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Bicaldo IEC, Padilla KSAR, Tu TH, Chen WT, Mendoza-Pascual MU, Vicera CVB, de Leon JR, Poblete KN, Austria ES, Lopez MLD, Kobayashi Y, Shiah FK, Papa RDS, Okuda N, Wang PL, Lin LH. The methane-oxidizing microbial communities of three maar lakes in tropical monsoon Asia. Front Microbiol 2024; 15:1410666. [PMID: 39044952 PMCID: PMC11263035 DOI: 10.3389/fmicb.2024.1410666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/21/2024] [Indexed: 07/25/2024] Open
Abstract
Methane-oxidizing bacteria (MOB) is a group of planktonic microorganisms that use methane as their primary source of cellular energy. For tropical lakes in monsoon Asia, there is currently a knowledge gap on MOB community diversity and the factors influencing their abundance. Herewith, we present a preliminary assessment of the MOB communities in three maar lakes in tropical monsoon Asia using Catalyzed Reporter Deposition, Fluorescence In-Situ Hybridization (CARD-FISH), 16S rRNA amplicon sequencing, and pmoA gene sequencing. Correlation analysis between MOB abundances and lakes' physicochemical parameters following seasonal monsoon events were performed to explain observed spatial and temporal patterns in MOB diversity. The CARD-FISH analyses detected the three MOB types (I, II, and NC10) which aligned with the results from 16S rRNA amplicons and pmoA gene sequencing. Among community members based on 16S rRNA genes, Proteobacterial Type I MOB (e.g., Methylococcaceae and Methylomonadaceae), Proteobacterial Type II (Methylocystaceae), Verrucomicrobial (Methylacidiphilaceae), Methylomirabilota/NC10 (Methylomirabilaceae), and archaeal ANME-1a were found to be the dominant methane-oxidizers in three maar lakes. Analysis of microbial diversity and distribution revealed that the community compositions in Lake Yambo vary with the seasons and are more distinct during the stratified period. Temperature, DO, and pH were significantly and inversely linked with type I MOB and Methylomirabilota during stratification. Only MOB type I was influenced by monsoon changes. This research sought to establish a baseline for the diversity and ecology of planktonic MOB in tropical monsoon Asia to better comprehend their contribution to the CH4 cycle in tropical freshwater ecosystems.
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Affiliation(s)
- Iona Eunice C. Bicaldo
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Karol Sophia Agape R. Padilla
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Philippine Genome Center, University of the Philippines, Quezon City, Philippines
- Department of Science and Technology, Science Education Institute, Taguig, Philippines
| | - Tzu-Hsuan Tu
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Wan Ting Chen
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
| | - Milette U. Mendoza-Pascual
- Department of Environmental Science, School of Science and Engineering, Ateneo Research Institute for Science and Engineering, Ateneo de Manila University, Quezon City, Philippines
| | | | - Justine R. de Leon
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- Department of Biological Sciences, University of Santo Tomas, Manila, Philippines
| | | | | | - Mark Louie D. Lopez
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Yuki Kobayashi
- Center for Ecological Research, Kyoto University, Shiga, Japan
| | - Fuh-Kwo Shiah
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan
| | - Rey Donne S. Papa
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- Department of Biological Sciences, University of Santo Tomas, Manila, Philippines
| | - Noboru Okuda
- Center for Ecological Research, Kyoto University, Shiga, Japan
- Research Center for Inland Seas, Kobe University, Kobe, Japan
- Research Institute for Humanity and Nature, Kamigamo Motoyama, Kita Ward, Kyoto, Japan
| | - Pei-Ling Wang
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
- Research Center for Future Earth, National Taiwan University, Taipei, Taiwan
| | - Li-Hung Lin
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
- Research Center for Future Earth, National Taiwan University, Taipei, Taiwan
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Alhajeri NS, Tawfik A, Elsamadony M, Al-Fadhli FM, Meng F. Synergistic algal/bacterial interaction in membrane bioreactor for detoxification of 1,2-dichloroethane-rich petroleum wastewater. JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134125. [PMID: 38565016 DOI: 10.1016/j.jhazmat.2024.134125] [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: 12/26/2023] [Revised: 03/12/2024] [Accepted: 03/23/2024] [Indexed: 04/04/2024]
Abstract
The study addressed the challenge of treating petroleum industry wastewater with high concentrations of 1,2-dichloroethane (1,2-DCA) ranging from 384 to 1654 mg/L, which poses a challenge for bacterial biodegradation and algal photodegradation. To overcome this, a collaborative approach using membrane bioreactors (MBRs) that combine algae and bacteria was employed. This synergistic method effectively mitigated the toxicity of 1,2-DCA and curbed MBR fouling. Two types of MBRs were tested: one (B-MBR) used bacterial cultures and the other (AB-MBR) incorporated a mix of algal and bacterial cultures. The AB-MBR significantly contributed to 1,2-DCA removal, with algae accounting for over 20% and bacteria for approximately 49.5% of the dechlorination process. 1,2-DCA metabolites, including 2-chloroethanol, 2-chloro-acetaldehyde, 2-chloroacetic acid, and acetic acid, were partially consumed as carbon sources by algae. Operational efficiency peaked at a 12-hour hydraulic retention time (HRT) in AB-MBR, enhancing enzyme activities crucial for 1,2-DCA degradation such as dehydrogenase (DH), alcohol dehydrogenase (ADH), and acetaldehyde dehydrogenase (ALDH). The microbial diversity in AB-MBR surpassed that in B-MBR, with a notable increase in Proteobacteria, Bacteroidota, Planctomycetota, and Verrucomicrobiota. Furthermore, AB-MBR showed a significant rise in the dominance of 1,2-DCA-degrading genus such as Pseudomonas and Acinetobacter. Additionally, algal-degrading phyla (e.g., Nematoda, Rotifera, and Streptophyta) were more prevalent in AB-MBR, substantially reducing the issue of membrane fouling.
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Affiliation(s)
- Nawaf S Alhajeri
- Department of Environmental Sciences, College of Life Sciences, Kuwait University, P.O. Box 5969, Safat 13060, Kuwait.
| | - Ahmed Tawfik
- Department of Environmental Sciences, College of Life Sciences, Kuwait University, P.O. Box 5969, Safat 13060, Kuwait
| | - Mohamed Elsamadony
- Department of Mechanical Engineering, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia; Interdisciplinary Research Center for Refining & Advanced Chemicals, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia
| | - Fahad M Al-Fadhli
- Department of Chemical Engineering, College of Engineering and Petroleum, Kuwait University, P.O. Box 5969, Safat 13060, Kuwait
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510006, China
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Grabowska-Grucza K, Kiersztyn B. Relationships between Legionella and Aeromonas spp. and associated lake bacterial communities across seasonal changes in an anthropogenic eutrophication gradient. Sci Rep 2023; 13:17076. [PMID: 37816753 PMCID: PMC10564844 DOI: 10.1038/s41598-023-43234-3] [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: 08/01/2023] [Accepted: 09/21/2023] [Indexed: 10/12/2023] Open
Abstract
Anthropogenic eutrophication of lakes threatens their homeostasis and carries an increased risk of development of potentially pathogenic microorganisms. In this paper we show how eutrophication affects seasonal changes in the taxonomic structure of bacterioplankton and whether these changes are associated with the relative abundance of pathogenic bacteria of the genera Legionella and Aeromonas. The subject of the study was a unique system of interconnected lakes in northern Poland (Great Masurian Lakes system), characterized by the presence of eutrophic gradient. We found that the taxonomic structure of the bacterial community in eutrophic lakes was significantly season dependent. No such significant seasonal changes were observed in meso-eutrophic lakes. We found that there is a specific taxonomic composition of bacteria associated with the occurrence of Legionella spp. The highest positive significant correlations were found for families Pirellulaceae, Mycobacteriaceae and Gemmataceae. The highest negative correlations were found for the families Sporichthyaceae, Flavobacteriaceae, the uncultured families of class Verrucomicrobia and Chitinophagaceae. We used also an Automatic Neural Network model to estimate the relative abundance of Legionella spp. based on the relative abundance of dominant bacterial families. In the case of Aeromonas spp. we did not find a clear relationship with bacterial communities inhabiting lakes of different trophic state. Our research has shown that anthropogenic eutrophication causes significant changes in the taxonomic composition of lake bacteria and contributes to an increase in the proportion of potentially pathogenic Legionella spp.
