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Smith HJ, Dieser M, Foreman CM. Eight genome sequences of bacterial, environmental isolates from Canada Glacier, Antarctica. Microbiol Resour Announc 2024; 13:e0113023. [PMID: 38990023 PMCID: PMC11320961 DOI: 10.1128/mra.01130-23] [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: 11/27/2023] [Accepted: 06/19/2024] [Indexed: 07/12/2024] Open
Abstract
Sediments in cryoconite holes and meltwater streams in the McMurdo Dry Valleys, Antarctica, provide both substrates and conditions that support life in an arid polar desert. Here, we report the genomic sequences of eight environmental, bacterial isolates from Canada Glacier cryoconite holes and stream. These isolates span three major phyla.
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Affiliation(s)
- Heidi J. Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Markus Dieser
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical & Biological Engineering, Montana State University, Bozeman, Montana, USA
| | - Christine M. Foreman
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical & Biological Engineering, Montana State University, Bozeman, Montana, USA
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2
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Yalçın G, Yıldız D, Calderó-Pascual M, Yetim S, Şahin Y, Parakatselaki ME, Avcı F, Karakaya N, Ladoukakis ED, Berger SA, Ger KA, Jeppesen E, Beklioğlu M. Quality matters: Response of bacteria and ciliates to different allochthonous dissolved organic matter sources as a pulsed disturbance in shallow lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170140. [PMID: 38244618 DOI: 10.1016/j.scitotenv.2024.170140] [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: 09/25/2023] [Revised: 12/11/2023] [Accepted: 01/11/2024] [Indexed: 01/22/2024]
Abstract
Shallow lake ecosystems are particularly prone to disturbances such as pulsed dissolved organic matter (allochthonous-DOM; hereafter allo-DOM) loadings from catchments. However, the effects of allo-DOM with contrasting quality (in addition to quantity) on the planktonic communities of microbial loop are poorly understood. To determine the impact of different qualities of pulsed allo-DOM disturbance on the coupling between bacteria and ciliates, we conducted a mesocosm experiment with two different allo-DOM sources added to mesocosms in a single-pulse disturbance event: Alder tree leaf extract, a more labile (L) source and HuminFeed® (HF), a more recalcitrant source. Allo-DOM sources were used as separate treatments and in combination (HFL) relative to the control without allo-DOM additions (C). Our results indicate that the quality of allo-DOM was a major regulator of planktonic microbial community biomass and/or composition through which both bottom-up and top-down forces were involved. Bacteria biomass showed significant nonlinear responses in L and HFL with initial increases followed by decreases to pre-pulse conditions. Ciliate biomass was significantly higher in L compared to all other treatments. In terms of composition, bacterivore ciliate abundance was significantly higher in both L and HFL treatments, mainly driven by the bacterial biomass increase in the same treatments. GAMM models showed negative interaction between metazoan zooplankton biomass and ciliates, but only in the L treatment, indicating top-down control on ciliates. Ecosystem stability analyses revealed overperformance, high resilience and full recovery of bacteria in the HFL and L treatments, while ciliates showed significant shift in compositional stability in HFL and L with incomplete taxonomic recovery. Our study highlights the importance of allo-DOM quality shaping the response within the microbial loop not only through triggering different scenarios in biomass, but also the community composition, stability, and species interactions (top-down and bottom-up) in bacteria and plankton.
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Affiliation(s)
- Gülce Yalçın
- Limnology Laboratory, Biological Sciences Department, Middle East Technical University, 06800 Ankara, Turkey; Ecosystem Research and Implementation Center, Middle East Technical University, 06800 Ankara, Turkey.
| | - Dilvin Yıldız
- Limnology Laboratory, Biological Sciences Department, Middle East Technical University, 06800 Ankara, Turkey; Earth System Sciences, Graduate School of Natural and Applied Science, Middle East Technical University, Ankara, Turkey.
| | - Maria Calderó-Pascual
- Centre for Freshwater and Environmental Studies, Dundalk Institute of Technology, Dundalk, Marshes Upper, Co. Louth A91 K584, Ireland..
