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Underwood JC, Hall NC, Mumford AC, Harvey RW, Bliznik PA, Jeanis KM. Relation between the relative abundance and collapse of Aphanizomenon flos-aquae and microbial antagonism in Upper Klamath Lake, Oregon. FEMS Microbiol Ecol 2024; 100:fiae043. [PMID: 38533659 PMCID: PMC11022654 DOI: 10.1093/femsec/fiae043] [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: 10/06/2023] [Revised: 03/04/2024] [Accepted: 03/25/2024] [Indexed: 03/28/2024] Open
Abstract
Aphanizomenon flos-aquae (AFA) is the dominant filamentous cyanobacterium that develops into blooms in Upper Klamath Lake, Oregon, each year. During AFA bloom and collapse, ecosystem conditions for endangered Lost River and shortnose suckers deteriorate, thus motivating the need to identify processes that limit AFA abundance and decline. Here, we investigate the relations between AFA and other members of the microbial community (photosynthetic and nonphotosynthetic bacteria and archaea), how those relations impact abundance and collapse of AFA, and the types of microbial conditions that suppress AFA. We found significant spatial variation in AFA relative abundance during the 2016 bloom period using 16S rRNA sequencing. The Pelican Marina site had the lowest AFA relative abundance, and this was coincident with increased relative abundance of Candidatus Sericytochromatia, Flavobacterium, and Rheinheimera, some of which are known AFA antagonists. The AFA collapse coincided with phosphorus limitation relative to nitrogen and the increased relative abundance of Cyanobium and Candidatus Sericytochromatia, which outcompete AFA when dissolved inorganic nitrogen is available. The data collected in this study indicate the importance of dissolved inorganic nitrogen combined with microbial community structure in suppressing AFA abundance.
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Affiliation(s)
- Jennifer C Underwood
- U.S. Geological Survey, Water Mission Area, 3215 Marine Street, Boulder, CO 80303, United States
| | - Natalie C Hall
- U.S. Geological Survey, Maryland–Delaware–D.C. Water Science Center, 5522 Research Park Dr, Catonsville, MD 21228, United States
| | - Adam C Mumford
- U.S. Geological Survey, Maryland–Delaware–D.C. Water Science Center, 5522 Research Park Dr, Catonsville, MD 21228, United States
| | - Ronald W Harvey
- U.S. Geological Survey, Water Mission Area, 3215 Marine Street, Boulder, CO 80303, United States
| | - Paul A Bliznik
- U.S. Geological Survey, Water Mission Area, 3215 Marine Street, Boulder, CO 80303, United States
| | - Kaitlyn M Jeanis
- U.S. Geological Survey, Water Mission Area, 3215 Marine Street, Boulder, CO 80303, United States
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Yan Y, Han IL, Lee J, Li G, Srinivasan V, McCullough K, Klaus S, Kang D, Wang D, He P, Patel A, Bott C, Gu AZ. Revisiting the role of Acinetobacter spp. in side-stream enhanced biological phosphorus removal (S2EBPR) systems. WATER RESEARCH 2024; 251:121089. [PMID: 38277823 DOI: 10.1016/j.watres.2023.121089] [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: 07/31/2023] [Revised: 12/02/2023] [Accepted: 12/28/2023] [Indexed: 01/28/2024]
Abstract
We piloted the incorporation of side-stream enhanced biological phosphorus removal (S2EBPR) with A/B stage short-cut nitrogen removal processes to enable simultaneous carbon-energy-efficient nutrients removal. This unique configuration and system conditions exerted selective force on microbial populations distinct from those in conventional EBPR. Interestingly, effective P removal was achieved with the predominance of Acinetobacter (21.5 ± 0.1 %) with nearly negligible level of known conical PAOs (Ca. Accumulibacter and Tetrasphaera were 0.04 ± 0.10 % and 0.47 ± 0.32 %, respectively). Using a combination of techniques, such as fluorescence in situ hybridization (FISH) coupled with single cell Raman spectroscopy (SCRS), the metabolic tracing of Acinetobacter-like cells exerted PAO-like phenotypic profiling. In addition, comparative metagenomics analysis of the closely related Acinetobacter spp. revealed the EBPR relevant metabolic pathways. Further oligotyping analysis of 16s rRNA V4 region revealed sub-clusters (microdiversity) of the Acinetobacter and revealed that the sub-group (oligo type 1, identical (100 % alignment identity) hits from Acinetobacter_midas_s_49494, and Acinetobacter_midas_s_55652) correlated with EBPR activities parameters, provided strong evidence that the identified Acinetobacter most likely contributed to the overall P removal in our A/B-shortcut N-S2EBPR system. To the best of our knowledge, this is the first study to confirm the in situ EBPR activity of Acinetobacter using combined genomics and SCRS Raman techniques. Further research is needed to identify the specific taxon, and phenotype of the Acinetobacter that are responsible for the P-removal.
