbon source is vital for carbon-neutral wastewater treatment. In this study, a novel cross-flow honeycomb bionic microbial carrier (CF) was developed to improve the efficiency of simultaneous nitrification, denitrification, and P removal (SNDPR) in an integrated fixed-film activated sludge (IFAS) system. A parallel laboratory-scale sequencing batch reactor with the commercialized microbial carriers (CM) (CM-IFAS) was performed as the comparative system for over 233 d The results demonstrated that CF-IFAS exhibited a more consistent N removal efficiency and better performance than CM-IFAS. In the CF-IFAS, the highest N and P removal efficiencies were 95.40% and 100%, respectively. Typical cycle analysis revealed that nitrate was primarily removed by the denitrifying glycogen-accumulating organisms in the CF-IFAS and by denitrifying phosphate-accumulating organisms in the CM-IFAS. The neutral community model showed that the microbial community assembly in both the reactors was driven by deterministic selection rather than stochastic factors. Compared to those in CM-IFAS, the microorganisms in CF-IFAS were more closely related to each other and had more keystone species: norank_f_norank_o_norank_c_OM190, SM1A02, Defluviicoccus, norank_f_ Saprospiraceae, and norank_f_Rhodocyclaceae. The absolute contents of the genes associated with N removal (bacterial amoA, archaeal amoA, NarG, NapA, NirS, and NirK) were higher in CF-IFAS than in CM-IFAS; the N cycle activity was also stronger in the CF-IFAS. Overall, the microecological environment differed between both systems. This study provides novel insights into the potential of bionic carriers to improve SNDPR performance by shaping microbial communities, thereby providing scientific guidance for practical engineering.
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Affiliation(s)
- Tong Wu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR. China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR. China
| | - Shan-Shan Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR. China.
| | - Le Zhong
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR. China
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR. China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR. China
| | - Fan Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150008, PR. China
| | - Ji-Wei Pang
- China Energy Conservation and Environmental Protection Group, Beijing 100089, PR. China
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR. China
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Xie W, Yan Y, Hu J, Dong P, Hou D, Zhang H, Yao Z, Zhu X, Zhang D. Ecological Dynamics and Co-occurrences Among Prokaryotes and Microeukaryotes in a Diatom Bloom Process in Xiangshan Bay, China. MICROBIAL ECOLOGY 2022; 84:746-758. [PMID: 34665286 DOI: 10.1007/s00248-021-01899-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Diatom blooms can significantly affect the succession of microbial communities, yet little is known about the assembly processes and interactions of microbial communities during autumn bloom events. In this study, we investigated the ecological effects of an autumn diatom bloom on prokaryotic communities (PCCs) and microeukaryotic communities (MECs), focusing on their assembly processes and interactions. The PCCs were largely dominated by Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria, and Flavobacteria, while the MECs primarily included Diatomea, Dinoflagellata, and Chlorophyta. The succession of both PCCs and MECs was mainly driven by this diatom bloom and environmental factors, such as nitrate and silicate. Null modeling revealed that homogeneous selection had a more pronounced impact on the structure of PCCs compared with that of MECs. In particular, drift and dispersal limitation cannot be neglected in the assembly processes of MECs. Co-occurrence network analyses showed that Litorimicrobium, Cercozoa, Marine Group I (MGI), Cryptomonadales, Myrionecta, and Micromonas may affect the bloom process. In summary, these results elucidated the complex, robust interactions and obviously distinct assembly mechanisms of PCCs and MECs during a diatom bloom and extend our current comprehension of the ecological mechanisms and microbial interactions involved in an autumn diatom bloom process.
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Affiliation(s)
- Weijuan Xie
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315832, China
| | - Yi Yan
- School of Marine Sciences, Ningbo University, Ningbo, 315832, China
| | - Jian Hu
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315832, China
| | - Pengsheng Dong
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315832, China
| | - Dandi Hou
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315832, China
| | - Huajun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China.
- School of Marine Sciences, Ningbo University, Ningbo, 315832, China.
| | - Zhiyuan Yao
- School of Civil and Environmental Engineering, Ningbo University, Ningbo, 315211, China
| | - Xiangyu Zhu
- Environmental Monitoring Center of Ningbo, Ningbo, 315010, China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China.
- School of Marine Sciences, Ningbo University, Ningbo, 315832, China.