| | - Sinem Yetim
- Limnology Laboratory, Biological Sciences Department, Middle East Technical University, 06800 Ankara, Turkey
| | - Yiğit Şahin
- Department of Biotechnology, Graduate School of Natural and Applied Sciences, Ege University, 35100 Izmir, Turkey; Department of Bioengineering, Faculty of Engineering, Ege University, 35100, Izmir, Turkey
| | | | - Feride Avcı
- Limnology Laboratory, Biological Sciences Department, Middle East Technical University, 06800 Ankara, Turkey.
| | | | - Emmanuel D Ladoukakis
- Department of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Greece.
| | - Stella A Berger
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Plankton and Microbial Ecology, Zur alten Fischerhuette 2, 16775 Stechlin, Germany.
| | - Kemal Ali Ger
- Department of Ecology (DECOL), Federal University of Rio Grande do Norte, Natal, RN 59078-970, Brazil..
| | - Erik Jeppesen
- Limnology Laboratory, Biological Sciences Department, Middle East Technical University, 06800 Ankara, Turkey; Ecosystem Research and Implementation Center, Middle East Technical University, 06800 Ankara, Turkey; Department of Ecoscience, Aarhus University, 8000C Aarhus, Denmark; Sino-Danish Centre for Education and Research (SDC), University of Chinese Academy of Sciences, Beijing, China.
| | - Meryem Beklioğlu
- Limnology Laboratory, Biological Sciences Department, Middle East Technical University, 06800 Ankara, Turkey; Ecosystem Research and Implementation Center, Middle East Technical University, 06800 Ankara, Turkey.
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Hu Y, Fair H, Liu Q, Wang Z, Duan B, Lu X. Diversity and co-occurrence networks of bacterial and fungal communities on two typical debris-covered glaciers, southeastern Tibetan Plateau. Microbiol Res 2023; 273:127409. [PMID: 37186995 DOI: 10.1016/j.micres.2023.127409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/19/2023] [Accepted: 05/09/2023] [Indexed: 05/17/2023]
Abstract
Debris-covered glaciers (DCGs) are globally distributed and thought to contain greater microbial diversity than clean surface continental glaciers, but the ecological characteristics of microbial communities on the surface of DCGs have remained underexplored. Here, we investigated bacterial and fungal diversity and co-occurrence networks on the supraglacial debris habitat of two DCGs (Hailuogou and Dagongba Glaciers) in the southeastern Tibetan Plateau. We found that the supraglacial debris harbored abundant microbes with Proteobacteria occupying more than half (51.5%) of the total bacteria operational taxonomic units. The composition, diversity, and co-occurrence networks of both bacterial and fungal communities in the debris were significantly different between Hailuogou Glacier and Dagongba Glacier even though the glaciers are geographically adjacent within the same mountain range. Bacteria were more diverse in the debris of the Dagongba Glacier, where a lower surface velocity and thicker debris layer allowed the supraglacial debris to continuously weather and accumulate nutrients. Fungi were more diverse in the debris of the Hailuogou Glacier, which experiences a wetter monsoonal climate, is richer in calcium, has greater debris instability, and greater ice velocity than the Dagongba Glacier. These factors may provide ideal conditions for the dispersal and propagation of fungi spores on the Hailuogou Glacier. In addition, we found an obvious gradient of bacterial diversity along the supraglacial debris transect on the Hailuogou Glacier. Bacterial diversity was lower where debris cover was thin and scattered and became more diverse near the glacial terminus in thick, slow-moving debris. No such increasing bacterial pattern was detected on the Dagongba Glacier, which implies a positive relationship of debris age, thickness, and weathering on bacterial diversity. Additionally, a highly connected bacterial co-occurrence network with low modularity was found in the debris of the Hailuogou Glacier. In contrast, debris from the Dagongba Glacier exhibited less connected but more modularized co-occurrence networks of both bacterial and fungal communities. These findings indicate that less disturbed supraglacial debris conditions are crucial for microbes to form stable communities on DCGs.
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Affiliation(s)
- Yang Hu
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, Sichuan 610299, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Heather Fair
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | - Qiao Liu
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, Sichuan 610299, China
| | - Ziwei Wang
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, Sichuan 610299, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Baoli Duan
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, Sichuan 610299, China.
| | - Xuyang Lu
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, Sichuan 610299, China.