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Affiliation(s)
- Yuan Yan
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14850, United States
| | - I L Han
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14850, United States
| | - Jangho Lee
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14850, United States
| | - Guangyu Li
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14850, United States
| | - Varun Srinivasan
- Department of Civil and Environmental Engineering, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, United States
| | - Kester McCullough
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14850, United States; Hampton Roads Sanitation District, Virginia Beach, VA, 23454, United States; modelEAU, Département de génie civil et de génie des eaux, Université Laval, 1065 av. de la Médecine, Québec, Canada
| | - Stephanie Klaus
- Hampton Roads Sanitation District, Virginia Beach, VA, 23454, United States
| | - Da Kang
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14850, United States; Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310029, China
| | - Dongqi Wang
- Department of Civil and Environmental Engineering, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, United States; Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Peisheng He
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14850, United States
| | - Anand Patel
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14850, United States
| | - Charles Bott
- Hampton Roads Sanitation District, Virginia Beach, VA, 23454, United States.
| | - April Z Gu
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14850, United States.
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Wu Y, Wang X, Wu W, Yang J. Mendelian randomization analysis reveals an independent causal relationship between four gut microbes and acne vulgaris. Front Microbiol 2024; 15:1326339. [PMID: 38371936 PMCID: PMC10869500 DOI: 10.3389/fmicb.2024.1326339] [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: 10/24/2023] [Accepted: 01/18/2024] [Indexed: 02/20/2024] Open
Abstract
Background Numerous studies have suggested a correlation between gut microbiota and acne vulgaris; however, no specific causal link has been explored. Materials and methods To investigate the possible causal relationship between gut microbiota and acne vulgaris, this study employed a large-scale genome-wide association study (GWAS) summary statistic. Initially, a two-sample Mendelian randomization (MR) analysis was utilized to identify the specific gut microflora responsible for acne vulgaris. We used the Inverse Variance Weighted (IVW) method as the main MR analysis method. Additionally, we assessed heterogeneity and horizontal pleiotropy, while also examining the potential influence of individual single-nucleotide polymorphisms (SNPs) on the analysis results. In order to eliminate gut microbiota with reverse causal associations, we conducted reverse MR analysis. Multivariate Mendelian randomization analysis (MVMR) was then employed to verify the independence of the causal associations. Finally, we performed SNP annotation on the instrumental variables of independent gut microbiota and acne vulgaris to determine the genes where these genetic variations are located. We also explored the biological functions of these genes through enrichment analysis. Result The IVW method of forward MR identified nine gut microbes with a causal relationship with acne vulgaris (p < 0.05). The findings from the sensitivity analysis demonstrate the absence of heterogeneity or horizontal pleiotropy, and leave-one-out analysis indicates that the results are not driven by a single SNP. Additionally, the Reverse MR analysis excluded two reverse-correlated pathogenic gut microbes. And then, MVMR was used to analyze seven gut microbes, and it was found that Cyanobacterium and Family XIII were risk factors for acne vulgaris, while Ruminococcus1 and Ruminiclostridium5 were protective factors for acne vulgaris. After conducting biological annotation, we identified six genes (PLA2G4A, FADS2, TIMP17, ADAMTS9, ZC3H3, and CPSF4L) that may be associated with the pathogenic gut microbiota of acne vulgaris patients. The enrichment analysis results indicate that PLA2G4A/FADS2 is associated with fatty acid metabolism pathways. Conclusion Our study found independent causal relationships between four gut microbes and acne vulgaris, and revealed a genetic association between acne vulgaris patients and gut microbiota. Consider preventing and treating acne vulgaris by interfering with the relative content of these four gut microbes.
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Affiliation(s)
- Yujia Wu
- School of Basic Medical Sciences, Dali University, Dali, China
| | - Xiaoyun Wang
- School of Basic Medical Sciences, Dali University, Dali, China
| | - Wenjuan Wu
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Jiankang Yang
- School of Basic Medical Sciences, Dali University, Dali, China
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Egbadon EO, Wigley K, Nwoba ST, Carere CR, Weaver L, Baronian K, Burbery L, Gostomski PA. Microaerobic methane-driven denitrification in a biotrickle bed - Investigating the active microbial biofilm community composition using RNA-stable isotope probing. CHEMOSPHERE 2024; 346:140528. [PMID: 37907168 DOI: 10.1016/j.chemosphere.2023.140528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 10/01/2023] [Accepted: 10/22/2023] [Indexed: 11/02/2023]
Abstract
A microaerobic (2% O2 v/v) biotrickle bed reactor supplied continuously with 2% methane to drive nitrate removal (MAME-D) was investigated using 16S rDNA and rRNA amplicon sequencing in combination with RNA-stable isotope probing (RNA-SIP) to identify the active microorganisms. Methane removal rates varied from 500 to 1000 mmol m-3h-1 and nitrate removal rates from 25 to 58 mmol m-3h-1 over 55 days of operation. Biofilm samples from the column were incubated in serum bottles supplemented with 13CH4. 16S rDNA analysis indicated a simple community structure in which four taxa accounted for 45% of the total relative abundance (RA). Dominant genera included the methanotroph Methylosinus and known denitrifiers Nubsella and Pseudoxanthomonas; along with a probable denitrifier assigned to the order Obscuribacterales. The 16S rRNA results revealed the methanotrophs Methylocystis (15% RA) and Methylosinus (10% RA) and the denitrifiers Arenimonas (10% RA) and Pseudoxanthomonas (7% RA) were the most active genera. Obscuribacterales was the most active taxa in the community at 22% RA. Activity was confirmed by the Δ buoyant density changes with time for the taxa, indicating most of the community activity was associated with methane oxidation and subsequent consumption of methanotrophic metabolic intermediates by the denitrifiers. This is the first report of RNA stable isotope probing within a microaerobic methane driven denitrification system and the active community was markedly different from the full community identified via 16S-rDNA analysis.