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Brindefalk B, Brolin H, Säve‐Söderbergh M, Karlsson E, Sundell D, Wikström P, Jacobsson K, Toljander J, Stenberg P, Sjödin A, Dryselius R, Forsman M, Ahlinder J. Bacterial composition in Swedish raw drinking water reveals three major interacting ubiquitous metacommunities. Microbiologyopen 2022; 11:e1320. [PMID: 36314747 PMCID: PMC9511821 DOI: 10.1002/mbo3.1320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Surface raw water used as a source for drinking water production is a critical resource, sensitive to contamination. We conducted a study on Swedish raw water sources, aiming to identify mutually co-occurring metacommunities of bacteria, and environmental factors driving such patterns. METHODS The water sources were different regarding nutrient composition, water quality, and climate characteristics, and displayed various degrees of anthropogenic impact. Water inlet samples were collected at six drinking water treatment plants over 3 years, totaling 230 samples. The bacterial communities of DNA sequenced samples (n = 175), obtained by 16S metabarcoding, were analyzed using a joint model for taxa abundance. RESULTS Two major groups of well-defined metacommunities of microorganisms were identified, in addition to a third, less distinct, and taxonomically more diverse group. These three metacommunities showed various associations to the measured environmental data. Predictions for the well-defined metacommunities revealed differing sets of favored metabolic pathways and life strategies. In one community, taxa with methanogenic metabolism were common, while a second community was dominated by taxa with carbohydrate and lipid-focused metabolism. CONCLUSION The identification of ubiquitous persistent co-occurring bacterial metacommunities in freshwater habitats could potentially facilitate microbial source tracking analysis of contamination issues in freshwater sources.
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Affiliation(s)
- Björn Brindefalk
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
| | - Harald Brolin
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Melle Säve‐Söderbergh
- Science DivisionSwedish Food AgencyUppsalaSweden
- Institute of Environmental Medicine, Karolinska InstitutetStockholmSweden
| | - Edvin Karlsson
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
- Department of Ecology and Environmental Science (EMG)Umeå UniversityUmeåSweden
| | - David Sundell
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
| | - Per Wikström
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
| | - Karin Jacobsson
- Department of Biomedical Science and Veterinary Public HealthSwedish University of Agricultural SciencesUppsalaSweden
| | | | - Per Stenberg
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
- Department of Ecology and Environmental Science (EMG)Umeå UniversityUmeåSweden
| | - Andreas Sjödin
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
| | | | - Mats Forsman
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
| | - Jon Ahlinder
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
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50
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Zhao RZ, Zhang WJ, Zhang W, Zhao ZF, Qiu XC. A Preliminary Study of Bacterioplankton Community Structure in the Taiyangshan Wetland in Ningxia and Its Driving Factors. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:12224. [PMID: 36231526 PMCID: PMC9565018 DOI: 10.3390/ijerph191912224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/12/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
The Taiyangshan Wetland, a valuable wetland resource in the arid zone of central Ningxia, is critical for flood storage and drought resistance, climate regulation, and biodiversity protection. Nevertheless, the community structure and diversity of bacterioplankton in the Taiyangshan Wetland remains unclear. High-throughput sequencing was used to analyze the differences in bacterioplankton structure and major determinants in the Taiyangshan Wetland from April to October 2020. The composition and diversity of the bacterioplankton community varied significantly in different sampling periods but showed negligible differences across lake regions. Meanwhile, the relative abundances of bacterioplankton Bacteroidetes, Actinobacteria, Firmicutes, Chloroflexi, Tenericutes, Epsilonbacteraeota, and Patescibacteria were significantly different in different sampling periods, while the relative abundances of Cyanobacteria in different lake regions were quite different. Network analysis revealed that the topological attributes of co-occurrence pattern networks of bacterioplankton were high, and bacterioplankton community compositions were complicated in the month of July. A mantel test revealed that the bacterioplankton community in the entire wetland was affected by water temperature, electrical conductivity, dissolved oxygen, salinity, total nitrogen, ammonia nitrogen, chemical oxygen demand, fluoride, and sulfate. The bacterioplankton community structure was affected by ten environmental parameters (e.g., water temperature, dissolved oxygen, salinity, and permanganate index) in April, while the bacterioplankton community was only related to 1~2 environmental parameters in July and October. The bacterioplankton community structure in Lake Region IV was related to seven environmental parameters, including dissolved oxygen, pH, total nitrogen, and chemical oxygen demand, whereas the bacterioplankton community structures in the other three lake regions were related to two environmental parameters. This study facilitates the understanding of the bacterioplankton community in wetlands in arid areas and provides references to the evaluation of aquatic ecological management of the Taiyangshan Wetland.
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Affiliation(s)
- Rui-Zhi Zhao
- School of Civil and Hydraulic Engineering, Ningxia University, Yinchuan 750021, China
| | - Wei-Jiang Zhang
- School of Civil and Hydraulic Engineering, Ningxia University, Yinchuan 750021, China
| | - Wen Zhang
- Ningxia Supervision Institute for Veterinary Drugs and Animal Feedstuffs, Yinchuan 750004, China
| | - Zeng-Feng Zhao
- School of Civil and Hydraulic Engineering, Ningxia University, Yinchuan 750021, China
| | - Xiao-Cong Qiu
- School of Life Science, Ningxia University, Yinchuan 750021, China
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