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Lubis AR, Linh NV, Srinual O, Fontana CM, Tayyamath K, Wannavijit S, Ninyamasiri P, Uttarotai T, Tapingkae W, Phimolsiripol Y, Van Doan HV. Effects of passion fruit peel (Passiflora edulis) pectin and red yeast (Sporodiobolus pararoseus) cells on growth, immunity, intestinal morphology, gene expression, and gut microbiota in Nile tilapia (Oreochromis niloticus). Sci Rep 2024; 14:22704. [PMID: 39349558 PMCID: PMC11442623 DOI: 10.1038/s41598-024-73194-1] [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: 05/17/2024] [Accepted: 09/16/2024] [Indexed: 10/02/2024] Open
Abstract
This study explores the effects of dietary supplementation with passion fruit peel pectin (Passiflora edulis) and red yeast cell walls (Sporidiobolus pararoseus) on growth performance, immunity, intestinal morphology, gene expression, and gut microbiota of Nile tilapia (Oreochromis niloticus). Nile tilapia with an initial body weight of approximately 15 ± 0.06 g were fed four isonitrogenous (29.09-29.94%), isolipidic (3.01-4.28%), and isoenergetic (4119-4214 Cal/g) diets containing 0 g kg-1 pectin or red yeast cell walls (T1 - Control), 10 g kg-1 pectin (T2), 10 g kg-1 red yeast (T3), and a combination of 10 g kg-1 pectin and 10 g kg-1 red yeast (T4) for 8 weeks. Growth rates and immune responses were assessed at 4 and 8 weeks, while histology, relative immune and antioxidant gene expression, and gut microbiota analysis were conducted after 8 weeks of feeding. The results showed that the combined supplementation (T4) significantly enhanced growth performance metrics, including final weight, weight gain, specific growth rate, and feed conversion ratio, particularly by week 8, compared to T1, T2, and T3 (P < 0.05). Immunological assessments revealed increased lysozyme and peroxidase activities in both skin mucus and serum, with the T4 group showing the most pronounced improvements. Additionally, antioxidant and immune-related gene expression, including glutathione peroxidase (GPX), glutathione reductase (GSR), and interleukin-1 (IL1), were upregulated in the gut, while intestinal morphology exhibited improved villus height and width. Gut microbiota analysis indicated increased alpha and beta diversity, with a notable rise in beneficial phyla such as Actinobacteriota and Firmicutes in the supplemented groups. These findings suggest that the combined use of pectin and red yeast cell walls as prebiotics in aquaculture can enhance the health and growth of Nile tilapia, offering a promising alternative to traditional practices. Further research is needed to determine optimal dosages for maximizing these benefits.
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Affiliation(s)
- Anisa Rilla Lubis
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Nguyen Vu Linh
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
- Functional Feed Innovation Centre (FuncFeed), Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Orranee Srinual
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Camilla Maria Fontana
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Khambou Tayyamath
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Supreya Wannavijit
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Punika Ninyamasiri
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Toungporn Uttarotai
- Department of Highland Agriculture and Natural Resources, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Wanaporn Tapingkae
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | | | - Hien V Van Doan
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand.
- Functional Feed Innovation Centre (FuncFeed), Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand.
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Gaenssle ALO, Bertran-Llorens S, Deuss PJ, Jurak E. Enrichment of Aquatic Xylan-Degrading Microbial Communities. Microorganisms 2024; 12:1715. [PMID: 39203557 PMCID: PMC11356981 DOI: 10.3390/microorganisms12081715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 08/08/2024] [Accepted: 08/11/2024] [Indexed: 09/03/2024] Open
Abstract
The transition towards a sustainable society involves the utilization of lignocellulosic biomass as a renewable feedstock for materials, fuel, and base chemicals. Lignocellulose consists of cellulose, hemicellulose, and lignin, forming a complex, recalcitrant matrix where efficient enzymatic saccharification is pivotal for accessing its valuable components. This study investigated microbial communities from brackish Lauwersmeer Lake, in The Netherlands, as a potential source of xylan-degrading enzymes. Environmental sediment samples were enriched with wheat arabinoxylan (WAX) and beechwood glucuronoxylan (BEX), with enrichment on WAX showing higher bacterial growth and complete xylan degradation compared to BEX. Metagenomic sequencing revealed communities consisting almost entirely of bacteria (>99%) and substantial shifts in composition during the enrichment. The first generation of seven-day enrichments on both xylans led to a high accumulation of Gammaproteobacteria (49% WAX, 84% BEX), which were largely replaced by Alphaproteobacteria (42% WAX, 69% BEX) in the fourth generation. Analysis of the protein function within the sequenced genomes showed elevated levels of genes associated with the carbohydrate catabolic process, specifically targeting arabinose, xylose, and xylan, indicating an adaptation to the primary monosaccharides present in the carbon source. The data open up the possibility of discovering novel xylan-degrading proteins from other sources aside from the thoroughly studied Bacteroidota.
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Affiliation(s)
- Aline Lucie Odette Gaenssle
- Department of Bioproduct Engineering, University of Groningen, Nijenborgh 3, 9747 AG Groningen, The Netherlands
| | - Salvador Bertran-Llorens
- Department of Chemical Engineering, University of Groningen, Nijenborgh 3, 9747 AG Groningen, The Netherlands
| | - Peter Joseph Deuss
- Department of Chemical Engineering, University of Groningen, Nijenborgh 3, 9747 AG Groningen, The Netherlands
| | - Edita Jurak
- Department of Chemical Engineering, University of Groningen, Nijenborgh 3, 9747 AG Groningen, The Netherlands
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Yadav RK, Chaudhary S, Patil SA. Distinct microbial communities enriched in water-saturated and unsaturated reactors influence performance of integrated hydroponics-microbial electrochemical technology. BIORESOURCE TECHNOLOGY 2024; 406:130976. [PMID: 38879056 DOI: 10.1016/j.biortech.2024.130976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/03/2024] [Accepted: 06/12/2024] [Indexed: 06/23/2024]
Abstract
This study aimed to understand the wastewater treatment and electricity generation performance besides the microbial communities of the integrated Hydroponics-Microbial Electrochemical Technology (iHydroMET) systems operated with water-saturated and water-unsaturated reactors. The organics removal was slightly higher in the water-unsaturated system (93 ± 4 %) than in the water-saturated system (87 ± 2 %). The total nitrogen removal and electric voltage were considerably higher in the water-saturated system (42 ± 5 %; 111 ± 8 V per reactor) than in the water-unsaturated system (18 ± 3 %; 95 ± 9 V per reactor). The enhanced organics and nitrogen removal and high voltage output in respective conditions were due to the dominance of polysaccharide-degrading aerobes (e.g., Pirellula), anammox bacteria (e.g., Anammoximicrobium), denitrifiers (e.g., Thauera and Rheinheimera), and electroactive microorganisms (e.g., Geobacter). The differential performance governed by distinct microbial communities under the tested conditions indicates that an appropriate balancing of water saturation and unsaturation in reactors is crucial to achieving optimum iHydroMET performance.
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Affiliation(s)
- Ravi K Yadav
- Department of Earth and Environmental Sciences, Indian Institute of Science Education and Research Mohali (IISER Mohali), Knowledge City, Sector 81, SAS Nagar, 140306, Punjab, India
| | - Srishti Chaudhary
- Department of Earth and Environmental Sciences, Indian Institute of Science Education and Research Mohali (IISER Mohali), Knowledge City, Sector 81, SAS Nagar, 140306, Punjab, India
| | - Sunil A Patil
- Department of Earth and Environmental Sciences, Indian Institute of Science Education and Research Mohali (IISER Mohali), Knowledge City, Sector 81, SAS Nagar, 140306, Punjab, India.
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Watson SE, Taylor CH, Bell V, Bellamy TR, Hooper AS, Taylor H, Jouault M, Kille P, Perkins RG. Impact of copper sulphate treatment on cyanobacterial blooms and subsequent water quality risks. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 366:121828. [PMID: 39002464 DOI: 10.1016/j.jenvman.2024.121828] [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: 03/01/2024] [Revised: 07/02/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024]
Abstract
Control of algal blooms and associated biologically-induced water quality risks in drinking reservoirs is problematic. Copper sulphate (CuSO4) treatment is one intervention that has been utilised for >100 years. Evidence indicates a favourable short-term reduction in Cyanobacterial biomass (e.g. bloom termination), but here we indicate that it may also increase longer-term water quality risk. In 2022, we investigated the impacts of CuSO4 spraying on Cyanobacterial communities and nutrient levels within a drinking water supply reservoir using environmental DNA (eDNA) to assess community shifts, alongside monitoring nutrient fractions, orthophosphate (OP) and total phosphate (TP), post-treatment. CuSO4 application successfully reduced Cyanobacterial abundance, however elimination of Cyanobacteria resulted in a shift in bacterial dominance favouring Planctomycetota throughout the summer and a combination of Actinobacteriota and Verrucomicrobiota, throughout autumn. As Cyanobacterial abundance recovered post-treatment, Cyanobacterial genera demonstrated greater diversity compared to only three Cyanobacterial genera present across samples pre-treatment, and included taxa associated with water quality risk (e.g. taste and odour (T&O) metabolite and toxin producers). The increase in Cyanobacteria post-treatment was attributed to an increase in biologically available nutrients, primarily a significant increase in OP. Overall, findings suggest that the significant shift in biodiversity likely induces a less stable ecosystem with greater plasticity of response to changing environmental and biogeochemical variables. Legacy implications of CuSO4 spraying, in terms of shifts in ecosystem and nutrient balance over time, may have implications for drinking water quality, but importantly also for reservoir management options. As such, the effects of CuSO4 spraying should be considered carefully before consideration as a contender for in-reservoir biological control.
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Affiliation(s)
- S E Watson
- School of Earth and Environmental Science, Main Building, Cardiff University, Museum Avenue, CF10 3AX, UK.
| | - C H Taylor
- School of Bioscience, Sir Martin Evans Building, Cardiff University, Museum Avenue, CF10 3AX, UK
| | - V Bell
- School of Earth and Environmental Science, Main Building, Cardiff University, Museum Avenue, CF10 3AX, UK
| | - T R Bellamy
- School of Bioscience, Sir Martin Evans Building, Cardiff University, Museum Avenue, CF10 3AX, UK
| | - A S Hooper
- School of Earth and Environmental Science, Main Building, Cardiff University, Museum Avenue, CF10 3AX, UK
| | - H Taylor
- Jersey Water, St Helier, Jersey, JE1 1JW, UK
| | - M Jouault
- Jersey Water, St Helier, Jersey, JE1 1JW, UK
| | - P Kille
- School of Bioscience, Sir Martin Evans Building, Cardiff University, Museum Avenue, CF10 3AX, UK
| | - R G Perkins
- School of Earth and Environmental Science, Main Building, Cardiff University, Museum Avenue, CF10 3AX, UK
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Knittel K, Miksch S, Moncada C, Silva-Solar S, Moye J, Amann R, Arnosti C. Distinct actors drive different mechanisms of biopolymer processing in polar marine coastal sediments. Environ Microbiol 2024; 26:e16687. [PMID: 39168162 DOI: 10.1111/1462-2920.16687] [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: 05/08/2024] [Accepted: 07/24/2024] [Indexed: 08/23/2024]
Abstract
Heterotrophic bacteria in the ocean initiate biopolymer degradation using extracellular enzymes that yield low molecular weight hydrolysis products in the environment, or by using a selfish uptake mechanism that retains the hydrolysate for the enzyme-producing cell. The mechanism used affects the availability of hydrolysis products to other bacteria, and thus also potentially the composition and activity of the community. In marine systems, these two mechanisms of substrate processing have been studied in the water column, but to date, have not been investigated in sediments. In surface sediments from an Arctic fjord of Svalbard, we investigated mechanisms of biopolymer hydrolysis using four polysaccharides and mucin, a glycoprotein. Extracellular hydrolysis of all biopolymers was rapid. Moreover, rapid degradation of mucin suggests that it may be a key substrate for benthic microbes. Although selfish uptake is common in ocean waters, only a small fraction (0.5%-2%) of microbes adhering to sediments used this mechanism. Selfish uptake was carried out primarily by Planctomycetota and Verrucomicrobiota. The overall dominance of extracellular hydrolysis in sediments, however, suggests that the bulk of biopolymer processing is carried out by a benthic community relying on the sharing of enzymatic capabilities and scavenging of public goods.
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Affiliation(s)
- Katrin Knittel
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Chyrene Moncada
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Jannika Moye
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Carol Arnosti
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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He Y, Zhu Y, Shui X, Huang Z, Li K, Lei W. Gut microbiome and metabolomic profiles reveal the antiatherosclerotic effect of indole-3-carbinol in high-choline-fed ApoE -/- mice. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 129:155621. [PMID: 38678950 DOI: 10.1016/j.phymed.2024.155621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/27/2024] [Accepted: 04/09/2024] [Indexed: 05/01/2024]
Abstract
BACKGROUND The metabolites produced from choline contribute to atherosclerosis (AS) pathogenesis, and the gut microbiota is redundantly essential for this process. Indole-3-carbinol (I3C), found in cruciferous vegetables such as broccoli, cabbage, cauliflower and brussels sprouts, helps prevent hyperlipidemia, maintain the gut microbiota balance, and decrease the production of trimethylamine-N-oxide (TMAO) from choline in the diet. PURPOSE The objective of this research was to investigate the impact of I3C on choline-induced AS and to further elucidate the underlying mechanism involved. METHODS AS models of high-choline-induced ApoE-/- mice and TMAO-promoted foamy macrophages were established to observe the effect of I3C on the formation of atherosclerotic plaques and foam cells and changes in AS-related indicators (including blood biochemical indicators, TMA, TMAO, SRA, and SRB1), and integrated analyses of the microbiome and metabolome were used to reveal the mechanism of action of I3C. RESULTS We found that I3C inhibited high-choline-induced atheroma formation (50-100 mg/kg/d, in vivo) and slightly improved the lipid profile (15 mg/kg/d, in vivo). Moreover, I3C suppressed lipid influx at a concentration of 40 µmol/L in vitro, enhanced the diversity of the gut microbiota and the abundance of the phylum Verrucomicrobia, and consequently modified the gut microbial metabolites at a dosage of 50 mg/kg/d in the mice. Associative analyses based on microbiome and metabolomics revealed that 1-methyladenosine was a key modulator of the protective effect of I3C against AS in high-choline-induced ApoE-/- mice. CONCLUSION These findings demonstrate for the first time that I3C ameliorates AS progression through remodeling of the gut microbiome and metabolomics, which paves the way for the possible therapeutic use of this vegetable-derived natural compound and may reduce the clinical severity of AS-related cardiovascular diseases.