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Affiliation(s)
- Emmanuel O Egbadon
- Department of Chemical & Process Engineering, University of Canterbury, Christchurch, New Zealand
| | - Kathryn Wigley
- Department of Chemical & Process Engineering, University of Canterbury, Christchurch, New Zealand
| | - Sunday T Nwoba
- Department of Chemical & Process Engineering, University of Canterbury, Christchurch, New Zealand
| | - Carlo R Carere
- Department of Chemical & Process Engineering, University of Canterbury, Christchurch, New Zealand
| | - Louise Weaver
- Institute of Environmental Science and Research Ltd., Christchurch, New Zealand
| | - Kim Baronian
- Department of Chemical & Process Engineering, University of Canterbury, Christchurch, New Zealand
| | - Lee Burbery
- Institute of Environmental Science and Research Ltd., Christchurch, New Zealand
| | - Peter A Gostomski
- Department of Chemical & Process Engineering, University of Canterbury, Christchurch, New Zealand.
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Brescia F, Sillo F, Franchi E, Pietrini I, Montesano V, Marino G, Haworth M, Zampieri E, Fusini D, Schillaci M, Papa R, Santamarina C, Vita F, Chitarra W, Nerva L, Petruzzelli G, Mennone C, Centritto M, Balestrini R. The 'microbiome counterattack': Insights on the soil and root-associated microbiome in diverse chickpea and lentil genotypes after an erratic rainfall event. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:459-483. [PMID: 37226644 PMCID: PMC10667653 DOI: 10.1111/1758-2229.13167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 05/05/2023] [Indexed: 05/26/2023]
Abstract
Legumes maintain soil fertility thanks to their associated microbiota but are threatened by climate change that causes soil microbial community structural and functional modifications. The core microbiome associated with different chickpea and lentil genotypes was described after an unexpected climatic event. Results showed that chickpea and lentil bulk soil microbiomes varied significantly between two sampling time points, the first immediately after the rainfall and the second 2 weeks later. Rhizobia were associated with the soil of the more productive chickpea genotypes in terms of flower and fruit number. The root-associated bacteria and fungi were surveyed in lentil genotypes, considering that several parcels showed disease symptoms. The metabarcoding analysis revealed that reads related to fungal pathogens were significantly associated with one lentil genotype. A lentil core prokaryotic community common to all genotypes was identified as well as a genotype-specific one. A higher number of specific bacterial taxa and an enhanced tolerance to fungal diseases characterized a lentil landrace compared to the commercial varieties. This outcome supported the hypothesis that locally adapted landraces might have a high recruiting efficiency of beneficial soil microbes.
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Affiliation(s)
- Francesca Brescia
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Fabiano Sillo
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Elisabetta Franchi
- Eni S.p.A.R&D Environmental & Biological LaboratoriesSan Donato MilaneseItaly
| | - Ilaria Pietrini
- Eni S.p.A.R&D Environmental & Biological LaboratoriesSan Donato MilaneseItaly
| | - Vincenzo Montesano
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyBernalda (MT)Italy
| | - Giovanni Marino
- Institute for Sustainable Plant ProtectionNational Research Council of ItalySesto FiorentinoItaly
| | - Matthew Haworth
- Institute for Sustainable Plant ProtectionNational Research Council of ItalySesto FiorentinoItaly
| | - Elisa Zampieri
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Danilo Fusini
- Eni S.p.A.R&D Environmental & Biological LaboratoriesSan Donato MilaneseItaly
| | - Martino Schillaci
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Roberto Papa
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Chiara Santamarina
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Federico Vita
- Department of Bioscience, Biotechnology and EnvironmentUniversity of Bari Aldo MoroBariItaly
| | - Walter Chitarra
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and EconomicsConeglianoItaly
| | - Luca Nerva
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and EconomicsConeglianoItaly
| | | | - Carmelo Mennone
- Azienda Pantanello, ALSIA Research Center Metapontum AgrobiosBernalda (MT)Italy
| | - Mauro Centritto
- Institute for Sustainable Plant ProtectionNational Research Council of ItalySesto FiorentinoItaly
- ENI‐CNR Water Research Center ‘Hypatia of Alexandria’ALSIA Research Center Metapontum AgrobiosBernaldaItaly
| | - Raffaella Balestrini
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
- ENI‐CNR Water Research Center ‘Hypatia of Alexandria’ALSIA Research Center Metapontum AgrobiosBernaldaItaly
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Gogoleva N, Chervyatsova O, Balkin A, Kuzmina L, Shagimardanova E, Kiseleva D, Gogolev Y. Microbial tapestry of the Shulgan-Tash cave (Southern Ural, Russia): influences of environmental factors on the taxonomic composition of the cave biofilms. ENVIRONMENTAL MICROBIOME 2023; 18:82. [PMID: 37990336 PMCID: PMC10662634 DOI: 10.1186/s40793-023-00538-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/09/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND Cave biotopes are characterized by stable low temperatures, high humidity, and scarcity of organic substrates. Despite the harsh oligotrophic conditions, they are often inhabited by rich microbial communities. Abundant fouling with a wide range of morphology and coloration of colonies covers the walls of the Shulgan-Tash cave in the Southern Urals. This cave is also famous for the unique Paleolithic painting discovered in the middle of the last century. We aimed to investigate the diversity, distribution, and potential impact of these biofilms on the cave's Paleolithic paintings, while exploring how environmental factors influence the microbial communities within the cave. RESULTS The cave's biofilm morphotypes were categorized into three types based on the ultrastructural similarities. Molecular taxonomic analysis identified two main clusters of microbial communities, with Actinobacteria dominating in most of them and a unique "CaveCurd" community with Gammaproteobacteria prevalent in the deepest cave sections. The species composition of these biofilms reflects changes in environmental conditions, such as substrate composition, temperature, humidity, ventilation, and CO2 content. Additionally, it was observed that cave biofilms contribute to biocorrosion on cave wall surfaces. CONCLUSIONS The Shulgan-Tash cave presents an intriguing example of a stable extreme ecosystem with diverse microbiota. However, the intense dissolution and deposition of carbonates caused by Actinobacteria pose a potential threat to the preservation of the cave's ancient rock paintings.