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Shen J, Song Y, Cheng C, Duan F, Liu C, Chai Y, Wang S, Xiong Q, Wu J. Spectroscopic and compositional profiles of dissolved organic matters in urban snow from 2019 to 2021: Focusing on pollution features identification. WATER RESEARCH 2023; 229:119408. [PMID: 36462254 DOI: 10.1016/j.watres.2022.119408] [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: 08/29/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Snow owns stronger adsorption capacity for organic pollutants compared with rain. Huge amounts of anthropogenic dissolved organic matters (DOMs) in the atmosphere may enter the water environment with urban snow and increase water pollution risk. Extracting stable pollution features of urban snow is conducive to identifying the urban snow pollution from the water environment. Herein, we systematically explored the spectroscopic and compositional profiles of urban snow in Beijing from three snow events by multiple analytical tools and extracted stable pollution features of urban snow for the first time. Results showed that conventional pollutants with high concentration were detected in urban snow. The fluorescence signals of humic-like and some protein-like materials, the molecular weight distributions of chromophoric DOM at 254 nm and humic-like materials, and 172 kinds of lignin-like molecular formulas were extracted as stable features for urban snow. These stable features of urban snow laid the foundation for the identification of urban snow pollution and the analysis of the impact mechanisms of atmospheric pollution sources on the water environment.
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Affiliation(s)
- Jian Shen
- Research Center of Environmental Technology in Water Pollution Source Identification and Precise Supervision, School of Environment, Tsinghua University, Beijing, 100084, China; Research and Development Center of Advanced Environmental Supervision Technology and Instrument, Research Institute for Environmental Innovation (Suzhou) Tsinghua, Suzhou, 215163, China; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yiming Song
- Research Center of Environmental Technology in Water Pollution Source Identification and Precise Supervision, School of Environment, Tsinghua University, Beijing, 100084, China; Research and Development Center of Advanced Environmental Supervision Technology and Instrument, Research Institute for Environmental Innovation (Suzhou) Tsinghua, Suzhou, 215163, China; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Cheng Cheng
- Research Center of Environmental Technology in Water Pollution Source Identification and Precise Supervision, School of Environment, Tsinghua University, Beijing, 100084, China; Research and Development Center of Advanced Environmental Supervision Technology and Instrument, Research Institute for Environmental Innovation (Suzhou) Tsinghua, Suzhou, 215163, China; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Fengkui Duan
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Chuanyang Liu
- Research Center of Environmental Technology in Water Pollution Source Identification and Precise Supervision, School of Environment, Tsinghua University, Beijing, 100084, China; Research and Development Center of Advanced Environmental Supervision Technology and Instrument, Research Institute for Environmental Innovation (Suzhou) Tsinghua, Suzhou, 215163, China; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yidi Chai
- Research Center of Environmental Technology in Water Pollution Source Identification and Precise Supervision, School of Environment, Tsinghua University, Beijing, 100084, China; Research and Development Center of Advanced Environmental Supervision Technology and Instrument, Research Institute for Environmental Innovation (Suzhou) Tsinghua, Suzhou, 215163, China
| | - Siting Wang
- Research and Development Center of Advanced Environmental Supervision Technology and Instrument, Research Institute for Environmental Innovation (Suzhou) Tsinghua, Suzhou, 215163, China
| | - Qiuran Xiong
- Research Center of Environmental Technology in Water Pollution Source Identification and Precise Supervision, School of Environment, Tsinghua University, Beijing, 100084, China; Research and Development Center of Advanced Environmental Supervision Technology and Instrument, Research Institute for Environmental Innovation (Suzhou) Tsinghua, Suzhou, 215163, China; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Jing Wu
- Research Center of Environmental Technology in Water Pollution Source Identification and Precise Supervision, School of Environment, Tsinghua University, Beijing, 100084, China; Research and Development Center of Advanced Environmental Supervision Technology and Instrument, Research Institute for Environmental Innovation (Suzhou) Tsinghua, Suzhou, 215163, China; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
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5
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He Z, Ding B, Ali Q, Liu H, Zhao Y, Wang X, Han Y, Dong H, Divvela PK, Juan Y. Screening and isolation of cold-adapted cellulose degrading bacterium: A candidate for straw degradation and De novo genome sequencing analysis. Front Microbiol 2023; 13:1098723. [PMID: 36713214 PMCID: PMC9880256 DOI: 10.3389/fmicb.2022.1098723] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/19/2022] [Indexed: 01/14/2023] Open