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Affiliation(s)
- Yuan He
- Guangdong Provincial Engineering Technology Research Center for Molecular Diagnosis and Innovative Drugs Translation of Cardiopulmonary Vascular Diseases, University Joint Laboratory of Guangdong Province and Macao Region on Molecular Targets and Intervention of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China; Laboratory of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China
| | - Ying Zhu
- Guangdong Provincial Engineering Technology Research Center for Molecular Diagnosis and Innovative Drugs Translation of Cardiopulmonary Vascular Diseases, University Joint Laboratory of Guangdong Province and Macao Region on Molecular Targets and Intervention of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China; Laboratory of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China
| | - Xiaorong Shui
- Laboratory of Vascular Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China
| | - Zufeng Huang
- Guangdong Provincial Engineering Technology Research Center for Molecular Diagnosis and Innovative Drugs Translation of Cardiopulmonary Vascular Diseases, University Joint Laboratory of Guangdong Province and Macao Region on Molecular Targets and Intervention of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China; Laboratory of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China
| | - Kongwei Li
- Guangdong Provincial Engineering Technology Research Center for Molecular Diagnosis and Innovative Drugs Translation of Cardiopulmonary Vascular Diseases, University Joint Laboratory of Guangdong Province and Macao Region on Molecular Targets and Intervention of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China; Laboratory of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China
| | - Wei Lei
- Guangdong Provincial Engineering Technology Research Center for Molecular Diagnosis and Innovative Drugs Translation of Cardiopulmonary Vascular Diseases, University Joint Laboratory of Guangdong Province and Macao Region on Molecular Targets and Intervention of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China; Department of Precision Laboratory, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China.
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Meynet P, Joss A, Davenport RJ, Fenner K. Impact of long-term temperature shifts on activated sludge microbiome dynamics and micropollutant removal. WATER RESEARCH 2024; 258:121790. [PMID: 38833810 DOI: 10.1016/j.watres.2024.121790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/11/2024] [Accepted: 05/14/2024] [Indexed: 06/06/2024]
Abstract
Micropollutants removal efficiency strongly vary across different aerobic wastewater treatment plants, resulting in their frequent detection in surface and ground waters. Seasonal temperature variation is a major factor influencing plant performance, but it is still unclear how prolonged periods of temperature change impact microbiome and micropollutant biotransformation. This work investigates the effect of long-term temperature variation on the microbial dynamics in an activated sludge system, and the impact on micropollutant biotransformation. Sequencing batch reactors were used as model system and 4-40 °C temperature range was studied. 16S rRNA amplicon sequencing showed that temperature drives microbial structure (gDNA) and activity (RNA), rather than time, and this was stronger below 15 °C and above 25 °C. The microbial community was richest and more diverse at 20 °C, while rarer and more specific taxa became predominant over time, at more extreme temperatures. This suggested that less abundant taxa might be responsible for maintaining the biotransformation capability in the activated sludge at extreme temperatures. Micropollutant biotransformation rates mostly deviated from the classic Arrhenius model below 15 °C and above 25 °C, indicating that prolonged exposure to temperature changes leads to temperature-induced taxonomic shifts, resulting in the emerging of different sets of biotransformation pathways over different temperature ranges.
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Affiliation(s)
- Paola Meynet
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom; Department of Environmental Chemistry, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf 8600, Switzerland.
| | - Adriano Joss
- Department of Processing Engineering, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf 8600, Switzerland
| | - Russell J Davenport
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Kathrin Fenner
- Department of Environmental Chemistry, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf 8600, Switzerland; Department of Chemistry, University of Zürich, Zürich 8057, Switzerland
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Vesamäki JS, Laine MB, Nissinen R, Taipale SJ. Plastic and terrestrial organic matter degradation by the humic lake microbiome continues throughout the seasons. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13302. [PMID: 38852938 PMCID: PMC11162827 DOI: 10.1111/1758-2229.13302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/15/2024] [Indexed: 06/11/2024]
Abstract
Boreal freshwaters go through four seasons, however, studies about the decomposition of terrestrial and plastic compounds often focus only on summer. We compared microbial decomposition of 13C-polyethylene, 13C-polystyrene, and 13C-plant litter (Typha latifolia) by determining the biochemical fate of the substrate carbon and identified the microbial decomposer taxa in humic lake waters in four seasons. For the first time, the annual decomposition rate including separated seasonal variation was calculated for microplastics and plant litter in the freshwater system. Polyethylene decomposition was not detected, whereas polystyrene and plant litter were degraded in all seasons. In winter, decomposition rates of polystyrene and plant litter were fivefold and fourfold slower than in summer, respectively. Carbon from each substrate was mainly respired in all seasons. Plant litter was utilized efficiently by various microbial groups, whereas polystyrene decomposition was limited to Alpha- and Gammaproteobacteria. The decomposition was not restricted only to the growth season, highlighting that the decomposition of both labile organic matter and extremely recalcitrant microplastics continues throughout the seasons.
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Affiliation(s)
- Jussi S. Vesamäki
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Miikka B. Laine
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Riitta Nissinen
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
- Department of BiologyUniversity of TurkuTurkuFinland
| | - Sami J. Taipale
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
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Guden RM, Haegeman A, Ruttink T, Moens T, Derycke S. Nematodes alter the taxonomic and functional profiles of benthic bacterial communities: A metatranscriptomic approach. Mol Ecol 2024; 33:e17331. [PMID: 38533629 DOI: 10.1111/mec.17331] [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: 06/21/2023] [Revised: 02/25/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024]
Abstract
Marine sediments cover 70% of the Earth's surface, and harbour diverse bacterial communities critical for marine biogeochemical processes, which affect climate change, biodiversity and ecosystem functioning. Nematodes, the most abundant and species-rich metazoan organisms in marine sediments, in turn, affect benthic bacterial communities and bacterial-mediated ecological processes, but the underlying mechanisms by which they affect biogeochemical cycles remain poorly understood. Here, we demonstrate using a metatranscriptomic approach that nematodes alter the taxonomic and functional profiles of benthic bacterial communities. We found particularly strong stimulation of nitrogen-fixing and methane-oxidizing bacteria in the presence of nematodes, as well as increased functional activity associated with methane metabolism and degradation of various carbon compounds. This study provides empirical evidence that the presence of nematodes results in taxonomic and functional shifts in active bacterial communities, indicating that nematodes may play an important role in benthic ecosystem processes.
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Affiliation(s)
- Rodgee Mae Guden
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Annelies Haegeman
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Tom Moens
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Sofie Derycke
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
- Aquatic Environment and Quality, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Oostende, Belgium
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Lefler FW, Barbosa M, Berthold DE, Roten R, Bishop WM, Laughinghouse HD. Microbial Community Response to Granular Peroxide-Based Algaecide Treatment of a Cyanobacterial Harmful Algal Bloom in Lake Okeechobee, Florida (USA). Toxins (Basel) 2024; 16:206. [PMID: 38787058 PMCID: PMC11125911 DOI: 10.3390/toxins16050206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 05/25/2024] Open
Abstract
Cyanobacterial harmful algal blooms (cyanoHABs) occur in fresh water globally. These can degrade water quality and produce toxins, resulting in ecological and economic damages. Thus, short-term management methods (i.e., algaecides) are necessary to rapidly mitigate the negative impacts of cyanoHABs. In this study, we assess the efficacy of a hydrogen peroxide-based algaecide (PAK® 27) on a Microcystis dominated bloom which occurred within the Pahokee Marina on Lake Okeechobee, Florida, USA. We observed a significant reduction in chlorophyll a (96.81%), phycocyanin (93.17%), and Microcystis cell counts (99.92%), and a substantial reduction in microcystins (86.7%) 48 h after treatment (HAT). Additionally, there was a significant shift in bacterial community structure 48 HAT, which coincided with an increase in the relative abundance of photosynthetic protists. These results indicate that hydrogen peroxide-based algaecides are an effective treatment method for cyanoHAB control and highlight their effects on non-target microorganisms (i.e., bacteria and protists).
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Affiliation(s)
- Forrest W. Lefler
- Fort Lauderdale Research and Education Center, University of Florida—IFAS, Davie, FL 33314, USA; (F.W.L.); (M.B.); (D.E.B.)
| | - Maximiliano Barbosa
- Fort Lauderdale Research and Education Center, University of Florida—IFAS, Davie, FL 33314, USA; (F.W.L.); (M.B.); (D.E.B.)
| | - David E. Berthold
- Fort Lauderdale Research and Education Center, University of Florida—IFAS, Davie, FL 33314, USA; (F.W.L.); (M.B.); (D.E.B.)
| | - Rory Roten
- SePRO Research and Technology Campus, 16013 Watson Seed Farm Road, Whitakers, NC 27891, USA; (R.R.); (W.M.B.)
| | - West M. Bishop
- SePRO Research and Technology Campus, 16013 Watson Seed Farm Road, Whitakers, NC 27891, USA; (R.R.); (W.M.B.)
| | - H. Dail Laughinghouse
- Fort Lauderdale Research and Education Center, University of Florida—IFAS, Davie, FL 33314, USA; (F.W.L.); (M.B.); (D.E.B.)
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Hancock TL, Dahedl EK, Kratz MA, Urakawa H. Synechococcus dominance induced after hydrogen peroxide treatment of Microcystis bloom in the Caloosahatchee River, Florida. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 345:123508. [PMID: 38325511 DOI: 10.1016/j.envpol.2024.123508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/25/2024] [Accepted: 02/04/2024] [Indexed: 02/09/2024]
Abstract
Few field trials examining hydrogen peroxide as a cyanobacterial harmful algal bloom (cHAB) treatment have been conducted in subtropical and tropical regions. None have been tested in Florida, home to Lake Okeechobee and downstream waterways which periodically experience Microcystis bloom events. To investigate treatment effects in Florida, we applied a 490 μM (16.7 mg/L; 0.0015%) hydrogen peroxide spray to a minor bloom of Microcystis aeruginosa on the downstream side of Franklin Lock and Dam in the Caloosahatchee River. Although hydrogen peroxide decreased to background level one day post-treatment, succession was observed in phytoplankton community amplicon sequencing. The relative abundance of Microcystis decreased on day 3 by 86%, whereas the picocyanobacteria Synechococcus became dominant, increasing by 77% on day 3 and by 173% on day 14 to 57% of the phytoplankton community. Metatranscriptomics revealed Synechococcus likely benefitted from the antioxidant defense of upregulated peroxiredoxin, peroxidase/catalase, and rubrerythrin expressions immediately after treatment, and upregulated nitrate transport and urease to take advantage of available nitrogen. Our results indicated hydrogen peroxide induces succession of the phytoplankton community from Microcystis to non-toxic picocyanobacteria and could be used for selective suppression of harmful cyanobacteria.
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Affiliation(s)
- Taylor L Hancock
- School of Geosciences, University of South Florida, Tampa, FL, 33620, USA; Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Elizabeth K Dahedl
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Michael A Kratz
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Hidetoshi Urakawa
- School of Geosciences, University of South Florida, Tampa, FL, 33620, USA; Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, USA.
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12
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Kachiprath B, Solomon S, Gopi J, Jayachandran PR, Thajudeen J, Sarasan M, Mohan AS, Puthumana J, Chaithanya ER, Philip R. Exploring bacterial diversity in Arctic fjord sediments: a 16S rRNA-based metabarcoding portrait. Braz J Microbiol 2024; 55:499-513. [PMID: 38175355 PMCID: PMC10920534 DOI: 10.1007/s42770-023-01217-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 12/10/2023] [Indexed: 01/05/2024] Open
Abstract
The frosty polar environment houses diverse habitats mostly driven by psychrophilic and psychrotolerant microbes. Along with traditional cultivation methods, next-generation sequencing technologies have become common for exploring microbial communities from various extreme environments. Investigations on glaciers, ice sheets, ponds, lakes, etc. have revealed the existence of numerous microorganisms while details of microbial communities in the Arctic fjords remain incomplete. The current study focuses on understanding the bacterial diversity in two Arctic fjord sediments employing the 16S rRNA gene metabarcoding and its comparison with previous studies from various Arctic habitats. The study revealed that Proteobacteria was the dominant phylum from both the fjord samples followed by Bacteroidetes, Planctomycetes, Firmicutes, Actinobacteria, Cyanobacteria, Chloroflexi and Chlamydiae. A significant proportion of unclassified reads derived from bacteria was also detected. Psychrobacter, Pseudomonas, Acinetobacter, Aeromonas, Photobacterium, Flavobacterium, Gramella and Shewanella were the major genera in both the fjord sediments. The above findings were confirmed by the comparative analysis of fjord metadata with the previously reported (secondary metadata) Arctic samples. This study demonstrated the potential of 16S rRNA gene metabarcoding in resolving bacterial composition and diversity thereby providing new in situ insights into Arctic fjord systems.
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Affiliation(s)
- Bhavya Kachiprath
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Solly Solomon
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
- Fishery Survey of India, Cochin Zonal Base, Kochangadi Road, Kochi, Kerala, 682005, India
| | - Jayanath Gopi
- Applied Research Center for Environment and Marine Studies, King Fahd University of Petroleum and Minerals, Dhahran, 31261, Kingdom of Saudi Arabia
| | - P R Jayachandran
- Applied Research Center for Environment and Marine Studies, King Fahd University of Petroleum and Minerals, Dhahran, 31261, Kingdom of Saudi Arabia
| | - Jabir Thajudeen
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Government of India), Headland Sada, Vasco-da-Gama, Goa, 403804, India
| | - Manomi Sarasan
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Anjali S Mohan
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Jayesh Puthumana
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - E R Chaithanya
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Rosamma Philip
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India.