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Affiliation(s)
- Natalia Gogoleva
- Research Department for Limnology, Mondsee, Universität Innsbruck, Mondsee, 5310, Austria.
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia.
| | | | - Alexander Balkin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Institute for Cellular and Intracellular Symbiosis, Ural Branch of the Russian Academy of Sciences, Orenburg, 460000, Russia
| | - Lyudmila Kuzmina
- Ufa Institute of Biology, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, 450054, Russia
| | - Elena Shagimardanova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Loginov Moscow Clinical Scientific Center, Moscow, 111123, Russia
| | - Daria Kiseleva
- Institute of Geology and Geochemistry, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, 620016, Russia
- Institute of Fundamental Education, Ural Federal University named after the first President of Russia B.N. Yeltsin, Ekaterinburg, 620002, Russia
| | - Yuri Gogolev
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", Kazan, 420111, Russia
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Wan R, Zha Y, Wu M, Li X, Yang H, Liu H. Long-term effective remediation of black-odorous water via regulating calcium nitrate sustained-release. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:1065. [PMID: 37598137 DOI: 10.1007/s10661-023-11659-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 08/01/2023] [Indexed: 08/21/2023]
Abstract
Nitrate addition is reported as a cost-effective method for remediating black-odorous water, which is mainly induced by the deficiency of electron acceptor. However, excessive release of nitrate and lack of long-term effectiveness significantly limited the application of direct nitrate dosing technology. Herein, for remediating black-odorous water, we constructed a nitrate sustained-release ecological concrete (ecoN-concrete), in which calcium nitrate (Ca(NO3)2) was dosed into concrete block to regulate the release of nitrate. The results showed that chemical oxygen demand (COD), turbidity, ammonia, phosphate, and sulfate were significantly removed in an ecoN-concrete-contained reactor fed with black-odorous water, and its removal efficiency was largely dependent on Ca(NO3)2 dosage. Meanwhile, the released nitrate was lower than 25% of its total dosage and nitrite was lower than 1.5 mg/L during 14 days remediation. After three recycles, the removal efficiencies of COD and turbidity by using ecoN-concrete were still more than 85%, indicating an excellent nitrate sustained-release performance of ecoN-concrete, which can be applied for preventing water re-blackening and re-stinking. Further investigation illustrated that the ecoN-concrete (1) decreased the abundance of Desulfovibrio, Desulfomonile, and Desulforhabdus in the phylum of Desulfobacterota to alleviate the odorous gas production and (2) significantly increased the abundance of Bacillus and Thermomonas, which utilized the released-nitrate for consuming organic matters and ammonia. This study provided an artful Ca(NO3)2 dosing strategy and long-term effective method for black-odorous water remediation.
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Affiliation(s)
- Rui Wan
- School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China.
| | - Yunyi Zha
- School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China
| | - Mengqi Wu
- School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China
| | - Xiaoxiao Li
- School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China
- College of Environment, Hohai University, Nanjing, 210098, China
| | - Haifeng Yang
- Donghu Innovation Center, Anhui Phoneya Environmental Technology Co. Ltd, Hefei, 230601, China
| | - Hongming Liu
- College of Life Sciences, Anhui Normal University, Wuhu, 241001, China
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Pessi IS, Popin RV, Durieu B, Lara Y, Tytgat B, Savaglia V, Roncero-Ramos B, Hultman J, Verleyen E, Vyverman W, Wilmotte A. Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics. Microb Genom 2023; 9:mgen001056. [PMID: 37417735 PMCID: PMC10438808 DOI: 10.1099/mgen.0.001056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023] Open
Abstract
Benthic microbial mats dominated by Cyanobacteria are important features of polar lakes. Although culture-independent studies have provided important insights into the diversity of polar Cyanobacteria, only a handful of genomes have been sequenced to date. Here, we applied a genome-resolved metagenomics approach to data obtained from Arctic, sub-Antarctic and Antarctic microbial mats. We recovered 37 metagenome-assembled genomes (MAGs) of Cyanobacteria representing 17 distinct species, most of which are only distantly related to genomes that have been sequenced so far. These include (i) lineages that are common in polar microbial mats such as the filamentous taxa Pseudanabaena, Leptolyngbya, Microcoleus/Tychonema and Phormidium; (ii) the less common taxa Crinalium and Chamaesiphon; (iii) an enigmatic Chroococcales lineage only distantly related to Microcystis; and (iv) an early branching lineage in the order Gloeobacterales that is distributed across the cold biosphere, for which we propose the name Candidatus Sivonenia alaskensis. Our results show that genome-resolved metagenomics is a powerful tool for expanding our understanding of the diversity of Cyanobacteria, especially in understudied remote and extreme environments.