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Affiliation(s)
- Karolina Grabowska-Grucza
- Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Żwirki i Wigury 101, 02-089, Warszawa, Poland.
| | - Bartosz Kiersztyn
- Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Żwirki i Wigury 101, 02-089, Warszawa, Poland
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Chiriac MC, Haber M, Salcher MM. Adaptive genetic traits in pelagic freshwater microbes. Environ Microbiol 2023; 25:606-641. [PMID: 36513610 DOI: 10.1111/1462-2920.16313] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
Pelagic microbes have adopted distinct strategies to inhabit the pelagial of lakes and oceans and can be broadly categorized in two groups: free-living, specialized oligotrophs and patch-associated generalists or copiotrophs. In this review, we aim to identify genomic traits that enable pelagic freshwater microbes to thrive in their habitat. To do so, we discuss the main genetic differences of pelagic marine and freshwater microbes that are both dominated by specialized oligotrophs and the difference to freshwater sediment microbes, where copiotrophs are more prevalent. We phylogenomically analysed a collection of >7700 metagenome-assembled genomes, classified habitat preferences on different taxonomic levels, and compared the metabolic traits of pelagic freshwater, marine, and freshwater sediment microbes. Metabolic differences are mainly associated with transport functions, environmental information processing, components of the electron transport chain, osmoregulation and the isoelectric point of proteins. Several lineages with known habitat transitions (Nitrososphaeria, SAR11, Methylophilaceae, Synechococcales, Flavobacteriaceae, Planctomycetota) and the underlying mechanisms in this process are discussed in this review. Additionally, the distribution, ecology and genomic make-up of the most abundant freshwater prokaryotes are described in details in separate chapters for Actinobacteriota, Bacteroidota, Burkholderiales, Verrucomicrobiota, Chloroflexota, and 'Ca. Patescibacteria'.
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Affiliation(s)
| | - Markus Haber
- Institute of Hydrobiology, Biology Centre CAS, Ceske Budejovice, Czechia
| | - Michaela M Salcher
- Institute of Hydrobiology, Biology Centre CAS, Ceske Budejovice, Czechia
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Qian X, Liu A, Liang C, He L, Xu Z, Tang S. Analysis of gut microbiota in patients with acute myocardial infarction by 16S rRNA sequencing. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1340. [PMID: 36660636 PMCID: PMC9843380 DOI: 10.21037/atm-22-5671] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/12/2022] [Indexed: 12/28/2022]
Abstract
Background An increasing number of studies have shown that gut microbiota are associated with human cardiovascular disease, but the characteristics of intestinal flora in patients with acute myocardial infarction (AMI) are still unclear. In this study, we aimed to investigate the difference of intestinal microflora between patients with AMI and healthy people, and to find the effect of percutaneous coronary intervention (PCI) on intestinal microflora. Methods A total of 60 stool samples and 60 peripheral blood samples were collected from 20 previously diagnosed AMI patients and 20 healthy people serving as controls. Gut microbiota communities were analyzed via 16 ribosomal RNA-sequencing (16S rRNA). Gut microbiota-derived metabolites, trimethylamine N-oxide (TMAO) and short-chain fatty acids (SCFA), in the blood were detected using stable isotope dilution high-performance liquid chromatography with on line electrospray ionization tandem mass spectrometry (LC/MS/MS). Results The results showed that a distinct pattern of gut microbiota was observed in AMI patients compared to healthy controls. AMI patients had lower microbiological richness but no significant change in diversity. Bacteroidetes and Verrucomicobia showed an upward trend, whereas Proteobacteria showed a downward trend in AMI patients. During a longitudinal study to compare the changes in bacteria before and after treatment, we found routine cardiac admission therapy 1 week after PCI surgery had no effect on the microbial community structure in patients. There were significantly higher levels of plasma TMAO in AMI patients' microbiota than that in the control group. Contrarily, there was no obvious change in SCFA. Conclusions The gut microbiota of patients with AMI differs from that of normal people, and the metabolic products of microflora are more abundant in the plasma of AMI than control cases. Microflora may act on the cardiovascular system through metabolites, and regulation of the microfloral structure may be used in the future treatment of cardiovascular diseases.
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Affiliation(s)
- Xueyi Qian
- Precision Medicine Centre, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Ankang Liu
- Department of Cardiology, Shanghai Fengxian District Central Hospital, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital South Campus, Shanghai, China
| | - Chen Liang
- Department of Cardiology, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Lianjun He
- Precision Medicine Centre, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Zhenyu Xu
- Precision Medicine Centre, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Shengxing Tang
- Department of Cardiology, Yijishan Hospital of Wannan Medical College, Wuhu, China
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Yuan Y, Liu J, Gao B, Sillanpää M, Al-Farraj S. The effect of activated sludge treatment and catalytic ozonation on high concentration of ammonia nitrogen removal from landfill leachate. BIORESOURCE TECHNOLOGY 2022; 361:127668. [PMID: 35878770 DOI: 10.1016/j.biortech.2022.127668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/17/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
This study adopted the combination of activated sludge treatment and catalytic ozonation technology to efficiently remove the high concentration of ammonia nitrogen from landfill leachate. Through optimizing the parameters continuously, the COD, NH4+-N, UV254 and colority respectively descended to 417.75 ± 6.72 mg/L, 9.77 mg/L, 1.98 ± 0.04 and 40 times, and 3D fluorescence also reduced significantly within 14 days. Target genes of AOB-amoA, nxrA, napA, nirS and nosZ analysis indicated that ammonia-oxidizing bacteria, nitrated bacteria, and denitrifying bacteria played a key role on nitrogen removal, aerobic denitrifying bacteria was dominated especially. The nitrogen removal process was as follows: catalytic ozonation converted nitrogen-containing organic matter into NH4+-N, then NH4+-N was converted into NO2--N and NO3--N with the action of ammonia oxidation, nitrification and catalytic ozonation. Finally, the denitrification microorganisms transformed NO3--N or NO2--N to N2. Therefore, this coupled process realized the nitrogen removal effectively from landfill leachate.