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13
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Liu N, Kivenson V, Peng X, Cui Z, Lankiewicz TS, Gosselin KM, English CJ, Blair EM, O'Malley MA, Valentine DL. Pontiella agarivorans sp. nov., a novel marine anaerobic bacterium capable of degrading macroalgal polysaccharides and fixing nitrogen. Appl Environ Microbiol 2024; 90:e0091423. [PMID: 38265213 PMCID: PMC10880615 DOI: 10.1128/aem.00914-23] [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: 06/07/2023] [Accepted: 12/05/2023] [Indexed: 01/25/2024] Open
Abstract
Marine macroalgae produce abundant and diverse polysaccharides, which contribute substantially to the organic matter exported to the deep ocean. Microbial degradation of these polysaccharides plays an important role in the turnover of macroalgal biomass. Various members of the Planctomycetes-Verrucomicrobia-Chlamydia (PVC) superphylum are degraders of polysaccharides in widespread anoxic environments. In this study, we isolated a novel anaerobic bacterial strain NLcol2T from microbial mats on the surface of marine sediments offshore Santa Barbara, CA, USA. Based on 16S ribosomal RNA (rRNA) gene and phylogenomic analyses, strain NLcol2T represents a novel species within the Pontiella genus in the Kiritimatiellota phylum (within the PVC superphylum). Strain NLcol2T is able to utilize various monosaccharides, disaccharides, and macroalgal polysaccharides such as agar and ɩ-carrageenan. A near-complete genome also revealed an extensive metabolic capacity for anaerobic degradation of sulfated polysaccharides, as evidenced by 202 carbohydrate-active enzymes (CAZymes) and 165 sulfatases. Additionally, its ability of nitrogen fixation was confirmed by nitrogenase activity detected during growth on nitrogen-free medium, and the presence of nitrogenases (nifDKH) encoded in the genome. Based on the physiological and genomic analyses, this strain represents a new species of bacteria that may play an important role in the degradation of macroalgal polysaccharides and with relevance to the biogeochemical cycling of carbon, sulfur, and nitrogen in marine environments. Strain NLcol2T (= DSM 113125T = MCCC 1K08672T) is proposed to be the type strain of a novel species in the Pontiella genus, and the name Pontiella agarivorans sp. nov. is proposed.IMPORTANCEGrowth and intentional burial of marine macroalgae is being considered as a carbon dioxide reduction strategy but elicits concerns as to the fate and impacts of this macroalgal carbon in the ocean. Diverse heterotrophic microbial communities in the ocean specialize in these complex polymers such as carrageenan and fucoidan, for example, members of the Kiritimatiellota phylum. However, only four type strains within the phylum have been cultivated and characterized to date, and there is limited knowledge about the metabolic capabilities and functional roles of related organisms in the environment. The new isolate strain NLcol2T expands the known substrate range of this phylum and further reveals the ability to fix nitrogen during anaerobic growth on macroalgal polysaccharides, thereby informing the issue of macroalgal carbon disposal.
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Affiliation(s)
- Na Liu
- Interdepartmental Graduate Program in Marine Science, University of California Santa Barbara, Santa Barbara, California, USA
| | - Veronika Kivenson
- Interdepartmental Graduate Program in Marine Science, University of California Santa Barbara, Santa Barbara, California, USA
| | - Xuefeng Peng
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
| | - Zhisong Cui
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao, China
| | - Thomas S. Lankiewicz
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
| | - Kelsey M. Gosselin
- Interdepartmental Graduate Program in Marine Science, University of California Santa Barbara, Santa Barbara, California, USA
| | - Chance J. English
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Department of Ecology Evolution, and Marine Biology, University of California, Santa Barbara, California, USA
| | - Elaina M. Blair
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
| | - Michelle A. O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
- Biological Engineering Program, University of California, Santa Barbara, California, USA
| | - David L. Valentine
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Department of Earth Science, University of California Santa Barbara, Santa Barbara, California, USA
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14
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Liu L, Wei C, Li Y, Wang M, Mao Y, Tian X. A Comparative Study on Effects of Three Butyric Acid-Producing Additives on the Growth Performance, Non-specific Immunity, and Intestinal Microbiota of the Sea Cucumber Apostichopus japonicus. AQUACULTURE NUTRITION 2024; 2024:6973951. [PMID: 38404622 PMCID: PMC10894051 DOI: 10.1155/2024/6973951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 01/23/2024] [Accepted: 02/05/2024] [Indexed: 02/27/2024]
Abstract
The providers of butyric acid, Clostridium butyricum (CB), sodium butyrate (SB), and tributyrin (TB), have been extensively studied as aquafeed additives in recent years. However, no comparative study has been reported on the probiotic effects of CB, SB, and TB as feed additives on sea cucumber (Apostichopus japonicus). A 63-day feeding trial was performed to assess the effects of dietary live cells of C. butyricum (CB group, the basal diet supplemented with 1% CB), sodium butyrate (SB group, the basal diet supplemented with 1% SB), and tributyrin (TB group, the basal diet supplemented with 1% TB) on the growth, non-specific immunity, and intestinal microbiota of A. japonicus with a basal diet group as the control. Results indicated that all three additives considerably increased A. japonicus growth, with dietary CB having the optimal growth-promoting effect. Of the seven non-specific enzyme parameters measured in coelomocytes of A. japonicus (i.e., the activities of phagocytosis, respiratory burst, superoxide dismutase, alkaline phosphatase, acid phosphatase, catalase, and lysozyme), dietary CB, SB, and TB considerably increased the activities of six, five, and six of them, respectively. The immune genes (Aj-p105, Aj-p50, Aj-rel, and Aj-lys) expression in the mid-intestine tissues of A. japonicus was significantly increased by all three additives. The CB group had the highest expression of all four genes. Additionally, the relative expression of Aj-p105, Aj-p50, and Aj-lys genes was significantly up-regulated in the three additive groups after stimulation with inactivated Vibrio splendidus. Dietary CB enhanced the intestinal microbial diversity and richness in A. japonicus while dietary TB decreased them. Meanwhile, dietary CB, SB, and TB significantly enhanced the abundance of Firmicutes, unclassified_f_Rhodobacteraceae, and Proteobacteria, respectively, while dietary CB and SB reduced the abundance of Vibrio. Dietary CB and SB improved the stability of microbial ecosystem in the intestine of A. japonicus. In contrast, dietary TB appeared to have a negative effect on the stability of intestinal microbial ecosystem. All three additives improved the intestinal microbial functions associated with energy production and immunity regulation pathways, which may contribute directly to growth promotion and non-specific immunity enhancement in A. japonicus. Collectively, in terms of enhancing growth and non-specific immunity, as well as improving intestinal microbiota, dietary live cells of C. butyricum exhibited the most effective effects in A. japonicus.
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Affiliation(s)
- Longzhen Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Cong Wei
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yongmei Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Mingyang Wang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yuze Mao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xiangli Tian
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
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15
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Xian WD, Ding J, Chen J, Qu W, Cao P, Tang C, Liu X, Zhang Y, Li JL, Wang P, Li WJ, Wang J. Distinct Assembly Processes Structure Planktonic Bacterial Communities Among Near- and Offshore Ecosystems in the Yangtze River Estuary. MICROBIAL ECOLOGY 2024; 87:42. [PMID: 38356037 PMCID: PMC11385042 DOI: 10.1007/s00248-024-02350-x] [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: 08/08/2023] [Accepted: 01/17/2024] [Indexed: 02/16/2024]
Abstract
The estuarine system functions as natural filters due to its ability to facilitate material transformation, planktonic bacteria play a crucial role in the cycling of complex nutrients and pollutants within estuaries, and understanding the community composition and assembly therein is crucial for comprehending bacterial ecology within estuaries. Despite extensive investigations into the composition and community assembly of two bacterial fractions (free-living, FLB; particle-attached, PAB), the process by which bacterioplankton communities in these two habitats assemble in the nearshore and offshore zones of estuarine ecosystems remains poorly understood. In this study, we conducted sampling in the Yangtze River Estuary (YRE) to investigate potential variations in the composition and community assembly of FLB and PAB in nearshore and offshore regions. We collected 90 samples of surface, middle, and bottom water from 16 sampling stations and performed 16S rRNA gene amplicon analysis along with environmental factor measurements. The results unveiled that the nearshore communities demonstrated significantly greater species richness and Chao1 indices compared to the offshore communities. In contrast, the nearshore communities had lower values of Shannon and Simpson indices. When compared to the FLB, the PAB exhibit a higher level of biodiversity and abundance. However, no distinct alpha and beta diversity differences were observed between the bottom, middle, and surface water layers. The community assembly analysis indicated that nearshore communities are predominantly shaped by deterministic processes, particularly due to heterogeneous selection of PAB; In contrast, offshore communities are governed more by stochastic processes, largely due to homogenizing dispersal of FLB. Consequently, the findings of this study demonstrate that nearshore and PAB communities exhibit higher levels of species diversity, while stochastic and deterministic processes exert distinct influences on communities among near- and offshore regions. This study further sheds new light on our understanding of the mechanisms governing bacterial communities in estuarine ecosystems.
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Affiliation(s)
- Wen-Dong Xian
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Haida South Rd No. 1, Dinghai, Zhoushan, 316000, China
| | - Junjie Ding
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Haida South Rd No. 1, Dinghai, Zhoushan, 316000, China
| | - Jinhui Chen
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Haida South Rd No. 1, Dinghai, Zhoushan, 316000, China
| | - Wu Qu
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Haida South Rd No. 1, Dinghai, Zhoushan, 316000, China
| | - Pinglin Cao
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Haida South Rd No. 1, Dinghai, Zhoushan, 316000, China
| | - Chunyu Tang
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Haida South Rd No. 1, Dinghai, Zhoushan, 316000, China
| | - Xuezhu Liu
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Haida South Rd No. 1, Dinghai, Zhoushan, 316000, China
| | - Yiying Zhang
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Haida South Rd No. 1, Dinghai, Zhoushan, 316000, China
| | - Jia-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
| | - Pandeng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
| | - Jianxin Wang
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Haida South Rd No. 1, Dinghai, Zhoushan, 316000, China.
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16
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Wietz M, Engel A, Ramondenc S, Niwano M, von Appen WJ, Priest T, von Jackowski A, Metfies K, Bienhold C, Boetius A. The Arctic summer microbiome across Fram Strait: Depth, longitude, and substrate concentrations structure microbial diversity in the euphotic zone. Environ Microbiol 2024; 26:e16568. [PMID: 38268397 DOI: 10.1111/1462-2920.16568] [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: 07/27/2023] [Accepted: 12/12/2023] [Indexed: 01/26/2024]
Abstract
The long-term dynamics of microbial communities across geographic, hydrographic, and biogeochemical gradients in the Arctic Ocean are largely unknown. To address this, we annually sampled polar, mixed, and Atlantic water masses of the Fram Strait (2015-2019; 5-100 m depth) to assess microbiome composition, substrate concentrations, and oceanographic parameters. Longitude and water depth were the major determinants (~30%) of microbial community variability. Bacterial alpha diversity was highest in lower-photic polar waters. Community composition shifted from west to east, with the prevalence of, for example, Dadabacteriales and Thiotrichales in Arctic- and Atlantic-influenced waters, respectively. Concentrations of dissolved organic carbon peaked in the western, compared to carbohydrates in the chlorophyll-maximum of eastern Fram Strait. Interannual differences due to the time of sampling, which varied between early (June 2016/2018) and late (September 2019) phytoplankton bloom stages, illustrated that phytoplankton composition and resulting availability of labile substrates influence bacterial dynamics. We identified 10 species clusters with stable environmental correlations, representing signature populations of distinct ecosystem states. In context with published metagenomic evidence, our microbial-biogeochemical inventory of a key Arctic region establishes a benchmark to assess ecosystem dynamics and the imprint of climate change.
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Affiliation(s)
- Matthias Wietz
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Anja Engel
- Biological Oceanography, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Simon Ramondenc
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Matomo Niwano
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Wilken-Jon von Appen
- Physical Oceanography of the Polar Seas, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Taylor Priest
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Anabel von Jackowski
- Biological Oceanography, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Katja Metfies
- Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Oldenburg, Germany
| | - Christina Bienhold
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Antje Boetius
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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17
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Handler ER, Andersen SDJ, Gradinger R, McGovern M, Vader A, Poste AE. Seasonality in land-ocean connectivity and local processes control sediment bacterial community structure and function in a High Arctic tidal flat. FEMS Microbiol Ecol 2024; 100:fiad162. [PMID: 38111220 PMCID: PMC10799726 DOI: 10.1093/femsec/fiad162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 10/26/2023] [Accepted: 12/14/2023] [Indexed: 12/20/2023] Open
Abstract
Climate change is altering patterns of precipitation, cryosphere thaw, and land-ocean influxes, affecting understudied Arctic estuarine tidal flats. These transitional zones between terrestrial and marine systems are hotspots for biogeochemical cycling, often driven by microbial processes. We investigated surface sediment bacterial community composition and function from May to September along a river-intertidal-subtidal-fjord gradient. We paired metabarcoding of in situ communities with in vitro carbon-source utilization assays. Bacterial communities differed in space and time, alongside varying environmental conditions driven by local seasonal processes and riverine inputs, with salinity emerging as the dominant structuring factor. Terrestrial and riverine taxa were found throughout the system, likely transported with runoff. In vitro assays revealed sediment bacteria utilized a broader range of organic matter substrates when incubated in fresh and brackish water compared to marine water. These results highlight the importance of salinity for ecosystem processes in these dynamic tidal flats, with the highest potential for utilization of terrestrially derived organic matter likely limited to tidal flat areas (and times) where sediments are permeated by freshwater. Our results demonstrate that intertidal flats must be included in future studies on impacts of increased riverine discharge and transport of terrestrial organic matter on coastal carbon cycling in a warming Arctic.
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Affiliation(s)
- Eleanor R Handler
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Department of Arctic Biology, The University Centre in Svalbard, P.O. Box 156, 9171 Longyearbyen, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
| | - Sebastian D J Andersen
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Department of Arctic Biology, The University Centre in Svalbard, P.O. Box 156, 9171 Longyearbyen, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
| | - Rolf Gradinger
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
| | - Maeve McGovern
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
| | - Anna Vader
- Department of Arctic Biology, The University Centre in Svalbard, P.O. Box 156, 9171 Longyearbyen, Norway
| | - Amanda E Poste
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
- Norwegian Institute for Nature Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
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18
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Moncada C, Arnosti C, Brüwer JD, de Beer D, Amann R, Knittel K. Niche separation in bacterial communities and activities in porewater, loosely attached, and firmly attached fractions in permeable surface sediments. THE ISME JOURNAL 2024; 18:wrae159. [PMID: 39115410 PMCID: PMC11368169 DOI: 10.1093/ismejo/wrae159] [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: 06/06/2024] [Revised: 07/26/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
Abstract
Heterotrophic microbes are central to organic matter degradation and transformation in marine sediments. Currently, most investigations of benthic microbiomes do not differentiate between processes in the porewater and on the grains and, hence, only show a generalized picture of the community. This limits our understanding of the structure and functions of sediment microbiomes. To address this problem, we fractionated sandy surface sediment microbial communities from a coastal site in Isfjorden, Svalbard, into cells associated with the porewater, loosely attached to grains, and firmly attached to grains; we found dissimilar bacterial communities and metabolic activities in these fractions. Most (84%-89%) of the cells were firmly attached, and this fraction comprised more anaerobes, such as sulfate reducers, than the other fractions. The porewater and loosely attached fractions (3% and 8%-13% of cells, respectively) had more aerobic heterotrophs. These two fractions generally showed a higher frequency of dividing cells, polysaccharide (laminarin) hydrolysis rates, and per-cell O2 consumption than the firmly attached cells. Thus, the different fractions occupy distinct niches within surface sediments: the firmly attached fraction is potentially made of cells colonizing areas on the grain that are protected from abrasion, but might be more diffusion-limited for organic matter and electron acceptors. In contrast, the porewater and loosely attached fractions are less resource-limited and have faster growth. Their cell numbers are kept low possibly through abrasion and exposure to grazers. Differences in community composition and activity of these cell fractions point to their distinct roles and contributions to carbon cycling within surface sediments.