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Affiliation(s)
- Igor S. Pessi
- Department of Microbiology, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Sustainability Science (HELSUS), Helsinki, Finland
| | - Rafael V. Popin
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Benoit Durieu
- InBioS – Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Yannick Lara
- Early Life Traces & Evolution-Astrobiology, UR-Astrobiology, University of Liège, Liège, Belgium
| | - Bjorn Tytgat
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Valentina Savaglia
- InBioS – Centre for Protein Engineering, University of Liège, Liège, Belgium
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Beatriz Roncero-Ramos
- InBioS – Centre for Protein Engineering, University of Liège, Liège, Belgium
- Department of Plant Biology and Ecology, University of Sevilla, Sevilla, Spain
| | - Jenni Hultman
- Department of Microbiology, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Sustainability Science (HELSUS), Helsinki, Finland
- Natural Resources Institute Finland (LUKE), Helsinki, Finland
| | - Elie Verleyen
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Wim Vyverman
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Annick Wilmotte
- InBioS – Centre for Protein Engineering, University of Liège, Liège, Belgium
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Kamada S, Wakabayashi R, Naganuma T. Phylogenetic Revisit to a Review on Predatory Bacteria. Microorganisms 2023; 11:1673. [PMID: 37512846 PMCID: PMC10385382 DOI: 10.3390/microorganisms11071673] [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: 05/29/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Predatory bacteria, along with the biology of their predatory behavior, have attracted interest in terms of their ecological significance and industrial applications, a trend that has been even more pronounced since the comprehensive review in 2016. This mini-review does not cover research trends, such as the role of outer membrane vesicles in myxobacterial predation, but provides an overview of the classification and newly described taxa of predatory bacteria since 2016, particularly with regard to phylogenetic aspects. Among them, it is noteworthy that in 2020 there was a major phylogenetic reorganization that the taxa hosting Bdellovibrio and Myxococcus, formerly classified as Deltaproteobacteria, were proposed as the new phyla Bdellovibrionota and Myxococcota, respectively. Predatory bacteria have been reported from other phyla, especially from the candidate divisions. Predatory bacteria that prey on cyanobacteria and predatory cyanobacteria that prey on Chlorella have also been found. These are also covered in this mini-review, and trans-phylum phylogenetic trees are presented.
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Affiliation(s)
- Saki Kamada
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan
| | - Ryoka Wakabayashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan
| | - Takeshi Naganuma
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan
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Stevenson DS. A New Ecological and Evolutionary Perspective on the Emergence of Oxygenic Photosynthesis. ASTROBIOLOGY 2023; 23:230-237. [PMID: 36413050 DOI: 10.1089/ast.2021.0165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In this hypothesis article, we propose that the timing of the evolution of oxygenic photosynthesis and the diversification of cyanobacteria is firmly tied to the geological evolution of Earth in the Mesoarchean to Neoarchean. Specifically, the diversification of species capable of oxygenic photosynthesis is tied to the growth of subaerial (above sea-level/terrestrial) continental crust, which provided niches for their diversification. Moreover, we suggest that some formerly aerobic bacterial lineages evolved to become anoxygenic photosynthetic as a result of changes in selection following the reintroduction of ferruginous conditions in the oceans at 1.88 GYa. Both conclusions are fully compatible with phylogenetic evidence. The hypothesis carries with it a predictive component-at least for terrestrial organisms-that the development and expansion of photosynthesis species was dependent on the geological evolution of Earth.
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Eisenhofer R, Brice KL, Blyton MDJ, Bevins SE, Leigh K, Singh BK, Helgen KM, Hough I, Daniels CB, Speight N, Moore BD. Individuality and stability of the koala ( Phascolarctos cinereus) faecal microbiota through time. PeerJ 2023; 11:e14598. [PMID: 36710873 PMCID: PMC9879153 DOI: 10.7717/peerj.14598] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/29/2022] [Indexed: 01/24/2023] Open
Abstract
Gut microbiota studies often rely on a single sample taken per individual, representing a snapshot in time. However, we know that gut microbiota composition in many animals exhibits intra-individual variation over the course of days to months. Such temporal variations can be a confounding factor in studies seeking to compare the gut microbiota of different wild populations, or to assess the impact of medical/veterinary interventions. To date, little is known about the variability of the koala (Phascolarctos cinereus) gut microbiota through time. Here, we characterise the gut microbiota from faecal samples collected at eight timepoints over a month for a captive population of South Australian koalas (n individuals = 7), and monthly over 7 months for a wild population of New South Wales koalas (n individuals = 5). Using 16S rRNA gene sequencing, we found that microbial diversity was stable over the course of days to months. Each koala had a distinct faecal microbiota composition which in the captive koalas was stable across days. The wild koalas showed more variation across months, although each individual still maintained a distinct microbial composition. Per koala, an average of 57 (±16) amplicon sequence variants (ASVs) were detected across all time points; these ASVs accounted for an average of 97% (±1.9%) of the faecal microbial community per koala. The koala faecal microbiota exhibits stability over the course of days to months. Such knowledge will be useful for future studies comparing koala populations and developing microbiota interventions for this regionally endangered marsupial.