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Affiliation(s)
- Yuchen Yuan
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; Key Laboratory of Membrane Separation of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Jiadong Liu
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; Key Laboratory of Membrane Separation of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Bo Gao
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; Key Laboratory of Membrane Separation of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Mika Sillanpää
- Department of Chemical Engineering, School of Mining, Metallurgy and Chemical Engineering, University of Johannesburg, P. O. Box 17011, Doornfontein 2028, South Africa; Chemistry Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; Zhejiang Rongsheng Environmental Protection Paper Co. LTD, NO. 588 East Zhennan Road, Pinghu Economic Development Zone, Zhejiang 314213, China; Department of Civil Engineering, University Centre for Research & Development, Chandigarh University, Gharuan, Mohali, Punjab, India; International Research Centre of Nanotechnology for Himalayan Sustainability (IRCNHS), Shoolini University, Solan 173212, Himachal Pradesh, India
| | - Saleh Al-Farraj
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
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Qi W, Liu J, Yu T, Huang S, Song R, Qiao Z. Ae1/Sbe1 maize-derived high amylose improves gut barrier function and ameliorates type II diabetes in high-fat diet-fed mice by increasing Akkermansia. Front Nutr 2022; 9:999020. [PMID: 36245499 PMCID: PMC9556726 DOI: 10.3389/fnut.2022.999020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/12/2022] [Indexed: 01/10/2023] Open
Abstract
Type II diabetes mellitus (T2DM) has its origins in chronic inflammation due to immune dysregulation. Improving chronic inflammation can significantly reduce the probability of T2DM and the rate of disease progression. Resistance to starch 2 (RSII) high-amylose maize starch (HAMS) has been widely implicated in the improvement and regulation of T2DM. However, its exact molecular mechanisms have not been fully discovered. Here, we used CRISPR/Cas9 technology to knock out two starch-branching enzyme genes, Ae1 and Sbe1, in maize to obtain mutants containing higher levels of HAMS. In experiments in which HAMS was fed to mice on a high-fat diet (HFD), we confirmed the function of HAMS in ameliorating hyperglycemia. Mechanistically, we found that HAMS improves the gut barrier function by increasing the Akkermansia abundance in the gut. This increase led to the alleviation of chronic inflammation in mice on a HFD, resulting in improved insulin sensitivity and a decrease in blood glucose.
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Affiliation(s)
- Weiwei Qi
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
| | - Jingchao Liu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
| | - Tante Yu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
| | - Shengchan Huang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
| | - Rentao Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zhenyi Qiao
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai, China
- *Correspondence: Zhenyi Qiao
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Smrhova T, Jani K, Pajer P, Kapinusova G, Vylita T, Suman J, Strejcek M, Uhlik O. Prokaryotes of renowned Karlovy Vary (Carlsbad) thermal springs: phylogenetic and cultivation analysis. ENVIRONMENTAL MICROBIOME 2022; 17:48. [PMID: 36089611 PMCID: PMC9465906 DOI: 10.1186/s40793-022-00440-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 08/26/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND The extreme conditions of thermal springs constitute a unique aquatic habitat characterized by low nutrient contents and the absence of human impacts on the microbial community composition. Thus, these springs may host phylogenetically novel microorganisms with potential use in biotechnology. With this hypothesis in mind, we examined the microbial composition of four thermal springs of the world-renowned spa town of Karlovy Vary (Carlsbad), Czechia, which differ in their temperature and chemical composition. RESULTS Microbial profiling using 16S rRNA gene sequencing revealed the presence of phylogenetically novel taxa at various taxonomic levels, spanning from genera to phyla. Many sequences belonged to novel classes within the phyla Hydrothermae, Altiarchaeota, Verrucomicrobia, and TA06. Cultivation-based methods employing oligotrophic media resulted in the isolation of 44 unique bacterial isolates. These include strains that withstand concentrations of up to 12% NaClw/v in cultivation media or survive a temperature of 100 °C, as well as hitherto uncultured bacterial species belonging to the genera Thermomonas, Paenibacillus, and Cellulomonas. These isolates harbored stress response genes that allow them to thrive in the extreme environment of thermal springs. CONCLUSIONS Our study is the first to analyze the overall microbial community composition of the renowned Karlovy Vary thermal springs. We provide insight into yet another level of uniqueness of these springs. In addition to their unique health benefits and cultural significance, we demonstrate that these springs harbor phylogenetically distinct microorganisms with unusual life strategies. Our findings open up avenues for future research with the promise of a deeper understanding of the metabolic potential of these microorganisms.
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Affiliation(s)
- Tereza Smrhova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Kunal Jani
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Petr Pajer
- Military Health Institute, Ministry of Defence of the Czech Republic, Prague, Czech Republic
| | - Gabriela Kapinusova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Tomas Vylita
- Institute of Balneology and Spa Sciences, Karlovy Vary, Czech Republic
| | - Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic.
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Abstract
Buffalo is an important livestock species. Here, we present a comprehensive metagenomic survey of the microbial communities along the buffalo digestive tract. We analysed 695 samples covering eight different sites in three compartments (four-chambered stomach, intestine, and rectum). We mapped ~85% of the raw sequence reads to 4,960 strain-level metagenome-assembled genomes (MAGs) and 3,255 species-level MAGs, 90% of which appear to correspond to new species. In addition, we annotated over 5.8 million nonredundant proteins from the MAGs. In comparison with the rumen microbiome of cattle, the buffalo microbiota seems to present greater potential for fibre degradation and less potential for methane production. Our catalogue of microbial genomes and the encoded proteins provides insights into microbial functions and interactions at distinct sites along the buffalo digestive tract.
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Sulfuriroseicoccus oceanibius gen. nov., sp. nov., a representative of the phylum Verrucomicrobia with a special cytoplasmic membrane. Antonie van Leeuwenhoek 2022; 115:337-352. [PMID: 35044567 DOI: 10.1007/s10482-021-01689-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/18/2021] [Indexed: 10/19/2022]
Abstract
Here, we describe a novel bacterial strain, designated T37T, which was isolated from the marine sediment of Xiaoshi Island, PR China. Growth of strain T37T occurs at 15-40 °C (optimum 37 °C), pH 6.0-9.0 (optimum 7.5), and in the presence of 0.5-5.5% (w/v) NaCl (optimum 1.5%). Characteristic biochemical traits of the novel strain include MK-9 as the major menaquinone. The major fatty acids identified were iso-C14:0 and C16:1 ω9c (oleic acid). Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and phosphoglycolipids were the major cellular polar lipids. The G + C content of genomic DNA was 58.4 mol%. Unusual outer membrane features deduced from the analysis of cell morphology point towards the formation of an enlarged periplasmic space putatively used for the digestion of macromolecules. Phylogenetic analyses based on 16S rRNA genes and the genome indicated that strain T37T represents a novel species and genus affiliated with a distinct family level lineage of the verrucomicrobial subdivision 1. Our polyphasic taxonomy approach places the novel strain in a new genus within the current family Verrucomicrobiaceae, order Verrucomicrobiales, class Verrucomicrobiae. Strain T37T (= KCTC 72799 T = MCCC 1H00391T) is the type strain of a novel species, for which the name Sulfuriroseicoccus oceanibius gen. nov., sp. nov. is proposed.