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Affiliation(s)
- Chyrene Moncada
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Carol Arnosti
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Jan D Brüwer
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Dirk de Beer
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Katrin Knittel
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
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19
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Lasota J, Ważny R, Kaźmierczak M, Błońska E. The effect of shrubs admixture in pine forest stands on soil bacterial and fungal communities and accumulation of polycyclic aromatic hydrocarbons. Sci Rep 2023; 13:16512. [PMID: 37783867 PMCID: PMC10545714 DOI: 10.1038/s41598-023-43925-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: 05/17/2023] [Accepted: 09/30/2023] [Indexed: 10/04/2023] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are a group of persistent toxic pollutants. The species composition of the stand is important in shaping the quality of soil organic matter and, consequently, the PAH content. The main purpose of the research was to determine the role of shrubs in shaping PAH accumulation in forest soils. The study covered the soils of the pine stands of the Rybnik Forest District, which experiences some of the highest deposition of industrial emissions in Europe. Pine stands with admixture of shrubs (alder buckthorn Frangula alnus and European hazelnut Coryllus avellana) growing in the same soil conditions were selected for the study. Samples for analyses were collected from the organic horizon (O) (from a depth of 0-7 cm) and humus mineral horizon (A) (from a depth of 7-15 cm). The organic C and total N concentrations, pH, alkaline cation content, soil enzyme activity and PAH content were determined. Additionally, the taxonomic composition of soil bacterial and fungal communities was determined. The highest activity of enzymes was noted in soils under influence of shrubs. The enzymatic activity was positively correlated with the content of total N, organic C, pH H2O and KCl and negatively with the C/N ratio. The highest PAH content was recorded in the soils of pine stands without the admixture of shrubs. Our research indicates the importance of shrubs in shaping the properties of surface horizons of forest soil and, consequently on the accumulation of PAHs. Shrubs stimulate biochemical activity of soils which results in lower PAHs accumulation by providing more easily decomposable organic matter.
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Affiliation(s)
- Jarosław Lasota
- Department of Ecology and Silviculture, Faculty of Forestry, University of Agriculture in Krakow, 29 Listopada 46 Str., 31-425, Kraków, Poland
| | - Rafał Ważny
- Małopolska Centre of Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7a, 30-387, Kraków, Poland
| | - Marzena Kaźmierczak
- Department of Ecology and Silviculture, Faculty of Forestry, University of Agriculture in Krakow, 29 Listopada 46 Str., 31-425, Kraków, Poland
| | - Ewa Błońska
- Department of Ecology and Silviculture, Faculty of Forestry, University of Agriculture in Krakow, 29 Listopada 46 Str., 31-425, Kraków, Poland.
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Arumugam U, Sudarsanan GB, Karuppannan AK, Palaniappan S. Metagenomic Studies Reveal the Evidence of Akkermansia muciniphila and Other Probiotic Bacteria in the Gut of Healthy and Enterocytozoon hepatopenaei (EHP)-Infected Farmed Penaeus vannamei. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10165-4. [PMID: 37749431 DOI: 10.1007/s12602-023-10165-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2023] [Indexed: 09/27/2023]
Abstract
Penaeus vannamei (whiteleg shrimp) is the most widely cultured shrimp globally. Enterocytozoon hepatopenaei (EHP), a microsporidian parasite, infects P. vannamei and causes severe growth retardation, subsequent production, and economic losses in the shrimp culture. The influence of EHP infection in the shrimp gut microbiota is poorly studied, and this would be an interesting area to investigate since the gut microbiome of shrimp influences a number of key host processes such as digestion and immunity. In this study, a metagenomic approach was followed to compare the overall species richness of the gut microbiota of EHP-infected and healthy P. vannamei. Bacterial genomic DNA from the healthy and EHP-infected gut sample were profiled for the bacterial 16S rRNA gene, targeting the V3-V4 conserved region. Operational taxonomic units (OTUs), an approximation of definitive taxonomic identity, were identified based on the sequence similarity within the sample reads and clustered together using a cut-off of 97% identity using UCLUST. The OTUs were then used for the computation of alpha diversity and beta diversity for each sample. EHP-infected gut sample showed lower bacterial abundance throughout the family, class, order, genus, and species levels when compared to healthy gut sample. This study shows that the shrimp gut microbiota is sensitive and exhibits a high level of plasticity during a microsporidian infection like EHP. Furthermore, Akkermansia muciniphila, a novel probiotic bacterium, has been reported in the shrimp gut for the first time.
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Affiliation(s)
- Uma Arumugam
- State Referral Laboratory for Aquatic Animal Health, Tamil Nadu Dr. J. Jayalalithaa Fisheries University, Madhavaram Campus, Chennai, 600051, Tamil Nadu, India.
| | - Ganesh Babu Sudarsanan
- State Referral Laboratory for Aquatic Animal Health, Tamil Nadu Dr. J. Jayalalithaa Fisheries University, Madhavaram Campus, Chennai, 600051, Tamil Nadu, India
| | - Anbu Kumar Karuppannan
- Bioinformatics Center, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Vepery, Chennai, 600007, Tamil Nadu, India
| | - Subash Palaniappan
- State Referral Laboratory for Aquatic Animal Health, Tamil Nadu Dr. J. Jayalalithaa Fisheries University, Madhavaram Campus, Chennai, 600051, Tamil Nadu, India
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21
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He K, Xiong J, Yang W, Zhao L, Wang T, Qian W, Hu S, Wang Q, Aleem MT, Miao W, Yan W. Metagenome of Gut Microbiota Provides a Novel Insight into the Pathogenicity of Balantioides coli in Weaned Piglets. Int J Mol Sci 2023; 24:10791. [PMID: 37445967 DOI: 10.3390/ijms241310791] [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: 05/10/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
Balantioides coli plays an important role in the diarrhea of weaned piglets, but its pathogenic potential and interaction with gut microbes remain unclear. To investigate the impact of B. coli colonization on the gut bacterial structure and function of weaned piglets, a metagenomic analysis based on shotgun sequencing was performed on fresh fecal samples collected from ten B. coli-colonized piglets and eight B. coli-free ones in this study. The results showed that decreasing diversity and shifted composition and function of the bacterial community were detected in the weaned piglets infected by B. coli. In contrast to the B. coli-negative group, the relative abundances of some members of the Firmicutes phylum including Clostridium, Ruminococcus species, and Intestinimonas butyriciproducens, which produce short-chain fatty acids, were significantly reduced in the B. coli-positive group. Notably, some species of the Prevotella genus (such as Prevotella sp. CAG:604 and Prevotella stercorea) were significantly increased in abundance in the B. coli-positive piglets. A functional analysis of the gut microbiota demonstrated that the differential gene sets for the metabolism of carbohydrates and amino acids were abundant in both groups, and the more enriched pathways in B. coli-infected piglets were associated with the sugar-specific phosphotransferase system (PTS) and the two-component regulatory system, as well as lipopolysaccharide (LPS) biosynthesis. Furthermore, several species of Prevotella were significantly positively correlated to the synthesis of lipid A, leading to the exporting of endotoxins and, thereby, inducing inflammation in the intestines of weaned piglets. Taken together, these findings revealed that colonization by B. coli was distinctly associated with the dysbiosis of gut bacterial structure and function in weaned piglets. Lower relative abundances of Clostridiaceae and Ruminococcaceae and higher abundances of Prevotella species were biomarkers of B. coli infection in weaned piglets.
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Affiliation(s)
- Kai He
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
- National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wentao Yang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Lizhuo Zhao
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Tianqi Wang
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Weifeng Qian
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Suhui Hu
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Qiangqiang Wang
- National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Muhammad Tahir Aleem
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Sciences and Health Professions, Cleveland State University, Cleveland, OH 44115, USA
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wenchao Yan
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
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Baloza M, Henkel S, Kasten S, Holtappels M, Molari M. The Impact of Sea Ice Cover on Microbial Communities in Antarctic Shelf Sediments. Microorganisms 2023; 11:1572. [PMID: 37375074 DOI: 10.3390/microorganisms11061572] [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: 03/17/2023] [Revised: 05/30/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
The area around the Antarctic Peninsula (AP) is facing rapid climatic and environmental changes, with so far unknown impacts on the benthic microbial communities of the continental shelves. In this study, we investigated the impact of contrasting sea ice cover on microbial community compositions in surface sediments from five stations along the eastern shelf of the AP using 16S ribosomal RNA (rRNA) gene sequencing. Redox conditions in sediments with long ice-free periods are characterized by a prevailing ferruginous zone, whereas a comparatively broad upper oxic zone is present at the heavily ice-covered station. Low ice cover stations were highly dominated by microbial communities of Desulfobacterota (mostly Sva1033, Desulfobacteria, and Desulfobulbia), Myxococcota, and Sva0485, whereas Gammaproteobacteria, Alphaproteobacteria, Bacteroidota, and NB1-j prevail at the heavy ice cover station. In the ferruginous zone, Sva1033 was the dominant member of Desulfuromonadales for all stations and, along with eleven other taxa, showed significant positive correlations with dissolved Fe concentrations, suggesting a significant role in iron reduction or an ecological relationship with iron reducers. Our results indicate that sea ice cover and its effect on organic carbon fluxes are the major drivers for changes in benthic microbial communities, favoring potential iron reducers at stations with increased organic matter fluxes.
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Affiliation(s)
- Marwa Baloza
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Faculty 2 Biology/Chemistry, University of Bremen, Leobener Str., 28359 Bremen, Germany
| | - Susann Henkel
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Sabine Kasten
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Faculty of Geosciences, University of Bremen, Klagenfurter Str., 28359 Bremen, Germany
- MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Moritz Holtappels
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Massimiliano Molari
- HGF-MPG Joint Research Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
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23
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Bar-Shalom R, Rozenberg A, Lahyani M, Hassanzadeh B, Sahoo G, Haber M, Burgsdorf I, Tang X, Squatrito V, Gomez-Consarnau L, Béjà O, Steindler L. Rhodopsin-mediated nutrient uptake by cultivated photoheterotrophic Verrucomicrobiota. THE ISME JOURNAL 2023:10.1038/s41396-023-01412-1. [PMID: 37120702 DOI: 10.1038/s41396-023-01412-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/31/2023] [Accepted: 04/05/2023] [Indexed: 05/01/2023]
Abstract
Rhodopsin photosystems convert light energy into electrochemical gradients used by the cell to produce ATP, or for other energy-demanding processes. While these photosystems are widespread in the ocean and have been identified in diverse microbial taxonomic groups, their physiological role in vivo has only been studied in few marine bacterial strains. Recent metagenomic studies revealed the presence of rhodopsin genes in the understudied Verrucomicrobiota phylum, yet their distribution within different Verrucomicrobiota lineages, their diversity, and function remain unknown. In this study, we show that more than 7% of Verrucomicrobiota genomes (n = 2916) harbor rhodopsins of different types. Furthermore, we describe the first two cultivated rhodopsin-containing strains, one harboring a proteorhodopsin gene and the other a xanthorhodopsin gene, allowing us to characterize their physiology under laboratory-controlled conditions. The strains were isolated in a previous study from the Eastern Mediterranean Sea and read mapping of 16S rRNA gene amplicons showed the highest abundances of these strains at the deep chlorophyll maximum (source of their inoculum) in winter and spring, with a substantial decrease in summer. Genomic analysis of the isolates suggests that motility and degradation of organic material, both energy demanding functions, may be supported by rhodopsin phototrophy in Verrucomicrobiota. Under culture conditions, we show that rhodopsin phototrophy occurs under carbon starvation, with light-mediated energy generation supporting sugar transport into the cells. Overall, this study suggests that photoheterotrophic Verrucomicrobiota may occupy an ecological niche where energy harvested from light enables bacterial motility toward organic matter and supports nutrient uptake.
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Affiliation(s)
- Rinat Bar-Shalom
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Andrey Rozenberg
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Matan Lahyani
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Babak Hassanzadeh
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Gobardhan Sahoo
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
- Department of Ecology and Environmental Sciences, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Markus Haber
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
- Institute of Hydrobiology, Biology Centre CAS, Na Sadkach 7, 37005, Ceske Budejovice, Czechia
| | - Ilia Burgsdorf
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Xinyu Tang
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Valeria Squatrito
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Laura Gomez-Consarnau
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
- Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, BC, México
| | - Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel.
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24
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Li S, Cai M, Wang Q, Yuan Z, Li R, Wang C, Sun Y. Effect of long-term exposure to dyeing wastewater treatment plant effluent on growth and gut microbiota of adult zebrafish (Danio rerio). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:53674-53684. [PMID: 36864334 DOI: 10.1007/s11356-023-26167-2] [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: 07/04/2022] [Accepted: 02/23/2023] [Indexed: 06/19/2023]
Abstract
Strict standards have been put forward for the treatment and discharge of dyeing wastewater worldwide. However, there are still traces amount of pollutants, especially emerging pollutants in dyeing wastewater treatment plant (DWTP) effluent. Few studies have focused on the chronic biological toxicity effect and mechanism of DWTP effluent. In this study, 3-month chronic compound toxic effects were investigated by the exposure of DWTP effluent using adult zebrafish. Significantly higher mortality and fatness and significantly lower body weight and body length were found in the treatment group. In addition, long-term exposure to DWTP effluent also obviously reduced liver-body weight ratio of zebrafish, causing abnormal liver development of zebrafish. Moreover, DWTP effluent led to obvious changes in the gut microbiota and microbial diversity of zebrafish. At phylum level, significantly higher of Verrucomicrobia but lower Tenericutes, Actinobacteria, and Chloroflexi were found in the control group. At genus level, the treatment group had significantly higher abundance of Lactobacillus, but significantly lower abundance of Akkermansia, Prevotella, Bacteroides, and Sutterella. These results suggested that long-term exposure to DWTP effluent led to imbalance of gut microbiota in zebrafish. In general, this research indicated that DWTP effluent pollutants could result in negative health outcomes to aquatic organisms.