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Affiliation(s)
- Raphael Eisenhofer
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia, Australia
| | - Kylie L. Brice
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Michaela DJ Blyton
- School of Chemistry and Molecular Biosciences, Faculty of Science, University of Queensland, Brisbane, Queensland, Australia
| | - Scott E. Bevins
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Kellie Leigh
- Science for Wildlife Ltd, Sydney, New South Wales, Australia
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia,Global Centre for Land Based Innovation, Western Sydney University, Penrith, New South Wales, Australia
| | - Kristofer M. Helgen
- Australian Museum Research Institute, Sydney, New South Wales, Australia,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of New South Wales, Sydney, New South Wales, Australia,Koala Life Foundation, Cleland Wildlife Park, Department for Environment and Water, 365c Mt Lofty Summit Road, Adelaide, South Australia, Australia
| | - Ian Hough
- Koala Life Foundation, Cleland Wildlife Park, Department for Environment and Water, 365c Mt Lofty Summit Road, Adelaide, South Australia, Australia
| | - Christopher B. Daniels
- Koala Life Foundation, Cleland Wildlife Park, Department for Environment and Water, 365c Mt Lofty Summit Road, Adelaide, South Australia, Australia
| | - Natasha Speight
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Ben D. Moore
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
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Chuvochina M, Mussig AJ, Chaumeil PA, Skarshewski A, Rinke C, Parks DH, Hugenholtz P. Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes. FEMS Microbiol Lett 2023; 370:fnad071. [PMID: 37480240 PMCID: PMC10408702 DOI: 10.1093/femsle/fnad071] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/13/2023] [Accepted: 07/20/2023] [Indexed: 07/23/2023] Open
Abstract
The Genome Taxonomy Database (GTDB) is a taxonomic framework that defines prokaryotic taxa as monophyletic groups in concatenated protein reference trees according to systematic criteria. This has resulted in a substantial number of changes to existing classifications (https://gtdb.ecogenomic.org). In the case of union of taxa, GTDB names were applied based on the priority of publication. The division of taxa or change in rank led to the formation of new Latin names above the rank of genus that were only made publicly available via the GTDB website without associated published taxonomic descriptions. This has sometimes led to confusion in the literature and databases. A number of the provisional GTDB names were later published in other studies, while many still lack authorships. To reduce further confusion, here we propose names and descriptions for 329 GTDB-defined prokaryotic taxa, 223 of which are suitable for validation under the International Code of Nomenclature of Prokaryotes (ICNP) and 49 under the Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode). For the latter, we designated 23 genomes as type material. An additional 57 taxa that do not currently satisfy the validation criteria of either code are proposed as Candidatus.
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Affiliation(s)
- Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics,, St Lucia QLD 4072, Brisbane, Australia
| | - Aaron J Mussig
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics,, St Lucia QLD 4072, Brisbane, Australia
| | - Pierre-Alain Chaumeil
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics,, St Lucia QLD 4072, Brisbane, Australia
| | - Adam Skarshewski
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics,, St Lucia QLD 4072, Brisbane, Australia
| | - Christian Rinke
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics,, St Lucia QLD 4072, Brisbane, Australia
| | - Donovan H Parks
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics,, St Lucia QLD 4072, Brisbane, Australia
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics,, St Lucia QLD 4072, Brisbane, Australia
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Sandzewicz M, Khomutovska N, Łach Ł, Kwiatowski J, Niyatbekov T, Suska-Malawska M, Jasser I. Salinity matters the most: How environmental factors shape the diversity and structure of cyanobacterial mat communities in high altitude arid ecosystems. Front Microbiol 2023; 14:1108694. [PMID: 37125173 PMCID: PMC10136773 DOI: 10.3389/fmicb.2023.1108694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 03/20/2023] [Indexed: 05/02/2023] Open
Abstract
Introduction Microbial mats are complex communities of benthic microorganisms that occur at the soil-water interphase in lakes' shores, streams, and ponds. In the cold, mountainous desert of Eastern Pamir (Tajikistan), where scarce water bodies are influenced by extreme environmental conditions, photosynthetic cyanobacteria form diverse mats. The mats are characterized by different morphology and thickness. Their habitats exhibit a wide range of conditions; from oligosaline to hypersaline, oligotrophic to hypertrophic, and from cold ponds to hot springs. The aim of the present study was to reveal the taxonomic composition and structure of these mats and to examine which environmental factors influence them. Methods Fifty-one mats were collected from small water bodies around Bulunkul, Karakul, and Rangkul Lakes in 2015 and 2017. The physical and chemical properties of the water were measured in situ, while the concentration of nutrients was analyzed ex-situ. To reveal the taxonomic composition of the mats, the hypervariable V3-V4 region of the 16S rRNA gene was examined using NGS technology. Results The results of bioinformatic analyses were compared with microscopic observations. They showed that Cyanobacteria was the dominant phylum, constituting on average 35% of bacterial ASVs, followed by Proteobacteria (28%), Bacteroidota (11%), and Firmicutes (9%). Synechococcales, Oscillatoriales, and Nostocales orders prevailed in Oxyphotobacteria, with a low contribution of Chroococcales, Gloeobacterales, and Chroococcidiopsidales. Occasionally the non-photosynthetic Vampirivibrionia (Melainabacteria) and Sericytochromatia from sister clades to Oxyphotobacteria were noted in the samples. Moreover, there was a high percentage of unidentified cyanobacterial sequences, as well as the recently described Hillbrichtia pamiria gen. et sp. nov., present in one of the samples. Salinity, followed by Na and K concentrations, correlated positively with the composition and structure of Oxyphotobacteria on different taxonomic levels and the abundance of all bacterial ASVs. Discussion The study suggests that the investigated communities possibly host more novel and endemic species. Among the environmental factors, salinity influenced the Oxyphotobacteria communities the most. Overall, the microenvironmental factors, i.e. the conditions in each of the reservoirs seemed to have a larger impact on the diversity of microbial mats in Pamir than the "subregional" factors, related to altitude, mean annual air temperature and distance between these subregions.