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Jiang X, Ma H, Zhao QL, Yang J, Xin CY, Chen B. Bacterial communities in paddy soil and ditch sediment under rice-crab co-culture system. AMB Express 2021; 11:163. [PMID: 34870775 PMCID: PMC8648911 DOI: 10.1186/s13568-021-01323-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/19/2021] [Indexed: 11/10/2022] Open
Abstract
As an important form of sustainable agriculture, rice-crab (Eriocheir sinensis) co-culture is rapid developing worldwide. However, the knowledge on the bacterial communities of the different components of the system is limited. In this study, we investigated the bacterial community structure in paddy soil and ditch sediment by using high-throughput sequencing technology. The results showed that compared with the ditch sediment, the content of NH4+-N in paddy soil decreased by 62.31%, and the content of AP (available phosphorus) increased by 172.02% (P < 0.05). The most abundant phyla in paddy soil and ditch sediment were Proteobacteria, Bacteroidetes and Chloroflexi, whose relative abundance was above 65%. Among the dominant genera, the relative abundance of an uncultured bacterium genus of Saprospiraceae and an uncultured bacterium genus of Lentimicrobiaceae in paddy soil was significantly lower than ditch sediment (P < 0.05). Alpha diversity indicated that the bacterial diversity of paddy soil and ditch sediment was similar. The bacterial community structure was affected by the relative abundance of bacteria, not the species of bacteria. Redundancy analysis (RDA) showed that the bacterial communities in paddy soil and ditch sediment were correlated with physicochemical properties. Our findings showed that the bacterial community structure was distinct in paddy soil and ditch sediment under rice-crab co-culture probably due to their different management patterns. These results can provide theoretical support for improving rice-crab co-culture technology.
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Emu Q, Guan H, Zhu J, Zhang L, Fan J, Ji Y, Lin Y, Li C, Dan X, Aguo Y, Wei X, Zhang M, Zhang B, Yang C, Li B, Xiong C. Grazing and Supplementation of Dietary Yeast Probiotics Shape the Gut Microbiota and Improve the Immunity of Black Fattening Goats ( Capra hircus). Front Microbiol 2021; 12:666837. [PMID: 34489878 PMCID: PMC8416523 DOI: 10.3389/fmicb.2021.666837] [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: 02/11/2021] [Accepted: 07/27/2021] [Indexed: 12/31/2022] Open
Abstract
This study aimed to investigate the effects of different feeding modes on the growth performance, gut microbiota, and immunity of Black Fattening Goat (Capra hircus). A total of 30 goats were grouped in three groups by their feeding modes (pasture grazing group, PG; barn feeding group, BF; barn feeding + probiotics, BF + P; n = 10) and the study was performed for 114 days. After a 2-week adaptation period, the first growth performance test was conducted, and the blood and fecal samplings (day 0) were collected on January 17, 2020, while the second and third test and samplings were conducted on days 53 and 100 of feeding. The species-composition of fecal microbiota was analyzed by 16S ribosomal RNA gene-sequencing using PacBio single molecule real time (SMRT) sequencing technology. Both the BF and BF + P groups had the highest (P < 0.05) body’s weight and length, and chest circumference at days 53 and 100, especially at day 100, the body’s weight of both the BF groups were more than 18 kg. The levels of immunoglobulin A (IgA) and immunoglobulin G (IgG) were found to be significantly higher (P < 0.05) in the PG and BF + P groups at day 100. The PG group exhibited the highest number of operational taxonomic unit (OTUs) and alpha diversity. Firmicutes, Bacteroidetes, and Verrucomicrobia were the predominant phyla in all the fecal samples. The relative abundance of Akkermansia muciniphila and Ruminococcus flavefaciens were found to be significantly higher (P < 0.05) in PG group and BF + P group at day 100, respectively, which might partially explain the significantly higher (P < 0.05) levels of IgA and IgG in these two groups. These findings suggested that BF supplemented with 5 g probiotics (Saccharomyces cerevisiae and mannan oligosaccharides) per day has the potential to enhance the growth and immunity of Black Fattening Goats.
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Affiliation(s)
- Quzhe Emu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Hao Guan
- Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, China
| | - Jiangjiang Zhu
- Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, China
| | - Lin Zhang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Jinsheng Fan
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Yang Ji
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Yaqiu Lin
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Chunmei Li
- Husbandry and Veterinary Technology Promotion Center of Fushun County, Zigong, China
| | - Xiaobo Dan
- Rongxian Agricultural Technology Extension Center, Zigong, China
| | - Yueda Aguo
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Xiaolan Wei
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Min Zhang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Bin Zhang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Chao Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Bo Li
- Rongxian Agricultural Technology Extension Center, Zigong, China
| | - Chaorui Xiong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
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Zhang R, Liu Y, Zhao X, Zhao Z, Zhang H, Huang X, Xu W, Shen Y, Lan W. High-throughput sequencing reveals the spatial distribution variability of microbial community in coastal waters in Shenzhen. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1429-1436. [PMID: 33755841 DOI: 10.1007/s10646-021-02391-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
Seashore habitats are located between terrestrial and marine ecosystems, which are a hotspot for anthropogenic impacts. Shenzhen is one of the most developed cities in south China, but the microbial functions of its coastal ecosystems remain poorly understood. The study applied 16S rRNA gene sequencing methods to identify the bacterial community from twenty sites of Shenzhen inshore waters. The microbial structure of the samples between eastern Shenzhen and western Shenzhen seashores is notably different, suggesting the spatial variability. Proteobacteria, Cyanobacteria, Actinobacteria, and Bacteroidetes were dominant phyla in the community, and the relative abundance of Bacteroidetes was significantly higher in eastern seashores. Specifically, samples from western Shenzhen contained much more Prochlorococcus, while Synechococcus was more abundant in eastern samples. Moreover, the metabolism of terpenoids and polyketides, and transport and catabolism were significantly more abundant in eastern samples, while antibiotic-resistant pathways were enriched in western samples. The results have important significance to understand bacterial ecosystem of coastal water and promote water quality management and protection activity in Shenzhen. This study can also help developing an optimal strategy for the green economy development and the policy planning of Guangdong-Hong Kong-Macao Greater Bay Area.
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Affiliation(s)
- Rui Zhang
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, Guangdong, PR China
- College of Food Science and Technology, Modern Biochemistry Experimental Center, Guangdong Ocean University, Zhanjiang, 518088, Guangdong, PR China
| | - Yu Liu
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, Guangdong, PR China
- College of Food Science and Technology, Modern Biochemistry Experimental Center, Guangdong Ocean University, Zhanjiang, 518088, Guangdong, PR China
| | - Xianfeng Zhao
- Shenzhen R&D Key Laboratory of Alien Pest Detection Technology, The Shenzhen Academy of Science and Technology for Inspection and Quarantine, Technology Center for Animal and Plant Inspection and Quarantine, Shenzhen Customs, Shenzhen, 518045, Guangdong, PR China
| | - Zhihui Zhao
- College of Agriculture, Guangdong Ocean University, Zhanjiang, 524088, Guangdong, PR China
| | - Honglian Zhang
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, Guangdong, PR China
- College of Food Science and Technology, Modern Biochemistry Experimental Center, Guangdong Ocean University, Zhanjiang, 518088, Guangdong, PR China
| | - Xiaoping Huang
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, Guangdong, PR China
- College of Food Science and Technology, Modern Biochemistry Experimental Center, Guangdong Ocean University, Zhanjiang, 518088, Guangdong, PR China
| | - Weiqing Xu
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, Guangdong, PR China
- College of Food Science and Technology, Modern Biochemistry Experimental Center, Guangdong Ocean University, Zhanjiang, 518088, Guangdong, PR China
| | - Yuchun Shen
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, Guangdong, PR China
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, Guangdong, PR China
| | - Wensheng Lan
- Shenzhen R&D Key Laboratory of Alien Pest Detection Technology, The Shenzhen Academy of Science and Technology for Inspection and Quarantine, Technology Center for Animal and Plant Inspection and Quarantine, Shenzhen Customs, Shenzhen, 518045, Guangdong, PR China.