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Affiliation(s)
- Shuangshuang Li
- College of Energy and Environmental Engineering, Hebei University of Engineering, Handan, 056038, China
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, Dalian, 116023, China
| | - Mingcan Cai
- College of Energy and Environmental Engineering, Hebei University of Engineering, Handan, 056038, China
| | - Qing Wang
- College of Energy and Environmental Engineering, Hebei University of Engineering, Handan, 056038, China
| | - Zixi Yuan
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, State Environmental Protection Key Laboratory of Food Chain Pollution Control, School of Ecology and Environment, Beijing Technology and Business University, Beijing, 100048, China
| | - Ruixuan Li
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, State Environmental Protection Key Laboratory of Food Chain Pollution Control, School of Ecology and Environment, Beijing Technology and Business University, Beijing, 100048, China
| | - Chun Wang
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, Dalian, 116023, China.
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, State Environmental Protection Key Laboratory of Food Chain Pollution Control, School of Ecology and Environment, Beijing Technology and Business University, Beijing, 100048, China.
| | - Yingxue Sun
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, State Environmental Protection Key Laboratory of Food Chain Pollution Control, School of Ecology and Environment, Beijing Technology and Business University, Beijing, 100048, China
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25
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Chen Y, Zhou L, Yu Q, Li E, Xie J. Effects of Sulfamethoxazole and Florfenicol on Growth, Antioxidant Capacity, Immune Responses and Intestinal Microbiota in Pacific White Shrimp Litopenaeus vannamei at Low Salinity. Antibiotics (Basel) 2023; 12:antibiotics12030575. [PMID: 36978441 PMCID: PMC10044552 DOI: 10.3390/antibiotics12030575] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/16/2023] Open
Abstract
Antibiotic residue may pose a serious risk to aquaculture, and the culture of Litopenaeus vannamei in a low-salinity environment is a growing trend over the world. Here, we aimed to understand the combined effect of low salinity and sulfamethoxazole (SMZ) and florfenicol (FLO) antibiotics on L. vannamei. The growth performance, immune functions, antioxidant capacity and intestinal microbiota were investigated. Compared with the control group, the weight gain and survival rate significantly decreased (p < 0.05) in shrimp after they were exposed to low-salinity (salinity 3) water and the mixture of antibiotics and low-salt conditions for 28 days. The antioxidant activities of SOD and T-AOC, shown at low salinity and in the higher concentration of the SMZ treatment group (SMZH), were significantly decreased, while the GST activity was significantly increased in each treatment group in comparison with the control group. The expression of immune-related genes, including TOLL, LvIMD, PPO and HSP, in the low concentration of the SMZ treatment group (SMZL) was higher than that in the other groups. The diversity of intestine microbiota was disturbed with a lower Shannon index in the low-salinity and SMZH groups, and a higher Simpson index in the SMZH group. Proteobacteria, Actinobacteria and Bacteroidetes were the dominant phyla in the gut of L. vannamei. At the genus level, Microbacterium, Shewanella, Aeromonas, Acinetobacter, Gemmobacter, Paracoccus and Lysobacter were significantly decreased in the low-salinity group. However, the abundance of opportunistic pathogens belonging to the genus Aeromonas in the FLO group was increased. The predicted microbe-mediated functions showed that the pathway for “amino acid metabolism” and “replication and repair” was significantly inhibited in both the low-salinity and antibiotic-exposed groups. All the findings in this study indicate that the combined effect of antibiotics and low salinity on L. vannamei negatively impacted the physiological and intestinal microbiota functions.
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Affiliation(s)
- Yunsong Chen
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, 58 Renmin Road, Haikou 570228, China
| | - Li Zhou
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, 58 Renmin Road, Haikou 570228, China
| | - Qiuran Yu
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Erchao Li
- School of Life Sciences, East China Normal University, Shanghai 200241, China
- Correspondence: (E.L.); (J.X.)
| | - Jia Xie
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, 58 Renmin Road, Haikou 570228, China
- Correspondence: (E.L.); (J.X.)
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26
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Jameson BD, Murdock SA, Ji Q, Stevens CJ, Grundle DS, Kim Juniper S. Network analysis of 16S rRNA sequences suggests microbial keystone taxa contribute to marine N 2O cycling. Commun Biol 2023; 6:212. [PMID: 36823449 PMCID: PMC9950131 DOI: 10.1038/s42003-023-04597-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
The mechanisms by which large-scale microbial community function emerges from complex ecological interactions between individual taxa and functional groups remain obscure. We leveraged network analyses of 16S rRNA amplicon sequences obtained over a seven-month timeseries in seasonally anoxic Saanich Inlet (Vancouver Island, Canada) to investigate relationships between microbial community structure and water column N2O cycling. Taxa separately broadly into three discrete subnetworks with contrasting environmental distributions. Oxycline subnetworks were structured around keystone aerobic heterotrophs that correlated with nitrification rates and N2O supersaturations, linking N2O production and accumulation to taxa involved in organic matter remineralization. Keystone taxa implicated in anaerobic carbon, nitrogen, and sulfur cycling in anoxic environments clustered together in a low-oxygen subnetwork that correlated positively with nitrification N2O yields and N2O production from denitrification. Close coupling between N2O producers and consumers in the anoxic basin is indicated by strong correlations between the low-oxygen subnetwork, PICRUSt2-predicted nitrous oxide reductase (nosZ) gene abundances, and N2O undersaturation. This study implicates keystone taxa affiliated with common ODZ groups as a potential control on water column N2O cycling and provides a theoretical basis for further investigations into marine microbial interaction networks.
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Affiliation(s)
- Brett D Jameson
- School of Earth & Ocean Sciences, University of Victoria, P.O. Box 1700 Station CSC, Victoria, BC, V8W 2Y2, Canada.
| | - Sheryl A Murdock
- Department of Biology, University of Victoria, P.O. Box 1700 CSC, Victoria, BC, V8W 2Y2, Canada
- Bermuda Institute of Ocean Sciences, 17 Biological Station, St. George's, GE01, Bermuda
| | - Qixing Ji
- Bermuda Institute of Ocean Sciences, 17 Biological Station, St. George's, GE01, Bermuda
- Thrust of Earth, Ocean & Atmospheric Sciences, Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou, Guangdong, 511400, China
| | - Catherine J Stevens
- School of Earth & Ocean Sciences, University of Victoria, P.O. Box 1700 Station CSC, Victoria, BC, V8W 2Y2, Canada
| | - Damian S Grundle
- Bermuda Institute of Ocean Sciences, 17 Biological Station, St. George's, GE01, Bermuda
- School of Ocean Futures & School of Earth & Space Exploration, Arizona State University, Tempe, AZ, 85287-7904, USA
| | - S Kim Juniper
- School of Earth & Ocean Sciences, University of Victoria, P.O. Box 1700 Station CSC, Victoria, BC, V8W 2Y2, Canada
- Department of Biology, University of Victoria, P.O. Box 1700 CSC, Victoria, BC, V8W 2Y2, Canada
- Ocean Networks Canada, 2474 Arbutus Road, Victoria, BC, V8N 1V8, Canada
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27
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Singh AK, Kumari M, Sharma N, Rai AK, Singh SP. Metagenomic views on taxonomic and functional profiles of the Himalayan Tsomgo cold lake and unveiling its deterzome potential. Curr Genet 2022; 68:565-579. [PMID: 35927361 DOI: 10.1007/s00294-022-01247-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 07/08/2022] [Accepted: 07/17/2022] [Indexed: 12/14/2022]
Abstract
Cold habitat is considered a potential source for detergent industry enzymes. This study aims at the metagenomic investigation of Tsomgo lake for taxonomic and functional annotation, unveiling the deterzome potential of the residing microbiota at this site. The present investigation revealed molecular profiling of microbial community structure and functional potential of the high-altitude Tsomgo lake samples of two different temperatures, harvested during March and August. Bacteria were found to be the most dominant phyla, with traces of genomic pieces of evidence belonging to archaea, viruses, and eukaryotes. Proteobacteria and Actinobacteria were noted to be the most abundant bacterial phyla in the cold lake. In-depth metagenomic investigation of the cold aquatic habitat revealed novel genes encoding detergent enzymes, amylase, protease, and lipase. Further, metagenome-assembled genomes (MAGs) belonging to the psychrophilic bacterium, Arthrobacter alpinus, were constructed from the metagenomic data. The annotation depicted the presence of detergent enzymes and genes for low-temperature adaptation in Arthrobacter alpinus. Psychrophilic microbial isolates were screened for lipase, protease, and amylase activities to further strengthen the metagenomic findings. A novel strain of Acinetobacter sp. was identified with the dual enzymatic activity of protease and amylase. The bacterial isolates exhibited hydrolyzing activity at low temperatures. This metagenomic study divulged novel genomic resources for detergent industry enzymes, and the bacterial isolates secreting cold-active amylase, lipase, and protease enzymes. The findings manifest that Tsomgo lake is a potential bioresource of cold-active enzymes, vital for various industrial applications.
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Affiliation(s)
- Ashutosh Kumar Singh
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Sector 81, SAS Nagar, Mohali, India
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Megha Kumari
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong, Gangtok, Sikkim, India
| | - Nitish Sharma
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Sector 81, SAS Nagar, Mohali, India
| | - Amit Kumar Rai
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong, Gangtok, Sikkim, India.
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Sector 81, SAS Nagar, Mohali, India.
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Singh A, Kumar M, Chakdar H, Pandiyan K, Kumar SC, Zeyad MT, Singh BN, Ravikiran KT, Mahto A, Srivastava AK, Saxena AK. Influence of host genotype in establishing root associated microbiome of indica rice cultivars for plant growth promotion. Front Microbiol 2022; 13:1033158. [PMID: 36452918 PMCID: PMC9702084 DOI: 10.3389/fmicb.2022.1033158] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/20/2022] [Indexed: 08/29/2023] Open
Abstract
Rice plants display a unique root ecosystem comprising oxic-anoxic zones, harboring a plethora of metabolic interactions mediated by its root microbiome. Since agricultural land is limited, an increase in rice production will rely on novel methods of yield enhancement. The nascent concept of tailoring plant phenotype through the intervention of synthetic microbial communities (SynComs) is inspired by the genetics and ecology of core rhizobiome. In this direction, we have studied structural and functional variations in the root microbiome of 10 indica rice varieties. The studies on α and β-diversity indices of rhizospheric root microbiome with the host genotypes revealed variations in the structuring of root microbiome as well as a strong association with the host genotypes. Biomarker discovery, using machine learning, highlighted members of class Anaerolineae, α-Proteobacteria, and bacterial genera like Desulfobacteria, Ca. Entotheonella, Algoriphagus, etc. as the most important features of indica rice microbiota having a role in improving the plant's fitness. Metabolically, rice rhizobiomes showed an abundance of genes related to sulfur oxidation and reduction, biofilm production, nitrogen fixation, denitrification, and phosphorus metabolism. This comparative study of rhizobiomes has outlined the taxonomic composition and functional diversification of rice rhizobiome, laying the foundation for the development of next-generation microbiome-based technologies for yield enhancement in rice and other crops.
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Affiliation(s)
- Arjun Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
- ICAR-Central Soil Salinity Research Institute, RRS, Lucknow, India
| | - Murugan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Kuppusamy Pandiyan
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
- Ginning Training Center, ICAR-Central Institute for Research on Cotton Technology, Nagpur, India
| | - Shiv Charan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | | | | | - K. T. Ravikiran
- ICAR-Central Soil Salinity Research Institute, RRS, Lucknow, India
| | - Arunima Mahto
- National Institute of Plant Genome Research, New Delhi, India
| | | | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
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29
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Abstract
Invertebrates, particularly sponges, have been a dominant source of new marine natural products. For example, lasonolide A (LSA) is a potential anticancer molecule isolated from the marine sponge Forcepia sp., with nanomolar growth inhibitory activity and a unique cytotoxicity profile against the National Cancer Institute 60-cell-line screen. Here, we identified the putative biosynthetic pathway for LSA. Genomic binning of the Forcepia sponge metagenome revealed a Gram-negative bacterium belonging to the phylum Verrucomicrobia as the candidate producer of LSA. Phylogenetic analysis showed that this bacterium, here named "Candidatus Thermopylae lasonolidus," only has 88.78% 16S rRNA identity with the closest relative, Pedosphaera parvula Ellin514, indicating that it represents a new genus. The lasonolide A (las) biosynthetic gene cluster (BGC) was identified as a trans-acyltransferase (AT) polyketide synthase (PKS) pathway. Compared with its host genome, the las BGC exhibits a significantly different GC content and pentanucleotide frequency, suggesting a potential horizontal acquisition of the gene cluster. Furthermore, three copies of the putative las pathway were identified in the candidate producer genome. Differences between the three las repeats were observed, including the presence of three insertions, two single-nucleotide polymorphisms, and the absence of a stand-alone acyl carrier protein in one of the repeats. Even though the verrucomicrobial producer shows signs of genome reduction, its genome size is still fairly large (about 5 Mbp), and, compared to its closest free-living relative, it contains most of the primary metabolic pathways, suggesting that it is in the early stages of reduction. IMPORTANCE While sponges are valuable sources of bioactive natural products, a majority of these compounds are produced in small quantities by uncultured symbionts, hampering the study and clinical development of these unique compounds. Lasonolide A (LSA), isolated from marine sponge Forcepia sp., is a cytotoxic molecule active at nanomolar concentrations, which causes premature chromosome condensation, blebbing, cell contraction, and loss of cell adhesion, indicating a novel mechanism of action and making it a potential anticancer drug lead. However, its limited supply hampers progression to clinical trials. We investigated the microbiome of Forcepia sp. using culture-independent DNA sequencing, identified genes likely responsible for LSA synthesis in an uncultured bacterium, and assembled the symbiont's genome. These insights provide future opportunities for heterologous expression and cultivation efforts that may minimize LSA's supply problem.
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Vaksmaa A, Egger M, Lüke C, Martins PD, Rosselli R, Asbun AA, Niemann H. Microbial communities on plastic particles in surface waters differ from subsurface waters of the North Pacific Subtropical Gyre. MARINE POLLUTION BULLETIN 2022; 182:113949. [PMID: 35932724 DOI: 10.1016/j.marpolbul.2022.113949] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
The long-term fate of plastics in the ocean and their interactions with marine microorganisms remain poorly understood. In particular, the role of sinking plastic particles as a transport vector for surface microbes towards the deep sea has not been investigated. Here, we present the first data on the composition of microbial communities on floating and suspended plastic particles recovered from the surface to the bathypelagic water column (0-2000 m water depth) of the North Pacific Subtropical Gyre. Microbial community composition of suspended plastic particles differed from that of plastic particles afloat at the sea surface. However, in both compartments, a diversity of hydrocarbon-degrading bacteria was identified. These findings indicate that microbial community members initially present on floating plastics are quickly replaced by microorganisms acquired from deeper water layers, thus suggesting a limited efficiency of sinking plastic particles to vertically transport microorganisms in the North Pacific Subtropical Gyre.