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Affiliation(s)
- Małgorzata Sandzewicz
- Institute of Environmental Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Nataliia Khomutovska
- Institute of Environmental Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Łukasz Łach
- Institute of Environmental Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Jan Kwiatowski
- Institute of Environmental Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Toirbek Niyatbekov
- Institute of Botany, Plant Physiology and Genetics, Academy Science Republic of Tajikistan, Dushanbe, Tajikistan
| | - Małgorzata Suska-Malawska
- Institute of Environmental Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Iwona Jasser
- Institute of Environmental Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
- *Correspondence: Iwona Jasser,
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Procter M, Kundu B, Sudalaimuthuasari N, AlMaskari RS, Saeed EE, Hazzouri KM, Amiri KMA. Microbiome of Citrullus colocynthis (L.) Schrad. Reveals a Potential Association with Non-Photosynthetic Cyanobacteria. Microorganisms 2022; 10:microorganisms10102083. [PMID: 36296358 PMCID: PMC9607294 DOI: 10.3390/microorganisms10102083] [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: 09/22/2022] [Revised: 10/13/2022] [Accepted: 10/18/2022] [Indexed: 01/24/2023] Open
Abstract
Citrullus colocynthis grows in the sandy desert soil of the Arabian Peninsula with limited access to water, aside from occasional precipitation or dew. Understanding its ability to produce water-filled fruit and nutrient-rich seeds despite the harsh environment, can be useful for agricultural applications. However, information regarding the microbiome of C. colocynthis is lacking. We hypothesized that C. colocynthis associates with bacteria that aid its survival, like what has been observed in other desert plants. Here, we used 16S rRNA gene data to gain insight into the microbiome of C. colocynthis to identify its associated bacteria. In total, 9818 and 6983 OTUs were generated from root, soil, and leaf samples combined. Overall, bulk soils had the highest alpha diversity, followed by rhizosphere and root zone soils. Furthermore, C. colocynthis is associated with known plant-growth-promoting bacteria (including Acidobacteria, Bacterioidetes, and Actinobacteria), and interestingly a class of non-photosynthetic Cyanobacteria (Melainabacteria) that is more abundant on the inside and outside of the root surface than control samples, suggesting its involvement in the rhizophagy process. This study will provide a foundation for functional studies to further understand how C. colocynthis-microbes interactions help them grow in the desert, paving the path for possible agricultural applications.
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Affiliation(s)
- Miranda Procter
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
| | - Biduth Kundu
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
| | - Naganeeswaran Sudalaimuthuasari
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
| | - Raja S. AlMaskari
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
| | - Esam E. Saeed
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
| | - Khaled M. Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
- Correspondence: (K.M.H.); (K.M.A.A.)
| | - Khaled M. A. Amiri
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
- Correspondence: (K.M.H.); (K.M.A.A.)
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Salmaso N, Vasselon V, Rimet F, Vautier M, Elersek T, Boscaini A, Donati C, Moretto M, Pindo M, Riccioni G, Stefani E, Capelli C, Lepori F, Kurmayer R, Mischke U, Klemenčič AK, Novak K, Greco C, Franzini G, Fusato G, Giacomazzi F, Lea A, Menegon S, Zampieri C, Macor A, Virgilio D, Zanut E, Zorza R, Buzzi F, Domaizon I. DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 834:155175. [PMID: 35421505 DOI: 10.1016/j.scitotenv.2022.155175] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
The taxonomic identification of organisms based on the amplification of specific genetic markers (metabarcoding) implicitly requires adequate discriminatory information and taxonomic coverage of environmental DNA sequences in taxonomic databases. These requirements were quantitatively examined by comparing the determination of cyanobacteria and microalgae obtained by metabarcoding and light microscopy. We used planktic and biofilm samples collected in 37 lakes and 22 rivers across the Alpine region. We focused on two of the most used and best represented genetic markers in the reference databases, namely the 16S rRNA and 18S rRNA genes. A sequence gap analysis using blastn showed that, in the identity range of 99-100%, approximately 30% (plankton) and 60% (biofilm) of the sequences did not find any close counterpart in the reference databases (NCBI GenBank). Similarly, a taxonomic gap analysis showed that approximately 50% of the cyanobacterial and eukaryotic microalgal species identified by light microscopy were not represented in the reference databases. In both cases, the magnitude of the gaps differed between the major taxonomic groups. Even considering the species determined under the microscope and represented in the reference databases, 22% and 26% were still not included in the results obtained by the blastn at percentage levels of identity ≥95% and ≥97%, respectively. The main causes were the absence of matching sequences due to amplification and/or sequencing failure and potential misidentification in the microscopy step. Our results quantitatively demonstrated that in metabarcoding the main obstacles in the classification of 16S rRNA and 18S rRNA sequences and interpretation of high-throughput sequencing biomonitoring data were due to the existence of important gaps in the taxonomic completeness of the reference databases and the short length of reads. The study focused on the Alpine region, but the extent of the gaps could be much greater in other less investigated geographic areas.