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14
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Tyagi I, Tyagi K, Bhutiani R, Chandra K, Kumar V. Bacterial diversity assessment of world's largest sewage-fed fish farms with special reference to water quality: a Ramsar site. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:42372-42386. [PMID: 33813698 DOI: 10.1007/s11356-021-13756-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
Bacterial community structure is one of the essential components of aquaculture dynamics and plays an important role in maintaining wetland health. The present work is an effort to study the structure of bacterial communities in the world's largest sewage-fed fish farms, the East Kolkata Wetlands (EKWs), along with their predicted functional metabolic pathways and correlation with environmental variables. Sequencing data analysis revealed the abundance of genera such as Arcobacter (0-50%), Pseudomonas (0-15%), Sulfurospirillum (0-9%), Cloacibacterium (0-6%), hgcI clade (7-29%), C39 (0-9%), V6 (3-36%), Fluiivicola (1-6%) and Cyanobium (3-8%) in the EKWs. Further, water quality analysis of three treatment groups, i.e. Sewage, Sewage F-1 and Sewage F-2, revealed that dissolved oxygen (DO), biochemical oxygen demand (BOD) and chemical oxygen demand (COD) differed significantly and violated the standard prescribed norms (Central Pollution Control Board, CPCB, New Delhi) for fishery propagation and irrigation in India. Further, the correlation matrix analysis between the abundance of bacterial genera and environmental variables indicated that DO, BOD and COD were mainly responsible for bacterial community structure and their proliferation in the EKWs. Our results indicated that the abundance of genera such as Arcobacter, Pseudomonas, Sulfurospirillum and Cloacibacterium has an inverse relationship with BOD and COD. Our observations based on the bacterial community structure and deteriorated water quality indicate the ineffective functioning and poor management of this man-made constructed wetland.
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Affiliation(s)
- Inderjeet Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 700053, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 700053, India
| | - Rakesh Bhutiani
- Department of Environmental Sciences, Gurukul Kangri Vishwavidyalaya, Haridwar, 249404, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 700053, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 700053, India.
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15
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Piel T, Sandrini G, Muyzer G, Brussaard CPD, Slot PC, van Herk MJ, Huisman J, Visser PM. Resilience of Microbial Communities after Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms. Microorganisms 2021; 9:microorganisms9071495. [PMID: 34361929 PMCID: PMC8304526 DOI: 10.3390/microorganisms9071495] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 12/23/2022] Open
Abstract
Applying low concentrations of hydrogen peroxide (H2O2) to lakes is an emerging method to mitigate harmful cyanobacterial blooms. While cyanobacteria are very sensitive to H2O2, little is known about the impacts of these H2O2 treatments on other members of the microbial community. In this study, we investigated changes in microbial community composition during two lake treatments with low H2O2 concentrations (target: 2.5 mg L−1) and in two series of controlled lake incubations. The results show that the H2O2 treatments effectively suppressed the dominant cyanobacteria Aphanizomenon klebahnii, Dolichospermum sp. and, to a lesser extent, Planktothrix agardhii. Microbial community analysis revealed that several Proteobacteria (e.g., Alteromonadales, Pseudomonadales, Rhodobacterales) profited from the treatments, whereas some bacterial taxa declined (e.g., Verrucomicrobia). In particular, the taxa known to be resistant to oxidative stress (e.g., Rheinheimera) strongly increased in relative abundance during the first 24 h after H2O2 addition, but subsequently declined again. Alpha and beta diversity showed a temporary decline but recovered within a few days, demonstrating resilience of the microbial community. The predicted functionality of the microbial community revealed a temporary increase of anti-ROS defenses and glycoside hydrolases but otherwise remained stable throughout the treatments. We conclude that the use of low concentrations of H2O2 to suppress cyanobacterial blooms provides a short-term pulse disturbance but is not detrimental to lake microbial communities and their ecosystem functioning.
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Affiliation(s)
- Tim Piel
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
| | - Giovanni Sandrini
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
| | - Gerard Muyzer
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
| | - Corina P. D. Brussaard
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherland Institute for Sea Research, 1790 AB Den Burg, The Netherlands
| | - Pieter C. Slot
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
| | - Maria J. van Herk
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
| | - Jef Huisman
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
| | - Petra M. Visser
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; (T.P.); (G.S.); (G.M.); (C.P.D.B.); (P.C.S.); (M.J.v.H.); (J.H.)
- Correspondence: ; Tel.: +31-20-5257073
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16
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Cartozzo C, Singh B, Swall J, Simmons T. Postmortem submersion interval (PMSI) estimation from the microbiome of sus scrofa bone in a freshwater lake. J Forensic Sci 2021; 66:1334-1347. [PMID: 33818789 DOI: 10.1111/1556-4029.14692] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/13/2021] [Accepted: 02/01/2021] [Indexed: 01/22/2023]
Abstract
While many studies have developed microbial succession-based models for the prediction of postmortem interval (PMI) in terrestrial systems, similar well-replicated long-term decomposition studies are lacking for aquatic systems. Therefore, this study sought to identify temporal changes in bacterial community structure associated with porcine skeletal remains (n = 198) for an extended period in a fresh water lake. Every ca. 250 ADD, one cage, containing 5 ribs and 5 scapulae, was removed from the lake for a total of nineteen collections. Water was also sampled at each interval. Variable region 4 (V4) of 16S rDNA was amplified and sequenced for all collected samples using Illumina MiSeq FGx Sequencing platform; resulting data were analyzed with the mothur (v1.39.5) and R (v3.6.0). Bacterial communities associated with ribs differed significantly from those associated with scapulae. This difference was mainly attributed to Clostridia, Holophagae, and Spirochaete relative abundances. For each bone type, α-diversity increased with ADD; similarly, β-diversity bacterial community structure changed significantly with ADD and were explained using environmental parameters and inferred functional pathways. Models developed using 24 rib and 34 scapula family-level taxa allowed the prediction of PMSI with root mean square error of 522.97 ADD (~57 days) and 333.8 ADD (~37 days), respectively.