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Affiliation(s)
- Annika Vaksmaa
- Department of Marine Microbiology & Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 't Horntje, the Netherlands.
| | - Matthias Egger
- The Ocean Cleanup, Rotterdam, the Netherlands; Egger Research and Consulting, St. Gallen, Switzerland
| | - Claudia Lüke
- Radboud University, Department of Microbiology, Nijmegen, the Netherlands
| | | | - Riccardo Rosselli
- Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, Spain; LABAQUA S.A.U, C/Dracma 16-18, Pol. Ind. Las Atalayas, 03114 Alicante, Spain
| | - Alejandro Abdala Asbun
- Department of Marine Microbiology & Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 't Horntje, the Netherlands
| | - Helge Niemann
- Department of Marine Microbiology & Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 't Horntje, the Netherlands; Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, the Netherlands
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31
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Thiele S, Storesund JE, Fernández-Méndez M, Assmy P, Øvreås L. A Winter-to-Summer Transition of Bacterial and Archaeal Communities in Arctic Sea Ice. Microorganisms 2022; 10:1618. [PMID: 36014036 PMCID: PMC9414599 DOI: 10.3390/microorganisms10081618] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/21/2022] [Accepted: 07/28/2022] [Indexed: 12/02/2022] Open
Abstract
The Arctic is warming 2-3 times faster than the global average, leading to a decrease in Arctic sea ice extent, thickness, and associated changes in sea ice structure. These changes impact sea ice habitat properties and the ice-associated ecosystems. Sea-ice algal blooms provide various algal-derived carbon sources for the bacterial and archaeal communities within the sea ice. Here, we detail the transition of these communities from winter through spring to early summer during the Norwegian young sea ICE (N-ICE2015) expedition. The winter community was dominated by the archaeon Candidatus Nitrosopumilus and bacteria belonging to the Gammaproteobacteria (Colwellia, Kangiellaceae, and Nitrinocolaceae), indicating that nitrogen-based metabolisms, particularly ammonia oxidation to nitrite by Cand. Nitrosopumilus was prevalent. At the onset of the vernal sea-ice algae bloom, the community shifted to the dominance of Gammaproteobacteria (Kangiellaceae, Nitrinocolaceae) and Bacteroidia (Polaribacter), while Cand. Nitrosopumilus almost disappeared. The bioinformatically predicted carbohydrate-active enzymes increased during spring and summer, indicating that sea-ice algae-derived carbon sources are a strong driver of bacterial and archaeal community succession in Arctic sea ice during the change of seasons. This implies a succession from a nitrogen metabolism-based winter community to an algal-derived carbon metabolism-based spring/ summer community.
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Affiliation(s)
- Stefan Thiele
- Department of Biological Science, University of Bergen, Thormøhlensgate 53 A/B, 5020 Bergen, Norway
- Bjerknes Centre for Climate Research, Jahnebakken 5, 5007 Bergen, Norway
| | | | - Mar Fernández-Méndez
- Norwegian Polar Institute, Fram Centre, Hjalmar Johansens Gate 14, 9296 Tromsø, Norway
- Biological Oceanography, GEOMAR Helmholtz Centre of Ocean Research, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Philipp Assmy
- Norwegian Polar Institute, Fram Centre, Hjalmar Johansens Gate 14, 9296 Tromsø, Norway
| | - Lise Øvreås
- Department of Biological Science, University of Bergen, Thormøhlensgate 53 A/B, 5020 Bergen, Norway
- Bjerknes Centre for Climate Research, Jahnebakken 5, 5007 Bergen, Norway
- Department of Arctic Biology, University Center in Svalbard, UNIS, 9171 Longyearbyen, Norway
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32
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Prekrasna I, Pavlovska M, Miryuta N, Dzhulai A, Dykyi E, Convey P, Kozeretska I, Bedernichek T, Parnikoza I. Antarctic Hairgrass Rhizosphere Microbiomes: Microscale Effects Shape Diversity, Structure, and Function. Microbes Environ 2022; 37. [PMID: 35705309 PMCID: PMC9530728 DOI: 10.1264/jsme2.me21069] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The rhizosphere microbiome of the native Antarctic hairgrass Deschampsia antarctica from the central maritime Antarctic was investigated using 16S RNA metagenomics and compared to those of the second native Antarctic plant Colobanthus quitensis and closely related temperate D. cespitosa. The rhizosphere microbial communities of D. antarctica and D. cespitosa had high taxon richness, while that of C. quitensis had markedly lower diversity. The majority of bacteria in the rhizosphere communities of the hairgrass were affiliated to Proteobacteria, Bacteroidetes, and Actinobacteria. The rhizosphere of C. quitensis was dominated by Actinobacteria. All microbial communities included high proportions of unique amplicon sequence variants (ASVs) and there was high heterogeneity between samples at the ASV level. The soil parameters examined did not explain this heterogeneity. Bacteria belonging to Actinobacteria, Bacteroidetes, and Proteobacteria were sensitive to fluctuations in the soil surface temperature. The values of the United Soil Surface Temperature Influence Index (UTII, Iti) showed that variations in most microbial communities from Galindez Island were associated with microscale variations in temperature. Metabolic predictions in silico using PICRUSt 2.0, based on the taxonomically affiliated part of the microbiomes, showed similarities with the rhizosphere community of D. antarctica in terms of the predicted functional repertoire. The results obtained indicate that these communities are involved in the primary processes of soil development (particularly the degradation of lignin and lignin-derived compounds) in the central maritime Antarctic and may be beneficial for the growth of Antarctic vascular plants. However, due to the limitations associated with interpreting PICRUSt 2.0 outputs, these predictions need to be verified experimentally.
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Affiliation(s)
| | - Mariia Pavlovska
- State Institution National Antarctic Scientific Center.,National University of Life and Environmental Sciences of Ukraine
| | | | - Artem Dzhulai
- State Institution National Antarctic Scientific Center
| | - Evgen Dykyi
- State Institution National Antarctic Scientific Center
| | - Peter Convey
- British Antarctic Survey, NERC.,Department of Zoology, University of Johannesburg
| | | | | | - Ivan Parnikoza
- State Institution National Antarctic Scientific Center.,Institute of Molecular Biology and Genetics.,National University of "Kyiv-Mohyla Academy"
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Abstract
Lagoons are fragile marine ecosystems that are considerably affected by anthropogenic pollutants. We performed a spatiotemporal characterization of the microbiome of two Moroccan lagoons, Marchica and Oualidia, both classified as Ramsar sites, the former on the Mediterranean coast and the latter on the Atlantic coast. We investigated their microbial diversity and abundance using 16S rRNA amplicon- and shotgun-based metagenomics approaches during the summers of 2014 and 2015. The bacterial microbiome was composed primarily of Proteobacteria (25–53%, 29–29%), Cyanobacteria (34–12%, 11–0.53%), Bacteroidetes (24–16%, 23–43%), Actinobacteria (7–11%, 13–7%), and Verrucomicrobia (4–1%, 15–14%) in Marchica and Oualidia in 2014 and 2015, respectively. Interestingly, 48 strains were newly reported in lagoon ecosystems, while eight unknown viruses were detected in Mediterranean Marchica only. Statistical analysis showed higher microbial diversity in the Atlantic lagoon than in the Mediterranean lagoon and a robust relationship between alpha diversity and geographic sampling locations. This first-ever metagenomics study on Moroccan aquatic ecosystems enriched the national catalog of marine microorganisms. They will be investigated as candidates for bioindication properties, biomonitoring potential, biotechnology valorization, biodiversity protection, and lagoon health assessment.
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34
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Giljan G, Arnosti C, Kirstein IV, Amann R, Fuchs BM. Strong seasonal differences of bacterial polysaccharide utilization in the North Seas over an annual cycle. Environ Microbiol 2022; 24:2333-2347. [PMID: 35384240 DOI: 10.1111/1462-2920.15997] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/26/2022] [Accepted: 04/02/2022] [Indexed: 11/29/2022]
Abstract
Marine heterotrophic bacteria contribute considerably to global carbon cycling, in part by utilizing phytoplankton-derived polysaccharides. The patterns and rates of two different polysaccharide utilization modes - extracellular hydrolysis and selfish uptake - have previously been found to change during spring phytoplankton bloom events. Here we investigated seasonal changes in bacterial utilization of three polysaccharides, laminarin, xylan, and chondroitin sulfate. Strong seasonal differences were apparent in mode and speed of polysaccharide utilization, as well as in bacterial community compositions. Compared to the winter month of February, during the spring bloom in May, polysaccharide utilization was detected earlier in the incubations and a higher portion of all bacteria took up laminarin selfishly. Highest polysaccharide utilization was measured in June and September, mediated by bacterial communities that were significantly different from spring assemblages. Extensive selfish laminarin uptake, for example, was detectible within a few hours in June, while extracellular hydrolysis of chondroitin was dominant in September. In addition to the well-known Bacteroidota and Gammaproteobacteria clades, the numerically minor verrucomicrobial clade Pedosphaeraceae could be identified as a rapid laminarin utilizer. In summary, polysaccharide utilization proved highly variable over the seasons, both in mode and speed, and also by the bacterial clades involved. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Greta Giljan
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Carol Arnosti
- Department of Marine Sciences, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Inga V Kirstein
- Alfred-Wegner-Institute Helmholtz-Center for Polar and Marine Research, Biological Station Helgoland, Helgoland, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Bernhard M Fuchs
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
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35
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Irazoqui JM, Eberhardt MF, Adjad MM, Amadio AF. Identification of key microorganisms in facultative stabilization ponds from dairy industries, using metagenomics. PeerJ 2022; 10:e12772. [PMID: 35310160 PMCID: PMC8929167 DOI: 10.7717/peerj.12772] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/19/2021] [Indexed: 01/07/2023] Open
Abstract
Wastewater stabilization ponds are a natural form of wastewater treatment. Their low operation and maintenance costs have made them popular, especially in developing countries. In these systems, effluents are retained for long periods of time, allowing the microbial communities present in the ponds to degrade the organic matter present, using both aerobic and anaerobic processes. Even though these systems are widespread in low income countries, there are no studies about the microorganisms present in them and how they operate. In this study, we analised the microbial communities of two serial full-scale stabilization ponds systems using whole genome shotgun sequencing. First, a taxonomic profiling of the reads was performed, to estimate the microbial diversity. Then, the reads of each system were assembled and binned, allowing the reconstruction of 110 microbial genomes. A functional analysis of the genomes allowed us to find how the main metabolic pathways are carried out, and we propose several organisms that would be key to this kind of environment, since they play an important role in these metabolic pathways. This study represents the first genome-centred approach to understand the metabolic processes in facultative ponds. A better understanding of these microbial communities and how they stabilize the effluents of dairy industries is necessary to improve them and to minimize the environmental impact of dairy industries wastewater.
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Affiliation(s)
- Jose M. Irazoqui
- Instituto de Investigacion de la Cadena Lactea (INTA-CONICET), Rafaela, Santa Fe, Argentina
| | - Maria F. Eberhardt
- Instituto de Investigacion de la Cadena Lactea (INTA-CONICET), Rafaela, Santa Fe, Argentina
| | - Maria M. Adjad
- Estacion Experimental Rafaela (INTA), Rafaela, Santa Fe, Argentina
| | - Ariel F. Amadio
- Instituto de Investigacion de la Cadena Lactea (INTA-CONICET), Rafaela, Santa Fe, Argentina
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36
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Han D, Son M, Eom KH, Park YT, Choi M, Kim J, Kim TH. Distribution of dissolved organic carbon linked to bacterial community composition during the summer melting season in Arctic fjords. Polar Biol 2022. [DOI: 10.1007/s00300-021-02995-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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37
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Chen W, Zhu R, Ye X, Sun Y, Tang Q, Liu Y, Yan F, Yu T, Zheng X, Tu P. Food-derived cyanidin-3-O-glucoside reverses microplastic toxicity via promoting discharge and modulating the gut microbiota in mice. Food Funct 2022; 13:1447-1458. [PMID: 35048920 DOI: 10.1039/d1fo02983e] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Microplastics (MPs) ingested and accumulated by organisms would ultimately pose a threat to humans via the food chain. A balanced gut microbiota contributes to many health benefits, which is readily influenced by environmental chemicals such as MPs. Cyanidin-3-O-glucoside (C3G), a bioactive compound of the anthocyanin family, possesses a variety of functional effects including anti-oxidant and anti-inflammatory, as well as gut microbiota modulation. C3G has been demonstrated to prevent polystyrene (PS) induced toxicities in Caco-2 cells and Caenorhabditis elegans (C. elegans) via activating autophagy and promoting discharge. In the present study, we aimed to explore the alleviation effect of C3G on PS induced toxicities in C57BL/6 mice. Our results showed that the supplementation of C3G effectively reduced the tissue accumulation and promoted the fecal PS discharge, leading to alleviation of the PS-caused oxidative stress and inflammatory response. Meanwhile, C3G modulated PS-associated gut microbiome perturbations and regulated functional bacteria in inflammation such as Desulfovibrio, Helicobacter, Oscillospiraceae and Lachnoclostridium. Also, C3G administration initiated alterations in functional pathways in response to xenobiotic PS, and reduced bacterial functional genes related to inflammation and human diseases. These findings may offer evidence for the protective role of C3G in the intervention of PS-induced toxicity and gut dysbiosis.
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Affiliation(s)
- Wen Chen
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, People's Republic of China; Zhejiang Key Laboratory for Agro-food Processing, Zhejiang University, Hangzhou 310058, People's Republic of China; National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou 310058, People's Republic of China.
| | - Ruiyu Zhu
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Xiang Ye
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, People's Republic of China; Zhejiang Key Laboratory for Agro-food Processing, Zhejiang University, Hangzhou 310058, People's Republic of China; National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou 310058, People's Republic of China.
| | - Yuhao Sun
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, People's Republic of China; Zhejiang Key Laboratory for Agro-food Processing, Zhejiang University, Hangzhou 310058, People's Republic of China; National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou 310058, People's Republic of China.
| | - Qiong Tang
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, People's Republic of China; Zhejiang Key Laboratory for Agro-food Processing, Zhejiang University, Hangzhou 310058, People's Republic of China; National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou 310058, People's Republic of China.
| | - Yangyang Liu
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, People's Republic of China; Zhejiang Key Laboratory for Agro-food Processing, Zhejiang University, Hangzhou 310058, People's Republic of China; National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou 310058, People's Republic of China.
| | - Fujie Yan
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, People's Republic of China; Zhejiang Key Laboratory for Agro-food Processing, Zhejiang University, Hangzhou 310058, People's Republic of China; National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou 310058, People's Republic of China.
| | - Ting Yu
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, People's Republic of China; Zhejiang Key Laboratory for Agro-food Processing, Zhejiang University, Hangzhou 310058, People's Republic of China; National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou 310058, People's Republic of China.
| | - Xiaodong Zheng
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, People's Republic of China; Zhejiang Key Laboratory for Agro-food Processing, Zhejiang University, Hangzhou 310058, People's Republic of China; National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou 310058, People's Republic of China.
| | - Pengcheng Tu
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, People's Republic of China; Zhejiang Key Laboratory for Agro-food Processing, Zhejiang University, Hangzhou 310058, People's Republic of China; National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou 310058, People's Republic of China.