Abstract
Degradation of crop straw in natural environment has been a bottleneck. There has been a recent increase in the exploration of cold-adapted microorganisms as they can solve the problem of corn straw degradation under low temperatures and offer new alternatives for the sustainable development of agriculture. The study was conducted in low-temperature (10°C) and high-efficiency cellulose-degrading bacteria were screened using carboxymethyl cellulose (CMC) selection medium and subjected to genome sequencing by the third-generation Pacbio Sequl and the second-generation Illumina Novaseq platform, and their cellulase activity was detected by 3,5-dinitrosalicylic acid (DNS) method. The results showed that the low-temperature (10°C) and high-efficiency cellulose-degrading bacterium Bacillus subtilis K1 was 4,060,823 bp in genome size, containing 4,213 genes, with 3,665, 3,656, 2,755, 3,240, 1,261, 3,336 and 4,003 genes annotated in the non-redundant protein sequence database (NR), Pfam, clusters of orthologous groups of proteins (COGs), Genome Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Annotation databases, respectively. In addition, a large number of lignocellulose degradation-related genes were annotated in the genome. The cellulose activity of B. subtilis K1 was higher, exhibiting the highest activity of endo-β-glucanase (24.69 U/ml), exo-β-glucanase (1.72 U/ml) and β-glucosaccharase (1.14 U/ml). It was found that through adding cold-adapted cellulose-degrading bacteriaK1 in the corn straw composting under 6°C (ambient temperature), the average temperature of straw composting was 58.7°C, and higher 86.7% as compared to control. The HA/FA was higher 94.02% than the control and the lignocellulose degradation rate was lower 18.01-41.39% than the control. The results provide a theoretical basis for clarifying the degradation potential of cold-adapted cellulose-degrading bacteria and improving the cellulose degradation efficiency.
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Affiliation(s)
- Zhigang He
- Institute of Plant Nutrition and Environmental Resources, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Baopeng Ding
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Qurban Ali
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Huiyu Liu
- Institute of Plant Nutrition and Environmental Resources, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Ying Zhao
- Institute of Plant Nutrition and Environmental Resources, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Xiujuan Wang
- Institute of Plant Nutrition and Environmental Resources, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Yingzuo Han
- Institute of Plant Nutrition and Environmental Resources, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Huan Dong
- Institute of Plant Nutrition and Environmental Resources, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | | | - Yinghua Juan
- Institute of Plant Nutrition and Environmental Resources, Liaoning Academy of Agricultural Sciences, Shenyang, China
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Guo B, Li W, Santibáñez P, Priscu JC, Liu Y, Liu K. Organic matter distribution in the icy environments of Taylor Valley, Antarctica. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 841:156639. [PMID: 35697215 DOI: 10.1016/j.scitotenv.2022.156639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/07/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Glaciers can accumulate and release organic matter affecting the structure and function of associated terrestrial and aquatic ecosystems. We analyzed 18 ice cores collected from six locations in Taylor Valley (McMurdo Dry Valleys), Antarctica to determine the spatial abundance and quality of organic matter, and the spatial distribution of bacterial density and community structure from the terminus of the Taylor Glacier to the coast (McMurdo Sound). Our results showed that dissolved and particulate organic carbon (DOC and POC) concentrations in the ice core samples increased from the Taylor Glacier to McMurdo Sound, a pattern also shown by bacterial cell density. Fluorescence Excitation Emission Matrices Spectroscopy (EEMs) and multivariate parallel factor (PARAFAC) modeling identified one humic-like (C1) and one protein-like (C2) component in ice cores whose fluorescent intensities all increased from the Polar Plateau to the coast. The fluorescence index showed that the bioavailability of dissolved organic matter (DOM) also decreased from the Polar Plateau to the coast. Partial least squares path modeling analysis revealed that bacterial abundance was the main positive biotic factor influencing both the quantity and quality of organic matter. Marine aerosol influenced the spatial distribution of DOC more than katabatic winds in the ice cores. Certain bacterial taxa showed significant correlations with DOC and POC concentrations. Collectively, our results show the tight connectivity among organic matter spatial distribution, bacterial abundance and meteorology in the McMurdo Dry Valley ecosystem.