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Affiliation(s)
- Claire Cartozzo
- Integrative Life Sciences, Virginia Commonwealth University, Richmond, VA, USA.,Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Baneshwar Singh
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Jenise Swall
- Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, Richmond, VA, USA
| | - Tal Simmons
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
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17
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PhenoGMM: Gaussian Mixture Modeling of Cytometry Data Quantifies Changes in Microbial Community Structure. mSphere 2021; 6:6/1/e00530-20. [PMID: 33536320 PMCID: PMC7860985 DOI: 10.1128/msphere.00530-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Microorganisms are vital components in various ecosystems on Earth. In order to investigate the microbial diversity, researchers have largely relied on the analysis of 16S rRNA gene sequences from DNA. Microbial flow cytometry can rapidly characterize the status of microbial communities. Upon measurement, large amounts of quantitative single-cell data are generated, which need to be analyzed appropriately. Cytometric fingerprinting approaches are often used for this purpose. Traditional approaches either require a manual annotation of regions of interest, do not fully consider the multivariate characteristics of the data, or result in many community-describing variables. To address these shortcomings, we propose an automated model-based fingerprinting approach based on Gaussian mixture models, which we call PhenoGMM. The method successfully quantifies changes in microbial community structure based on flow cytometry data, which can be expressed in terms of cytometric diversity. We evaluate the performance of PhenoGMM using data sets from both synthetic and natural ecosystems and compare the method with a generic binning fingerprinting approach. PhenoGMM supports the rapid and quantitative screening of microbial community structure and dynamics. IMPORTANCE Microorganisms are vital components in various ecosystems on Earth. In order to investigate the microbial diversity, researchers have largely relied on the analysis of 16S rRNA gene sequences from DNA. Flow cytometry has been proposed as an alternative technology to characterize microbial community diversity and dynamics. The technology enables a fast measurement of optical properties of individual cells. So-called fingerprinting techniques are needed in order to describe microbial community diversity and dynamics based on flow cytometry data. In this work, we propose a more advanced fingerprinting strategy based on Gaussian mixture models. We evaluated our workflow on data sets from both synthetic and natural ecosystems, illustrating its general applicability for the analysis of microbial flow cytometry data. PhenoGMM supports a rapid and quantitative analysis of microbial community structure using flow cytometry.
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18
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Dickey JR, Fordyce JA, Lebeis SL. Bacterial communities of the Salvia lyrata rhizosphere explained by spatial structure and sampling grain. MICROBIAL ECOLOGY 2020; 80:846-858. [PMID: 32888042 DOI: 10.1007/s00248-020-01594-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
Advancements in molecular technology have reduced the constraints that the grain of observation, or the spatial resolution and volume of the sampling unit, has on the characterization of plant-associated microbiomes. With discrete ecological sampling and massive parallel sequencing, we can more precisely portray microbiome community assembly and microbial recruitment to host tissue over space and time. Here, we differentiate rarefied community richness and relative abundance in bacterial microbiomes of Salvia lyrata dependent on three spatial depths, which are discrete physical distances from the soil surface within the rhizosphere microhabitat as a proxy for the root system zones. To assess the impact of sampling grain on rarefied community richness and relative abundance, we evaluated the variation of these metrics between samples pooled prior to DNA extraction and samples pooled after sequencing. A distance-based redundancy analysis with the quantitative Jaccard distance revealed that rhizosphere microbiomes vary in richness between rhizosphere soil depths. At all orders of diversity, rarefied microbial richness was consistently lowest at the deepest samples taken (approximately 4 cm from soil surface) in comparison with other rhizosphere soil depths. We additionally show that finer grain sampling (i.e., three samples of equal volume pooled after sequencing) recovers greater microbial richness when using 16S rRNA gene sequencing to describe microbial communities found within the rhizosphere system. In summary, to further elucidate the extent host-specific microbiomes assemble within the rhizosphere, the grain at which bacterial communities are sampled should reflect and encompass fine-scale heterogeneity of the system.
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Affiliation(s)
- Jonathan R Dickey
- Department of Ecology and Evolutionary Biology, The University of Tennessee, 569 Dabney Hall, Knoxville, TN, 37996, USA.
| | - James A Fordyce
- Department of Ecology and Evolutionary Biology, The University of Tennessee, 569 Dabney Hall, Knoxville, TN, 37996, USA
| | - Sarah L Lebeis
- Department of Microbiology, The University of Tennessee, 307 Ken and Blaire Mossman Bldg., Knoxville, TN, 37996, USA
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19
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McDaniel EA, Peterson BD, Stevens SLR, Tran PQ, Anantharaman K, McMahon KD. Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms. mSystems 2020; 5:e00299-20. [PMID: 32817383 PMCID: PMC7438021 DOI: 10.1128/msystems.00299-20] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/29/2020] [Indexed: 11/23/2022] Open
Abstract
Methylmercury is a potent bioaccumulating neurotoxin that is produced by specific microorganisms that methylate inorganic mercury. Methylmercury production in diverse anaerobic bacteria and archaea was recently linked to the hgcAB genes. However, the full phylogenetic and metabolic diversity of mercury-methylating microorganisms has not been fully unraveled due to the limited number of cultured experimentally verified methylators and the limitations of primer-based molecular methods. Here, we describe the phylogenetic diversity and metabolic flexibility of putative mercury-methylating microorganisms by hgcAB identification in publicly available isolate genomes and metagenome-assembled genomes (MAGs) as well as novel freshwater MAGs. We demonstrate that putative mercury methylators are much more phylogenetically diverse than previously known and that hgcAB distribution among genomes is most likely due to several independent horizontal gene transfer events. The microorganisms we identified possess diverse metabolic capabilities spanning carbon fixation, sulfate reduction, nitrogen fixation, and metal resistance pathways. We identified 111 putative mercury methylators in a set of previously published permafrost metatranscriptomes and demonstrated that different methylating taxa may contribute to hgcA expression at different depths. Overall, we provide a framework for illuminating the microbial basis of mercury methylation using genome-resolved metagenomics and metatranscriptomics to identify putative methylators based upon hgcAB presence and describe their putative functions in the environment.IMPORTANCE Accurately assessing the production of bioaccumulative neurotoxic methylmercury by characterizing the phylogenetic diversity, metabolic functions, and activity of methylators in the environment is crucial for understanding constraints on the mercury cycle. Much of our understanding of methylmercury production is based on cultured anaerobic microorganisms within the Deltaproteobacteria, Firmicutes, and Euryarchaeota. Advances in next-generation sequencing technologies have enabled large-scale cultivation-independent surveys of diverse and poorly characterized microorganisms from numerous ecosystems. We used genome-resolved metagenomics and metatranscriptomics to highlight the vast phylogenetic and metabolic diversity of putative mercury methylators and their depth-discrete activities in thawing permafrost. This work underscores the importance of using genome-resolved metagenomics to survey specific putative methylating populations of a given mercury-impacted ecosystem.
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Affiliation(s)
- Elizabeth A McDaniel
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Benjamin D Peterson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Environmental Chemistry and Technology Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Sarah L R Stevens
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA
- American Family Insurance Data Science Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Patricia Q Tran
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
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20
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Aguilar P, Sommaruga R. The balance between deterministic and stochastic processes in structuring lake bacterioplankton community over time. Mol Ecol 2020; 29:3117-3130. [PMID: 32628343 PMCID: PMC7540538 DOI: 10.1111/mec.15538] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 06/21/2020] [Accepted: 06/23/2020] [Indexed: 01/04/2023]
Abstract
One major goal in microbial ecology is to establish the importance of deterministic and stochastic processes for community assembly. This is relevant to explain and predict how diversity changes at different temporal scales. However, understanding of the relative quantitative contribution of these processes and particularly of how they may change over time is limited. Here, we assessed the importance of deterministic and stochastic processes based on the analysis of the bacterial microbiome in one alpine oligotrophic and in one subalpine mesotrophic lake, which were sampled over two consecutive years at different time scales. We found that in both lakes, homogeneous selection (i.e., a deterministic process) was the main assembly process at the annual scale and explained 66.7% of the bacterial community turnover, despite differences in diversity and temporal variability patterns between ecosystems. However, in the alpine lake, homogenizing dispersal (i.e., a stochastic process) was the most important assembly process at the short‐term (daily and weekly) sampling scale and explained 55% of the community turnover. Alpha diversity differed between lakes, and seasonal stability of the bacterial community was more evident in the oligotrophic lake than in the mesotrophic one. Our results demonstrate how important forces that govern temporal changes in bacterial communities act at different time scales. Overall, our study validates on a quantitative basis, the importance and dominance of deterministic processes in structuring bacterial communities in freshwater environments over long time scales.