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38
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Differences of gut microbiota composition in mice supplied with polysaccharides from γ-irradiated and non-irradiated Schizophyllum commune. Food Res Int 2022; 151:110855. [PMID: 34980391 DOI: 10.1016/j.foodres.2021.110855] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 11/09/2021] [Accepted: 11/29/2021] [Indexed: 01/02/2023]
Abstract
In this study, polysaccharides from normal (N-SFP) and γ-irradiated (I-SFP) Schizophyllum commune were supplied to Kunming mice for 30 days. The results showed that N-SFP and I-SFP supplementation prevent body weight gain, enhance kidney uric acid metabolism and increase the concentration of SCFAs to a certain extent. Moreover, N-SFP and I-SFP promote the growth of beneficial gut microbiota and inhibit the growth of harmful bacteria. Compared to N-SFP, I-SFP decreased the relative abundance of Muribaculaceae and Lactobacillaceae, and increased the beneficial gut microbiota, especially the family of Akkermansiaceae, Lachnospiraceae and Bacteroidaceae. In total, I-SFP showed better effects than N-SFP in preventing weight gain, and modulating the mice gut microbiota, which suggests that I-SFP could act as a potential health supplement in the prevention of obesity.
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Wietz M, Bienhold C, Metfies K, Torres-Valdés S, von Appen WJ, Salter I, Boetius A. The polar night shift: seasonal dynamics and drivers of Arctic Ocean microbiomes revealed by autonomous sampling. ISME COMMUNICATIONS 2021; 1:76. [PMID: 37938651 PMCID: PMC9723606 DOI: 10.1038/s43705-021-00074-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 11/03/2021] [Accepted: 11/15/2021] [Indexed: 06/15/2023]
Abstract
The Arctic Ocean features extreme seasonal differences in daylight, temperature, ice cover, and mixed layer depth. However, the diversity and ecology of microbes across these contrasting environmental conditions remain enigmatic. Here, using autonomous samplers and sensors deployed at two mooring sites, we portray an annual cycle of microbial diversity, nutrient concentrations and physical oceanography in the major hydrographic regimes of the Fram Strait. The ice-free West Spitsbergen Current displayed a marked separation into a productive summer (dominated by diatoms and carbohydrate-degrading bacteria) and regenerative winter state (dominated by heterotrophic Syndiniales, radiolarians, chemoautotrophic bacteria, and archaea). The autumn post-bloom with maximal nutrient depletion featured Coscinodiscophyceae, Rhodobacteraceae (e.g. Amylibacter) and the SAR116 clade. Winter replenishment of nitrate, silicate and phosphate, linked to vertical mixing and a unique microbiome that included Magnetospiraceae and Dadabacteriales, fueled the following phytoplankton bloom. The spring-summer succession of Phaeocystis, Grammonema and Thalassiosira coincided with ephemeral peaks of Aurantivirga, Formosa, Polaribacter and NS lineages, indicating metabolic relationships. In the East Greenland Current, deeper sampling depth, ice cover and polar water masses concurred with weaker seasonality and a stronger heterotrophic signature. The ice-related winter microbiome comprised Bacillaria, Naviculales, Polarella, Chrysophyceae and Flavobacterium ASVs. Low ice cover and advection of Atlantic Water coincided with diminished abundances of chemoautotrophic bacteria while others such as Phaeocystis increased, suggesting that Atlantification alters microbiome structure and eventually the biological carbon pump. These insights promote the understanding of microbial seasonality and polar night ecology in the Arctic Ocean, a region severely affected by climate change.
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Affiliation(s)
- Matthias Wietz
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Christina Bienhold
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Katja Metfies
- Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Sinhué Torres-Valdés
- Marine BioGeoScience, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Wilken-Jon von Appen
- Physical Oceanography of the Polar Seas, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Ian Salter
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Faroe Marine Research Institute, Tórshavn, Faroe Islands
| | - Antje Boetius
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
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Currie AA, Marshall AJ, Lohrer AM, Cummings VJ, Seabrook S, Cary SC. Sea Ice Dynamics Drive Benthic Microbial Communities in McMurdo Sound, Antarctica. Front Microbiol 2021; 12:745915. [PMID: 34777294 PMCID: PMC8581541 DOI: 10.3389/fmicb.2021.745915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/29/2021] [Indexed: 01/04/2023] Open
Abstract
Climate change is driving dramatic variability in sea ice dynamics, a key driver in polar marine ecosystems. Projected changes in Antarctica suggest that regional warming will force dramatic shifts in sea ice thickness and persistence, altering sea ice-associated primary production and deposition to the seafloor. To improve our understanding of the impacts of sea ice change on benthic ecosystems, we directly compared the benthic microbial communities underlying first-year sea ice (FYI) and multi-year sea ice (MYI). Using two tractable coastal habitats in McMurdo Sound, Antarctica, where FYI (Cape Evans) and MYI (New Harbour) prevail, we show that the structure and composition of the benthic microbial communities reflect the legacy of sea ice dynamics. At Cape Evans, an enrichment of known heterotrophic algal polysaccharide degrading taxa (e.g., Flavobacteriaceae, unclassified Gammaproteobacteria, and Rubritaleaceae) and sulfate-reducing bacteria (e.g., Desulfocapsaceae) correlated with comparatively higher chlorophyll a (14.2±0.8μgg-1) and total organic carbon content (0.33%±0.04), reflecting increased productivity and seafloor deposition beneath FYI. Conversely, at New Harbour, an enrichment of known archaeal (e.g., Nitrosopumilaceae) and bacterial (e.g., Woeseiaceae and Nitrospiraceae) chemoautotrophs was common in sediments with considerably lower chlorophyll a (1.0±0.24μgg-1) and total organic carbon content (0.17%±0.01), reflecting restricted productivity beneath MYI. We also report evidence of a submarine discharge of sub-permafrost brine from Taylor Valley into New Harbour. By comparing our two study sites, we show that under current climate-warming scenarios, changes to sea ice productivity and seafloor deposition are likely to initiate major shifts in benthic microbial communities, with heterotrophic organic matter degradation processes becoming increasingly important. This study provides the first assessment of how legacy sea ice conditions influence benthic microbial communities in Antarctica, contributing insight into sea ice-benthic coupling and ecosystem functioning in a polar environment.
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Affiliation(s)
- Ashleigh A Currie
- School of Science, University of Waikato, Hamilton, New Zealand.,Environmental Research Institute, International Centre for Terrestrial Antarctic Research, Hamilton, New Zealand
| | - Alexis J Marshall
- School of Science, University of Waikato, Hamilton, New Zealand.,Environmental Research Institute, International Centre for Terrestrial Antarctic Research, Hamilton, New Zealand
| | - Andrew M Lohrer
- National Institute of Water and Atmosphere, Hamilton, New Zealand
| | - Vonda J Cummings
- National Institute of Water and Atmosphere, Wellington, New Zealand
| | - Sarah Seabrook
- National Institute of Water and Atmosphere, Wellington, New Zealand
| | - S Craig Cary
- School of Science, University of Waikato, Hamilton, New Zealand.,Environmental Research Institute, International Centre for Terrestrial Antarctic Research, Hamilton, New Zealand
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41
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Ruocco N, Esposito R, Zagami G, Bertolino M, De Matteo S, Sonnessa M, Andreani F, Crispi S, Zupo V, Costantini M. Microbial diversity in Mediterranean sponges as revealed by metataxonomic analysis. Sci Rep 2021; 11:21151. [PMID: 34707182 PMCID: PMC8551288 DOI: 10.1038/s41598-021-00713-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
Although the Mediterranean Sea covers approximately a 0.7% of the world's ocean area, it represents a major reservoir of marine and coastal biodiversity. Among marine organisms, sponges (Porifera) are a key component of the deep-sea benthos, widely recognized as the dominant taxon in terms of species richness, spatial coverage, and biomass. Sponges are evolutionarily ancient, sessile filter-feeders that harbor a largely diverse microbial community within their internal mesohyl matrix. In the present work, we firstly aimed at exploring the biodiversity of marine sponges from four different areas of the Mediterranean: Faro Lake in Sicily and "Porto Paone", "Secca delle fumose", "Punta San Pancrazio" in the Gulf of Naples. Eight sponge species were collected from these sites and identified by morphological analysis and amplification of several conserved molecular markers (18S and 28S RNA ribosomal genes, mitochondrial cytochrome oxidase subunit 1 and internal transcribed spacer). In order to analyze the bacterial diversity of symbiotic communities among these different sampling sites, we also performed a metataxonomic analysis through an Illumina MiSeq platform, identifying more than 1500 bacterial taxa. Amplicon Sequence Variants (ASVs) analysis revealed a great variability of the host-specific microbial communities. Our data highlight the occurrence of dominant and locally enriched microbes in the Mediterranean, together with the biotechnological potential of these sponges and their associated bacteria as sources of bioactive natural compounds.
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Affiliation(s)
- Nadia Ruocco
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Roberta Esposito
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy ,grid.4691.a0000 0001 0790 385XDepartment of Biology, University of Naples Federico II, Complesso Universitario Di Monte Sant’Angelo, Via Cinthia 21, 80126 Naples, Italy
| | - Giacomo Zagami
- grid.10438.3e0000 0001 2178 8421Dipartimento Di Scienze Biologiche, Chimiche, Farmaceutiche Ed Ambientali, Università Di Messina, 98100 Messina, Italy
| | - Marco Bertolino
- grid.5606.50000 0001 2151 3065DISTAV, Università Degli Studi Di Genova, Corso Europa 26, 16132 Genoa, Italy
| | - Sergio De Matteo
- grid.10438.3e0000 0001 2178 8421Dipartimento Di Scienze Biologiche, Chimiche, Farmaceutiche Ed Ambientali, Università Di Messina, 98100 Messina, Italy
| | | | | | - Stefania Crispi
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy ,grid.5326.20000 0001 1940 4177Institute of Biosciences and BioResources Naples, National Research Council of Italy, Naples, Italy
| | - Valerio Zupo
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Maria Costantini
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
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42
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Tardy V, Etienne D, Masclaux H, Essert V, Millet L, Verneaux V, Lyautey E. Spatial distribution of sediment archaeal and bacterial communities relates to the source of organic matter and hypoxia - a biogeographical study on Lake Remoray (France). FEMS Microbiol Ecol 2021; 97:6362600. [PMID: 34472595 DOI: 10.1093/femsec/fiab126] [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: 04/16/2021] [Accepted: 08/31/2021] [Indexed: 11/15/2022] Open
Abstract
Bottom waters hypoxia spreads in many lakes worldwide causing severe consequences on whole lakes trophic network. Here, we aimed at understanding the origin of organic matter stored in the sediment compartment and the related diversity of sediment microbial communities in a lake with deoxygenated deep water layers. We used a geostatistical approach to map and compare both the variation of organic matter and microbial communities in sediment. Spatialisation of C/N ratio and δ13C signature of sediment organic matter suggested that Lake Remoray was characterized by an algal overproduction which could be related to an excess of nutrient due to the close lake-watershed connectivity. Three spatial patterns were observed for sediment microbial communities after the hypoxic event, each characterized by specific genetic structure, microbial diversity and composition. The relative abundance variation of dominant microbial groups across Lake Remoray such as Cyanobacteria, Gammaproteobacteria, Deltaproteobacteria and Chloroflexi provided us important information on the lake areas where hypoxia occurs. The presence of methanogenic species in the deeper part of the lake suggests important methane production during hypoxia period. Taken together, our results provide an extensive picture of microbial communities' distribution related to quantity and quality of organic matter in a seasonally hypoxic lake.
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Affiliation(s)
- Vincent Tardy
- Pôle R&D 'ECLA', 73376 Le Bourget-du-Lac, France.,Université Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - David Etienne
- Pôle R&D 'ECLA', 73376 Le Bourget-du-Lac, France.,Université Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - Hélène Masclaux
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Univ. Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Valentin Essert
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Univ. Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Laurent Millet
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Univ. Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Valérie Verneaux
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Univ. Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Emilie Lyautey
- Pôle R&D 'ECLA', 73376 Le Bourget-du-Lac, France.,Université Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France
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43
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Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms. ISME JOURNAL 2021; 16:630-641. [PMID: 34493810 PMCID: PMC8857213 DOI: 10.1038/s41396-021-01105-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 12/11/2022]
Abstract
Marine algae annually sequester petagrams of carbon dioxide into polysaccharides, which are a central metabolic fuel for marine carbon cycling. Diatom microalgae produce sulfated polysaccharides containing methyl pentoses that are challenging to degrade for bacteria compared to other monomers, implicating these sugars as a potential carbon sink. Free-living bacteria occurring in phytoplankton blooms that specialise on consuming microalgal sugars, containing fucose and rhamnose remain unknown. Here, genomic and proteomic data indicate that small, coccoid, free-living Verrucomicrobiota specialise in fucose and rhamnose consumption during spring algal blooms in the North Sea. Verrucomicrobiota cell abundance was coupled with the algae bloom onset and accounted for up to 8% of the bacterioplankton. Glycoside hydrolases, sulfatases, and bacterial microcompartments, critical proteins for the consumption of fucosylated and sulfated polysaccharides, were actively expressed during consecutive spring bloom events. These specialised pathways were assigned to novel and discrete candidate species of the Akkermansiaceae and Puniceicoccaceae families, which we here describe as Candidatus Mariakkermansia forsetii and Candidatus Fucivorax forsetii. Moreover, our results suggest specialised metabolic pathways could determine the fate of complex polysaccharides consumed during algae blooms. Thus the sequestration of phytoplankton organic matter via methyl pentose sugars likely depend on the activity of specialised Verrucomicrobiota populations.