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Affiliation(s)
- Bixi Guo
- State Key Laboratory of Tibetan Plateau Earth System Science (LATPES), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; Polar Oceans Research Group, Sheridan, MT 59749, USA
| | - Wei Li
- Polar Oceans Research Group, Sheridan, MT 59749, USA; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, CA 94550, USA
| | - Pamela Santibáñez
- Ministry of Science, Technology, Knowledge, & Innovation, Punta Arenas 6200000, Chile
| | - John C Priscu
- Polar Oceans Research Group, Sheridan, MT 59749, USA.
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System Science (LATPES), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System Science (LATPES), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
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Cariou M, Francois CM, Voisin J, Pigneret M, Hervant F, Volatier L, Mermillod-Blondin F. Effects of bioturbation by tubificid worms on biogeochemical processes, bacterial community structure and diversity in heterotrophic wetland sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 795:148842. [PMID: 34328914 DOI: 10.1016/j.scitotenv.2021.148842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/09/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Bioturbation activity of tubificid worms has been recognized as a key process influencing organic matter processing and nutrient cycling in benthic aquatic ecosystems. This activity is expected to modify benthic microbial communities by affecting the physical and chemical environment in sediments. Nevertheless, quantifications of bacterial community changes associated with bioturbation in freshwater ecosystems are still lacking. The present study aimed at evaluating the impact of tubificid worms on bacterial community structure using NGS approach (16S metabarcoding) and long (6 months) laboratory experiments on four heterotrophic wetland sediments. Worm bioturbation activity significantly stimulated biogeochemical processes at the water-sediment interface but only had a marginally significant effect on bacterial community structures. Yet, bacterial diversity was consistently reduced in presence of worms. Such decrease could be associated with the stimulation of organic matter mineralization by worms, leading to a reduction of the diversity of trophic niches available for bacterial species. The slight changes in bacterial community structures induced by bioturbation did not appear to control biogeochemical processes. Thus, the stimulation of biogeochemical processes by worm bioturbation was more associated with a stimulation of the initial bacterial community than with a drastic change in bacterial communities induced by worms.
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Affiliation(s)
- Marie Cariou
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622 Villeurbanne, France
| | - Clémentine M Francois
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622 Villeurbanne, France
| | - Jérémy Voisin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622 Villeurbanne, France
| | - Mathilde Pigneret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622 Villeurbanne, France
| | - Frédéric Hervant
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622 Villeurbanne, France
| | - Laurence Volatier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622 Villeurbanne, France
| | - Florian Mermillod-Blondin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622 Villeurbanne, France.
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8
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Niu H, Wu H, Chen K, Sun J, Cao M, Luo J. Effects of decapitated and root-pruned Sedum alfredii on the characterization of dissolved organic matter and enzymatic activity in rhizosphere soil during Cd phytoremediation. JOURNAL OF HAZARDOUS MATERIALS 2021; 417:125977. [PMID: 33992011 DOI: 10.1016/j.jhazmat.2021.125977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/06/2021] [Accepted: 04/24/2021] [Indexed: 06/12/2023]
Abstract
Decapitation and root pruning, can impact plant morphological and physiological characteristics, which may determine the efficiency of phytoremediation. However, the effects of decapitated and root-pruned plants on the characterization of dissolved organic matter (DOM) and enzymatic activity, which determine the bioavailability of soil pollutants, have rarely been reported. This study aims to characterize DOM and enzymatic activity in the rhizosphere soil of Sedum alfredii when treated by decapitation and root pruning. Decapitation, slight pruning (10% root cutting), and their combination stimulated S. alfredii to secrete more DOM in the rhizosphere soil compared with the control. Furthermore, the proportions of hydrophilic increased from 42.7% in the control to 57.1% in the decapitation and slight pruning combination. Soil urease, invertase, and neutral phosphatase activities were higher in the rhizosphere soil of decapitated and root-pruned S. alfredii, and the highest values were observed with their combination. DOM from the soils of decapitated and root-pruned S. alfredii had significantly higher Cd extraction ability compared with that of the untreated species. Based on the findings of this study, we suggest that decapitation and root pruning can improve the phytoremediation efficiency of S. alfredii by increasing the bioavailability of Cd in its rhizosphere.