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Affiliation(s)
- Pablo Aguilar
- Lake and Glacier Ecology Research Group, Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Ruben Sommaruga
- Lake and Glacier Ecology Research Group, Department of Ecology, University of Innsbruck, Innsbruck, Austria
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21
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Soil Water Contents Control the Responses of Dissolved Nitrogen Pools and Bacterial Communities to Freeze-Thaw in Temperate Soils. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6867081. [PMID: 32258137 PMCID: PMC7086428 DOI: 10.1155/2020/6867081] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 01/30/2020] [Accepted: 02/26/2020] [Indexed: 11/18/2022]
Abstract
Background Freeze-thaw influences soil-dissolved nitrogen (N) pools due to variations in bacterial communities in temperate regions. The availability of soil water is important to soil biogeochemical cycles under frozen conditions. However, it is unclear how soil water content (SWC) mediates the effects of freeze-thaw on soil-dissolved N pools and bacterial communities. Method In this study, freeze-thaw microcosms were incubated at three levels of SWC, including 10% (air-dried soils), 15% (natural SWC), and 30% (wet soils). In addition to measuring soil-dissolved N pools, variations in bacterial communities were examined using high-throughput sequencing. Results and Conclusions. Total dissolved N (TDN), NO3 --N, NH4 +-N, microbial biomass N (MBN), and net N mineralization rate (NNMR) were significantly influenced by SWC, freeze-thaw, and their interaction (NH4 +-N excluded). N immobilization was inhibited under both low and high SWC, which was accompanied by varied bacterial community composition. However, only higher SWC substantially modified the freeze-thaw effects on the soil-dissolved N pools, characterized by a decrease in N mineralization (especially for the content of NO3 --N and NNMR) and an increase in N immobilization (MBN). These scenarios could be significantly correlated to variations in bacterial community composition based on redundancy analysis, especially by species belonging to Bacteroidetes, Nitrospirae, Alphaproteobacteria, Gemmatimonadetes, and Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.Bacteroidetes, Nitrospirae, Alphaproteobacteria, Gemmatimonadetes, and Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.Nitrospirae, Alphaproteobacteria, Gemmatimonadetes, and Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.Alphaproteobacteria, Gemmatimonadetes, and Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.Gemmatimonadetes, and Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.
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Abstract
A major goal in microbial ecology is to understand how microbial community structure influences ecosystem functioning. Various methods to directly associate bacterial taxa to functional groups in the environment are being developed. In this study, we applied machine learning methods to relate taxonomic data obtained from marker gene surveys to functional groups identified by flow cytometry. This allowed us to identify the taxa that are associated with heterotrophic productivity in freshwater lakes and indicated that the key contributors were highly system specific, regularly rare members of the community, and that some could possibly switch between being low and high contributors. Our approach provides a promising framework to identify taxa that contribute to ecosystem functioning and can be further developed to explore microbial contributions beyond heterotrophic production. High-nucleic-acid (HNA) and low-nucleic-acid (LNA) bacteria are two operational groups identified by flow cytometry (FCM) in aquatic systems. A number of reports have shown that HNA cell density correlates strongly with heterotrophic production, while LNA cell density does not. However, which taxa are specifically associated with these groups, and by extension, productivity has remained elusive. Here, we addressed this knowledge gap by using a machine learning-based variable selection approach that integrated FCM and 16S rRNA gene sequencing data collected from 14 freshwater lakes spanning a broad range in physicochemical conditions. There was a strong association between bacterial heterotrophic production and HNA absolute cell abundances (R2 = 0.65), but not with the more abundant LNA cells. This solidifies findings, mainly from marine systems, that HNA and LNA bacteria could be considered separate functional groups, the former contributing a disproportionately large share of carbon cycling. Taxa selected by the models could predict HNA and LNA absolute cell abundances at all taxonomic levels. Selected operational taxonomic units (OTUs) ranged from low to high relative abundance and were mostly lake system specific (89.5% to 99.2%). A subset of selected OTUs was associated with both LNA and HNA groups (12.5% to 33.3%), suggesting either phenotypic plasticity or within-OTU genetic and physiological heterogeneity. These findings may lead to the identification of system-specific putative ecological indicators for heterotrophic productivity. Generally, our approach allows for the association of OTUs with specific functional groups in diverse ecosystems in order to improve our understanding of (microbial) biodiversity-ecosystem functioning relationships. IMPORTANCE A major goal in microbial ecology is to understand how microbial community structure influences ecosystem functioning. Various methods to directly associate bacterial taxa to functional groups in the environment are being developed. In this study, we applied machine learning methods to relate taxonomic data obtained from marker gene surveys to functional groups identified by flow cytometry. This allowed us to identify the taxa that are associated with heterotrophic productivity in freshwater lakes and indicated that the key contributors were highly system specific, regularly rare members of the community, and that some could possibly switch between being low and high contributors. Our approach provides a promising framework to identify taxa that contribute to ecosystem functioning and can be further developed to explore microbial contributions beyond heterotrophic production.
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Zhao Y, Wang X, Liu C, Wang S, Wang X, Hou H, Wang J, Li H. Purification of harvested rainwater using slow sand filters with low-cost materials: Bacterial community structure and purifying effect. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 674:344-354. [PMID: 31005836 DOI: 10.1016/j.scitotenv.2019.03.474] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 03/30/2019] [Accepted: 03/30/2019] [Indexed: 06/09/2023]
Abstract
Slow sand filters (SSFs) have been shown to effectively improve water quality. The aim of the present study was to obtain low-cost materials (LCMs) as filter mediums (FMs) to efficiently purify harvested rainwater and to document the relationship between bacterial community structure and water purification. The red clay was mixed with crushed limestone and crushed brick, respectively. The mixtures or brick powder were used as the filter media for SSFs. Laboratory column tests were conducted in conjunction with the monitoring of representative water quality parameters (COD, NH4+, CFU and total coliforms) to estimate the performance of low-cost material slow sand filters (LCM-SSFs), including the time needed for biofilm maturation. The relationship between bacterial community structure and SSF performance was determined using a combination of 16S rRNA gene sequencing and an array of statistical techniques. The results demonstrated that LCM-SSFs perform well in purifying harvested rainwater, and are of superior economic benefit. LCMs had a stronger adsorptivity than quartz sand, which enhanced the purification of harvested rainwater before the biofilms matured, and shorten the time required for biofilm maturation. During the 90-day laboratory experiment, a mixture of crushed limestone and red clay exhibited the best performance. The abundance of Opitutae could be used as a potential indicator of NH4+ removal efficiency by SSFs. Schmutzdecke was characterized by abundant, diverse and evenly distributed bacterial communities that produced rich, stable and robust environmental functions, and that possessed an excellent purifying capacity. Environmental conditions associated with low ecological stress, such as neutral pH filter mediums and lucifugal experimental conditions, were conducive to the diversity and evenness of effluent bacterial communities and improved the performance of LCM-SSFs in purifying harvested rainwater.