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Chun SJ, Cui Y, Baek SH, Ahn CY, Oh HM. Seasonal succession of microbes in different size-fractions and their modular structures determined by both macro- and micro-environmental filtering in dynamic coastal waters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 784:147046. [PMID: 33894601 DOI: 10.1016/j.scitotenv.2021.147046] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 04/06/2021] [Accepted: 04/06/2021] [Indexed: 05/16/2023]
Abstract
Microbes interact with each other in response to various environmental changes in coastal marine ecosystems. To explore how the macroenvironment (environmental filtering) and species-engineered microenvironment (niche construction) affect the ecological network of the marine microbiome in the highly dynamic coastal waters of Korea, we analyzed the modular structures of the microbial community and identified microbial interconnections in different size fractions for a year. Fluctuations in the macroenvironment, such as temperature and nutrient concentrations driven by seasonal changes, are the major factors in determining successive microbial modules. Compared to particle-associated (PA) microbes, free-living (FL) microbes seemed to be more affected by macroenvironmental filtering. Modules related to nutrients were further divided into various modules according to different lifestyles. In addition, a large transient discharge of the Changjiang (Yangtze River) in summer also formed a distinct microbial module, which was related to the high ammonia concentration arising from phytoplankton degradation. Microbes belonging to the SAR11, SAR86, and SAR116 clades, Flavobacteriaceae, and MG IIa-L showed repeated interconnections in temperature-related modules, while the SAR202 clade, Marinimicrobia, DEV007 clade, and Arctic97B-4 and Sva0996 marine groups displayed repeated connections in nutrient-related modules. These 'skeleton'-forming microbes created species-engineered microenvironments, further fine-tuning microbial modular structures. Furthermore, they serve as keystone species for module stability by linking interdependent microbial partners within their own modules through universally beneficial metabolic activities. Therefore, they could reinforce the ecological resilience of microbial communities under abiotic and biotic perturbations in dynamic coastal waters. In conclusion, both macro- and micro-environmental filtering were important for determining the seasonal succession of microbial community structures.
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Affiliation(s)
- Seong-Jun Chun
- LMO Research Team, National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon 33657, Republic of Korea; Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yingshun Cui
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Seung Ho Baek
- South Sea Institute, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea
| | - Chi-Yong Ahn
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea.
| | - Hee-Mock Oh
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea.
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45
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Kavehei A, Hose GC, Chariton AA, Gore DB. Application of environmental DNA for assessment of contamination downstream of a legacy base metal mine. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125794. [PMID: 33862483 DOI: 10.1016/j.jhazmat.2021.125794] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/11/2021] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
Acid Rock Drainage (ARD) from legacy mines can negatively impact the biota in sediments and waters for tens of kilometers downstream. Here we used environmental (e)DNA metabarcoding to assess the impacts of metal contaminants on biota in sediment and water downstream of a legacy base metal sulfide mine in southeastern Australia, as exemplar of similar mines elsewhere. Concentrations of metals in water were below Australian water quality guideline values at 20 km downstream for copper (Cu), 40 km downstream for zinc (Zn) and 10 km downstream for lead (Pb). Sediment metal concentrations were below national guideline concentrations at 10 km downstream for Cu, 60 km downstream for Zn and 20 km downstream for Pb. In contrast, metabarcoding showed that biological communities from sediment samples at 10 km and 20 km downstream were similar to sites close to the mine and thus indicative of being impacted, despite metal concentrations being relatively low. As we illustrate, when combined with sediment and water chemistry, metabarcoding can provide more ecological robust perspective on the downstream effects of legacy mines, capturing the sensitivities of a diverse range of organisms.
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Affiliation(s)
- Armin Kavehei
- Department of Earth and Environmental Sciences, Macquarie University, Sydney 2109, Australia.
| | - Grant C Hose
- Department of Biological Sciences, Macquarie University, Sydney 2109, Australia
| | - Anthony A Chariton
- Department of Biological Sciences, Macquarie University, Sydney 2109, Australia
| | - Damian B Gore
- Department of Earth and Environmental Sciences, Macquarie University, Sydney 2109, Australia
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46
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Kim S, Islam MR, Kang I, Cho JC. Cultivation of Dominant Freshwater Bacterioplankton Lineages Using a High-Throughput Dilution-to-Extinction Culturing Approach Over a 1-Year Period. Front Microbiol 2021; 12:700637. [PMID: 34385989 PMCID: PMC8353197 DOI: 10.3389/fmicb.2021.700637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/09/2021] [Indexed: 11/13/2022] Open
Abstract
Although many culture-independent molecular analyses have elucidated a great diversity of freshwater bacterioplankton, the ecophysiological characteristics of several abundant freshwater bacterial groups are largely unknown due to the scarcity of cultured representatives. Therefore, a high-throughput dilution-to-extinction culturing (HTC) approach was implemented herein to enable the culture of these bacterioplankton lineages using water samples collected at various seasons and depths from Lake Soyang, an oligotrophic reservoir located in South Korea. Some predominant freshwater bacteria have been isolated from Lake Soyang via HTC (e.g., the acI lineage); however, large-scale HTC studies encompassing different seasons and water depths have not been documented yet. In this HTC approach, bacterial growth was detected in 14% of 5,376 inoculated wells. Further, phylogenetic analyses of 16S rRNA genes from a total of 605 putatively axenic bacterial cultures indicated that the HTC isolates were largely composed of Actinobacteria, Bacteroidetes, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Verrucomicrobia. Importantly, the isolates were distributed across diverse taxa including phylogenetic lineages that are widely known cosmopolitan and representative freshwater bacterial groups such as the acI, acIV, LD28, FukuN57, MNG9, and TRA3-20 lineages. However, some abundant bacterial groups including the LD12 lineage, Chloroflexi, and Acidobacteria could not be domesticated. Among the 71 taxonomic groups in the HTC isolates, representative strains of 47 groups could either form colonies on agar plates or be revived from frozen glycerol stocks. Additionally, season and water depth significantly affected bacterial community structure, as demonstrated by 16S rRNA gene amplicon sequencing analyses. Therefore, our study successfully implemented a dilution-to-extinction cultivation strategy to cultivate previously uncultured or underrepresented freshwater bacterial groups, thus expanding the basis for future multi-omic studies.
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Affiliation(s)
- Suhyun Kim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
| | - Md Rashedul Islam
- Bacteriophage Biology Laboratory, Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| | - Ilnam Kang
- Department of Biological Sciences, Center for Molecular and Cell Biology, Inha University, Incheon, South Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
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47
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Bacterial community structure and functional profiling of high Arctic fjord sediments. World J Microbiol Biotechnol 2021; 37:133. [PMID: 34255189 DOI: 10.1007/s11274-021-03098-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/23/2021] [Indexed: 10/20/2022]
Abstract
Kongsfjorden, an Arctic fjord is significantly affected by the glacier melt and Atlantification, both the processes driven by accelerated warming in the Arctic. This has lead to changes in primary production, carbon pool and microbial communities, especially that in the sediment. In this study, we have examined the bacterial community structure of surface (0-2 cm) and subsurface (3-9 cm) sediments of Kongsfjorden using the high throughput sequencing analysis. Results revealed that bacterial community structure of Kongsfjorden sediments were dominated by phylum Proteobacteria followed by Bacteroidetes and Epsilonbacteraeota. While α- and γ-Proteobacterial class were dominant in surface sediments; δ-Proteobacteria were found to be predominant in subsurface sediments. The bacterial community structure in the surface and subsurface sediments showed significant variations (p ≤ 0.05). Total organic carbon could be one of the major parameters controlling the bacterial diversity in the surface and subsurface sediments. Functional prediction analysis indicated that the bacterial community could be involved in the degradation of complex organic compounds such as glycans, glycosaminoglycans, polycyclic aromatic hydrocarbons and also in the biosynthesis of secondary metabolites.
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48
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Kinsela AS, Bligh MW, Vázquez-Campos X, Sun Y, Wilkins MR, Comarmond MJ, Rowling B, Payne TE, Waite TD. Biogeochemical Mobility of Contaminants from a Replica Radioactive Waste Trench in Response to Rainfall-Induced Redox Oscillations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8793-8805. [PMID: 34110792 DOI: 10.1021/acs.est.1c01604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Results of investigations into factors influencing contaminant mobility in a replica trench located adjacent to a legacy radioactive waste site are presented in this study. The trench was filled with nonhazardous iron- and organic matter (OM)-rich components, as well as three contaminant analogues strontium, cesium, and neodymium to examine contaminant behavior. Imposed redox/water-level oscillations, where oxygen-laden rainwater was added to the anoxic trench, resulted in marked biogeochemical changes including the removal of aqueous Fe(II) and circulation of dissolved carbon, along with shifts to microbial communities involved in cycling iron (Gallionella, Sideroxydans) and methane generation (Methylomonas, Methylococcaceae). Contaminant mobility depended upon element speciation and rainfall event intensity. Strontium remained mobile, being readily translocated under hydrological perturbations. Strong ion-exchange reactions and structural incorporation into double-layer clay minerals were likely responsible for greater retention of Cs, which, along with Sr, was unaffected by redox oscillations. Neodymium was initially immobilized within the anoxic trenches, due to either secondary mineral (phosphate) precipitation or via the chemisorption of organic- and carbonate-Nd complexes onto variably charged solid phases. Oxic rainwater intrusions altered Nd mobility via competing effects. Oxidation of Fe(II) led to partial retention of Nd within highly sorbing Fe(III)/OM phases, whereas pH decreases associated with rainwater influxes resulted in a release of adsorbed Nd to solution with both pH and OM presumed to be the key factors controlling Nd attenuation. Collectively, the behavior of simulated contaminants within this replica trench provided unique insights into trench water biogeochemistry and contaminant cycling in a redox oscillatory environment.
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Affiliation(s)
- Andrew S Kinsela
- UNSW Water Research Centre and School of Civil and Environmental Engineering, The University of New South Wales, Sydney 2052, Australia
| | - Mark W Bligh
- UNSW Water Research Centre and School of Civil and Environmental Engineering, The University of New South Wales, Sydney 2052, Australia
| | - Xabier Vázquez-Campos
- NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia
| | - Yingying Sun
- UNSW Water Research Centre and School of Civil and Environmental Engineering, The University of New South Wales, Sydney 2052, Australia
| | - Marc R Wilkins
- NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia
| | - M Josick Comarmond
- Environmental Research Theme, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Brett Rowling
- Environmental Research Theme, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Timothy E Payne
- Environmental Research Theme, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - T David Waite
- UNSW Water Research Centre and School of Civil and Environmental Engineering, The University of New South Wales, Sydney 2052, Australia
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49
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Miksch S, Meiners M, Meyerdierks A, Probandt D, Wegener G, Titschack J, Jensen MA, Ellrott A, Amann R, Knittel K. Bacterial communities in temperate and polar coastal sands are seasonally stable. ISME COMMUNICATIONS 2021; 1:29. [PMID: 36739458 PMCID: PMC9723697 DOI: 10.1038/s43705-021-00028-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/13/2021] [Accepted: 05/24/2021] [Indexed: 04/18/2023]
Abstract
Coastal sands are biocatalytic filters for dissolved and particulate organic matter of marine and terrestrial origin, thus, acting as centers of organic matter transformation. At high temporal resolution, we accessed the variability of benthic bacterial communities over two annual cycles at Helgoland (North Sea), and compared it with seasonality of communities in Isfjorden (Svalbard, 78°N) sediments, where primary production does not occur during winter. Benthic community structure remained stable in both, temperate and polar sediments on the level of cell counts and 16S rRNA-based taxonomy. Actinobacteriota of uncultured Actinomarinales and Microtrichales were a major group, with 8 ± 1% of total reads (Helgoland) and 31 ± 6% (Svalbard). Their high activity (frequency of dividing cells 28%) and in situ cell numbers of >10% of total microbes in Svalbard sediments, suggest Actinomarinales and Microtrichales as key heterotrophs for carbon mineralization. Even though Helgoland and Svalbard sampling sites showed no phytodetritus-driven changes of the benthic bacterial community structure, they harbored significantly different communities (p < 0.0001, r = 0.963). The temporal stability of benthic bacterial communities is in stark contrast to the dynamic succession typical of coastal waters, suggesting that pelagic and benthic bacterial communities respond to phytoplankton productivity very differently.
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Affiliation(s)
| | - Mirja Meiners
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - David Probandt
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Jürgen Titschack
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Senckenberg am Meer, Wilhelmshaven, Germany
| | - Maria A Jensen
- UNIS, The University Centre in Svalbard, Longyearbyen, Norway
| | - Andreas Ellrott
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Katrin Knittel
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
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50
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Maturana-Martínez C, Fernández C, González HE, Galand PE. Different Active Microbial Communities in Two Contrasted Subantarctic Fjords. Front Microbiol 2021; 12:620220. [PMID: 34248861 PMCID: PMC8264266 DOI: 10.3389/fmicb.2021.620220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 05/25/2021] [Indexed: 12/02/2022] Open
Abstract
Microorganisms play a crucial role in biogeochemical processes affecting the primary production and biogeochemical cycles of the ocean. In subpolar areas, the increment of the water temperature induced by climate change could lead to changes in the structure and activity of planktonic microbial communities. To understand how the structure of the microbial community in Chilean Patagonian fjords could be affected by climate change, we analyzed the composition of the prokaryotic community (bacteria-archaea) in two fjords (Pia and Yendegaia) with contrasting morphological and hydrological features. We targeted both the standing stock (16S rRNA genes) and the active fraction (16S rRNA transcripts) of the microbial communities during two consecutive austral winters. Our results showed that in both fjords, the active community had higher diversity and stronger biogeographic patterns when compared to the standing stock. Members of the Alpha-, Gamma-, and Deltaproteobacteria followed by archaea from the Marine Group I (Thaumarchaeota) dominated the active communities in both fjords. However, in Pia fjord, which has a marine-terminating glacier, the composition of the microbial community was directly influenced by the freshwater discharges from the adjacent glacier, and indirectly by a possible upwelling phenomenon that could bring deep sea bacteria such as SAR202 to the surface layer. In turn, in the Yendegaia, which has a land-terminating glacier, microbial communities were more similar to the ones described in oceanic waters. Furthermore, in Yendegaia fjord, inter-annual differences in the taxonomic composition and diversity of the microbial community were observed. In conclusion, Yendegaia fjord, without glacier calving, represents a fjord type that will likely be more common under future climate scenarios. Our results showing distinct Yendegaia communities, with for example more potential nitrogen-fixing microorganisms (Planctomycetes), indicate that as a result of climate change, changing planktonic communities could potentially impact biogeochemical processes and nutrient sources in subantarctic fjords.
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Affiliation(s)
- Claudia Maturana-Martínez
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, Banyuls-sur-Mer, France.,Centro de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes and Universidad Austral de Chile, Valdivia, Chile
| | - Camila Fernández
- Centro de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes and Universidad Austral de Chile, Valdivia, Chile.,Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, Banyuls-sur-Mer, France.,Departamento de Oceanografía and Centro de Investigación Oceanográfica COPAS Sur-Austral, Universidad de Concepción, Concepción, Chile
| | - Humberto E González
- Centro de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes and Universidad Austral de Chile, Valdivia, Chile
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, Banyuls-sur-Mer, France
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