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Affiliation(s)
- Hong Niu
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central University for Nationalities, Wuhan 430074, China
| | - Hang Wu
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central University for Nationalities, Wuhan 430074, China
| | - Ke Chen
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central University for Nationalities, Wuhan 430074, China
| | - Jie Sun
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central University for Nationalities, Wuhan 430074, China
| | - Min Cao
- University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Jie Luo
- College of Resources and Environment, Yangtze University, Wuhan, China.
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9
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Izabel-Shen D, Albert S, Winder M, Farnelid H, Nascimento FJA. Quality of phytoplankton deposition structures bacterial communities at the water-sediment interface. Mol Ecol 2021; 30:3515-3529. [PMID: 33993575 DOI: 10.1111/mec.15984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 02/16/2021] [Accepted: 05/11/2021] [Indexed: 11/28/2022]
Abstract
Phytoplankton comprises a large fraction of the vertical carbon flux to deep water via the sinking of particulate organic matter (POM). However, despite the importance of phytoplankton in the coupling of benthic-pelagic productivity, the extent to which its deposition in the sediment affects bacterial dynamics at the water-sediment interface is poorly understood. Here, we conducted a microcosm experiment in which varying mixtures of diatom and cyanobacteria, representing phytoplankton-derived POM of differing quality, served as inputs to sediment cores. Characterization of 16S rRNA gene of the bacterial communities at the water-sediment interface showed that bacterial α-diversity was not affected by POM addition, while bacterial β-diversity changed significantly along the POM quality gradient, with the variation driven by changes in relative abundance rather than in taxon replacement. Analysing individual taxa abundances across the POM gradient revealed two distinct bacterial responses, in which taxa within either diatom- or cyanobacteria-favoured groups were more phylogenetically closely related to one another than other taxa found in the water. Moreover, there was little overlap in taxon identity between sediment and water communities, suggesting the minor role played by sediment bacteria in influencing the observed changes in bacterial communities in the overlying water. Together, these results showed that variability in phytoplankton-originated POM can impact bacterial dynamics at the water-sediment interface. Our findings highlight the importance of considering the potential interactions between phytoplankton and bacteria in benthic-pelagic coupling in efforts to understand the structure and function of bacterial communities under a changing climate.
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Affiliation(s)
- Dandan Izabel-Shen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Séréna Albert
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Monika Winder
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Hanna Farnelid
- Center for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
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10
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Bacterial and archaeal community structure in benthic sediments from glacial lakes at the Múlajökull Glacier, central Iceland. Polar Biol 2020. [DOI: 10.1007/s00300-020-02770-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Nicholes MJ, Williamson CJ, Tranter M, Holland A, Poniecka E, Yallop ML, Anesio A. Bacterial Dynamics in Supraglacial Habitats of the Greenland Ice Sheet. Front Microbiol 2019; 10:1366. [PMID: 31333595 PMCID: PMC6616251 DOI: 10.3389/fmicb.2019.01366] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/31/2019] [Indexed: 11/13/2022] Open
Abstract
Current research into bacterial dynamics on the Greenland Ice Sheet (GrIS) is biased toward cryoconite holes, despite this habitat covering less than 8% of the ablation (melt) zone surface. In contrast, the expansive surface ice, which supports wide-spread Streptophyte micro-algal blooms thought to enhance surface melt, has been relatively neglected. This study aims to understand variability in bacterial abundance and production across an ablation season on the GrIS, in relation to micro-algal bloom dynamics. Bacterial abundance reached 3.3 ± 0.3 × 105 cells ml−1 in surface ice and was significantly linearly related to algal abundances during the middle and late ablation periods (R2 = 0.62, p < 0.05; R2 = 0.78, p < 0.001). Bacterial production (BP) of 0.03–0.6 μg C L−1 h−1 was observed in surface ice and increased in concert with glacier algal abundances, indicating that heterotrophic bacteria consume algal-derived dissolved organic carbon. However, BP remained at least 28 times lower than net primary production, indicating inefficient carbon cycling by heterotrophic bacteria and net accumulation of carbon in surface ice throughout the ablation season. Across the supraglacial environment, cryoconite sediment BP was at least four times greater than surface ice, confirming that cryoconite holes are the true “hot spots” of heterotrophic bacterial activity.