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Affiliation(s)
- Yuewen Zhao
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, China
| | - Xiuyan Wang
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, China.
| | - Changli Liu
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, China
| | - Shuaiwei Wang
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, China
| | - Xihua Wang
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, China
| | - Hongbing Hou
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, China
| | - Jingjing Wang
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, China
| | - Hongzhao Li
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, China
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Fiedler CJ, Schönher C, Proksch P, Kerschbaumer DJ, Mayr E, Zunabovic-Pichler M, Domig KJ, Perfler R. Assessment of Microbial Community Dynamics in River Bank Filtrate Using High-Throughput Sequencing and Flow Cytometry. Front Microbiol 2018; 9:2887. [PMID: 30555435 PMCID: PMC6281747 DOI: 10.3389/fmicb.2018.02887] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/12/2018] [Indexed: 11/13/2022] Open
Abstract
Surface-groundwater interactions play an important role in microbial community compositions of river bank filtrates. Surface water contaminations deriving from environmental influences are attenuated by biogeochemical processes in the hyporheic zone, which are essential for providing clean and high-quality drinking water in abstraction wells. Characterizing the flow regime of surface water into the groundwater body can provide substantial information on water quality, but complex hydraulic dynamics make predictions difficult. Thus, a bottom up approach using microbial community shifting patterns as an overall outcome of dynamic water characteristics could provide more detailed information on the influences that affect groundwater quality. The combination of high-throughput sequencing data together with flow cytometric measurements of total cell counts reveals absolute abundances among taxa, thus enhancing interpretation of bacterial dynamics. 16S rRNA high-throughput sequencing of 55 samples among six wells in a well field in Austria that is influenced by river bank filtrate within a time period of 3 months has revealed both, clear differences as well as strong similarity in microbiome compositions between wells and dates. A significant community shift from April to May occurred in four of six wells, suggesting that surface water flow regimes do affect these wells stronger than others. Triplicate sampling and subsequent sequencing of wells at different dates proved the method to be reproducible. Flow cytometric measurements of total cells indicate microbial shifts due to increased cell counts and emphasize the rise of allochthonous microorganisms. Typical freshwater bacterial lineages (Verrucomicrobia, Bacteroidetes, Actinobacteria, Cyanobacteria, Armatimonadetes) were identified as most increasing phyla during community shifts. The changes are most likely a result of increased water abstraction in the wells together with constant river water levels rather than rain events. The results provide important knowledge for future implementations of well utilization in dependency of the nearby Danube River water levels and can help drawing conclusions about the influence of surface water in the groundwater such that hygienically save and clean drinking water with a stable microbial community can be provided.
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Affiliation(s)
- Christina J Fiedler
- Laboratory of Microbiology, Institute of Sanitary Engineering and Water Pollution Control (SIG), Department of Water, Atmosphere and Environment, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christoph Schönher
- Laboratory of Microbiology, Institute of Sanitary Engineering and Water Pollution Control (SIG), Department of Water, Atmosphere and Environment, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Philipp Proksch
- Laboratory of Microbiology, Institute of Sanitary Engineering and Water Pollution Control (SIG), Department of Water, Atmosphere and Environment, University of Natural Resources and Life Sciences, Vienna, Austria
| | - David Johannes Kerschbaumer
- Laboratory of Microbiology, Institute of Sanitary Engineering and Water Pollution Control (SIG), Department of Water, Atmosphere and Environment, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Ernest Mayr
- Laboratory of Microbiology, Institute of Sanitary Engineering and Water Pollution Control (SIG), Department of Water, Atmosphere and Environment, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Marija Zunabovic-Pichler
- Laboratory of Microbiology, Institute of Sanitary Engineering and Water Pollution Control (SIG), Department of Water, Atmosphere and Environment, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Konrad J Domig
- Laboratory of Food Microbiology and Hygiene, Institute of Food Science, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Reinhard Perfler
- Laboratory of Microbiology, Institute of Sanitary Engineering and Water Pollution Control (SIG), Department of Water, Atmosphere and Environment, University of Natural Resources and Life Sciences, Vienna, Austria
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Correction: Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats. PLoS One 2018; 13:e0206396. [PMID: 30346995 PMCID: PMC6197661 DOI: 10.1371/journal.pone.0206396] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0195112.].
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Pietrangelo L, Bucci A, Maiuro L, Bulgarelli D, Naclerio G. Unraveling the Composition of the Root-Associated Bacterial Microbiota of Phragmites australis and Typha latifolia. Front Microbiol 2018; 9:1650. [PMID: 30116224 PMCID: PMC6083059 DOI: 10.3389/fmicb.2018.01650] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 07/02/2018] [Indexed: 01/08/2023] Open
Abstract
Phragmites australis and Typha latifolia are two macrophytes commonly present in natural and artificial wetlands. Roots of these plants engage in interactions with a broad range of microorganisms, collectively referred to as the microbiota. The microbiota contributes to the natural process of phytodepuration, whereby pollutants are removed from contaminated water bodies through plants. The outermost layer of the root corpus, the rhizoplane, is a hot-spot for these interactions where microorganisms establish specialized aggregates designated biofilm. Earlier studies suggest that biofilm-forming members of the microbiota play a crucial role in the process of phytodepuration. However, the composition and recruitment cue of the Phragmites, and Typha microbiota remain poorly understood. We therefore decided to investigate the composition and functional capacities of the bacterial microbiota thriving at the P. australis and T. latifolia root–soil interface. By using 16S rRNA gene Illumina MiSeq sequencing approach we demonstrated that, despite a different composition of the initial basin inoculum, the microbiota associated with the rhizosphere and rhizoplane of P. australis and T. latifolia tends to converge toward a common taxonomic composition dominated by members of the phyla Actinobacteria, Firmicutes, Proteobacteria, and Planctomycetes. This indicates the existence of a selecting process acting at the root–soil interface of these aquatic plants reminiscent of the one observed for land plants. The magnitude of this selection process is maximum at the level of the rhizoplane, where we identified different bacteria enriched in and discriminating between rhizoplane and rhizosphere fractions in a species-dependent and -independent way. This led us to hypothesize that the structural diversification of the rhizoplane community underpins specific metabolic capabilities of the microbiota. We tested this hypothesis by complementing the sequencing survey with a biochemical approach and scanning electron microscopy demonstrating that rhizoplane-enriched bacteria have a bias for biofilm-forming members. Together, our data will be critical to facilitate the rational exploitation of plant–microbiota interactions for phytodepuration.
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Affiliation(s)
- Laura Pietrangelo
- Department of Biosciences and Territory, University of Molise, Campobasso, Italy.,Plant Sciences, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Antonio Bucci
- Department of Biosciences and Territory, University of Molise, Campobasso, Italy
| | - Lucia Maiuro
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Campobasso, Italy
| | - Davide Bulgarelli
- Plant Sciences, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Gino Naclerio
- Department of Biosciences and Territory, University of Molise, Campobasso, Italy
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