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Affiliation(s)
- Miranda Jane Nicholes
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, Bristol, United Kingdom
| | - Christopher James Williamson
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, Bristol, United Kingdom.,School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Martyn Tranter
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, Bristol, United Kingdom
| | - Alexandra Holland
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, Bristol, United Kingdom
| | - Ewa Poniecka
- School of Earth and Ocean Sciences, Cardiff University, Cardiff, United Kingdom
| | - Marian Louise Yallop
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, Bristol, United Kingdom.,School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | | | - Alexandre Anesio
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, Bristol, United Kingdom.,Department of Environmental Science, Aarhus University, Roskilde, Denmark
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Ávila MP, Brandão LPM, Brighenti LS, Tonetta D, Reis MP, Stæhr PA, Asmala E, Amado AM, Barbosa FAR, Bezerra-Neto JF, Nascimento AMA. Linking shifts in bacterial community with changes in dissolved organic matter pool in a tropical lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 672:990-1003. [PMID: 30981171 DOI: 10.1016/j.scitotenv.2019.04.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/15/2019] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
Bacterioplankton communities have a pivotal role in the global carbon cycle. Still the interaction between microbial community and dissolved organic matter (DOM) in freshwater ecosystems remains poorly understood. Here, we report results from a 12-day mesocosm study performed in the epilimnion of a tropical lake, in which inorganic nutrients and allochthonous DOM were supplemented under full light and shading. Although the production of autochthonous DOM triggered by nutrient addition was the dominant driver of changes in bacterial community structure, temporal covariations between DOM optical proxies and bacterial community structure revealed a strong influence of community shifts on DOM fate. Community shifts were coupled to a successional stepwise alteration of the DOM pool, with different fractions being selectively consumed by specific taxa. Typical freshwater clades as Limnohabitans and Sporichthyaceae were associated with consumption of low molecular weight carbon, whereas Gammaproteobacteria and Flavobacteria utilized higher molecular weight carbon, indicating differences in DOM preference among clades. Importantly, Verrucomicrobiaceae were important in the turnover of freshly produced autochthonous DOM, ultimately affecting light availability and dissolved organic carbon concentrations. Our findings suggest that taxonomically defined bacterial assemblages play definite roles when influencing DOM fate, either by changing specific fractions of the DOM pool or by regulating light availability and DOC levels.
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Affiliation(s)
- Marcelo P Ávila
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Luciana P M Brandão
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Ludmila S Brighenti
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Denise Tonetta
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Mariana P Reis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil.
| | - Peter A Stæhr
- Department of Bioscience, Aarhus University, Frederiksborgvej 399, Box 358, 4000 Roskilde, Denmark
| | - Eero Asmala
- Department of Bioscience, Aarhus University, Frederiksborgvej 399, Box 358, 4000 Roskilde, Denmark; Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, 10900 Hanko, Finland
| | - André M Amado
- Limnology Laboratory, Department of Oceanography and Limnology, Universidade Federal do Rio Grande do Norte, Rio Grande do Norte, Brazil
| | - Francisco A R Barbosa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - José F Bezerra-Neto
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Andréa M A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil.
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Stibal M, Jacobsen CS, Häggblom MM. Editorial: Polar and Alpine Microbiology. FEMS Microbiol Ecol 2018; 94:5054038. [DOI: 10.1093/femsec/fiy136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 07/13/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Marek Stibal
- Department of Ecology, Faculty of Science, Charles University, 128 44 Prague, Czechia
| | | | - Max M Häggblom
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901-8525, USA
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