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Affiliation(s)
- Nico Salmaso
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy.
| | - Valentin Vasselon
- OFB, Pôle R&D ECLA, Site INRAE CARRTEL, 75bis av. de Corzent - CS 50511, FR-74203 Thonon les Bains cedex, France.
| | - Frédéric Rimet
- INRAE, UMR Carrtel, Université Savoie Mont Blanc, Pole R&D ECLA, 75bis av. de Corzent - CS 50511, FR-74203 Thonon les Bains cedex, France.
| | - Marine Vautier
- INRAE, UMR Carrtel, Université Savoie Mont Blanc, Pole R&D ECLA, 75bis av. de Corzent - CS 50511, FR-74203 Thonon les Bains cedex, France.
| | - Tina Elersek
- National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia.
| | - Adriano Boscaini
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy.
| | - Claudio Donati
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy.
| | - Marco Moretto
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy.
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy.
| | - Giulia Riccioni
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy
| | - Erika Stefani
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy.
| | - Camilla Capelli
- Institute of Earth Sciences, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Via Flora Ruchat-Roncati 15, 6850 Mendrisio, Switzerland.
| | - Fabio Lepori
- Institute of Earth Sciences, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Via Flora Ruchat-Roncati 15, 6850 Mendrisio, Switzerland.
| | - Rainer Kurmayer
- Research Department for Limnology, University of Innsbruck, Mondseestraße 9, 5310 Mondsee, Austria.
| | - Ute Mischke
- Bavarian Environment Agency, Ref. 83, Wielenbach, Germany.
| | | | - Katarina Novak
- Slovenian Environment Agency, Vojkova 1b, 1000 Ljubljana, Slovenia.
| | - Claudia Greco
- Italian National Institute for Environmental Protection and Research (ISPRA), Ozzano, Italy.
| | - Giorgio Franzini
- ARPAV, Regional Agency for Environmental Protection and Prevention of Veneto, Via A. Dominutti 8, 37135 Verona, Italy.
| | - Giampaolo Fusato
- ARPAV, Regional Agency for Environmental Protection and Prevention of Veneto, Via A. Dominutti 8, 37135 Verona, Italy.
| | - Federica Giacomazzi
- ARPAV, Regional Agency for Environmental Protection and Prevention of Veneto, Via A. Dominutti 8, 37135 Verona, Italy.
| | - Alessia Lea
- ARPAV, Regional Agency for Environmental Protection and Prevention of Veneto, Via Ospedale Civile 24, 35121 Padova, Italy.
| | - Silvia Menegon
- ARPAV, Regional Agency for Environmental Protection and Prevention of Veneto, Via Santa Barbara 5/a, 31100 Treviso, Italy.
| | - Chiara Zampieri
- ARPAV, Regional Agency for Environmental Protection and Prevention of Veneto, Via A. Dominutti 8, 37135 Verona, Italy.
| | - Arianna Macor
- ARPA FVG, Regional Environmental Protection Agency of Friuli Venezia Giulia, Via Cairoli 14, 33057 Palmanova, UD, Italy.
| | - Damiano Virgilio
- ARPA FVG, Regional Environmental Protection Agency of Friuli Venezia Giulia, Via Cairoli 14, 33057 Palmanova, UD, Italy.
| | - Elisa Zanut
- ARPA FVG, Regional Environmental Protection Agency of Friuli Venezia Giulia, Via Cairoli 14, 33057 Palmanova, UD, Italy.
| | - Raffaella Zorza
- ARPA FVG, Regional Environmental Protection Agency of Friuli Venezia Giulia, Via Cairoli 14, 33057 Palmanova, UD, Italy.
| | - Fabio Buzzi
- ARPA Lombardia, Sede di Lecco, U.O. Laghi e Monitoraggio Biologico Fiumi, Italy.
| | - Isabelle Domaizon
- INRAE, UMR Carrtel, Université Savoie Mont Blanc, Pole R&D ECLA, 75bis av. de Corzent - CS 50511, FR-74203 Thonon les Bains cedex, France.
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Non-Proteinogenic Amino Acid β-N-Methylamino-L-Alanine (BMAA): Bioactivity and Ecological Significance. Toxins (Basel) 2022; 14:toxins14080539. [PMID: 36006201 PMCID: PMC9414260 DOI: 10.3390/toxins14080539] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/28/2022] [Accepted: 08/04/2022] [Indexed: 11/21/2022] Open
Abstract
Research interest in a non-protein amino acid β-N-methylamino-L-alanine (BMAA) arose due to the discovery of a connection between exposure to BMAA and the occurrence of neurodegenerative diseases. Previous reviews on this topic either considered BMAA as a risk factor for neurodegenerative diseases or focused on the problems of detecting BMAA in various environmental samples. Our review is devoted to a wide range of fundamental biological problems related to BMAA, including the molecular mechanisms of biological activity of BMAA and the complex relationships between producers of BMAA and the environment in various natural ecosystems. At the beginning, we briefly recall the most important facts about the producers of BMAA (cyanobacteria, microalgae, and bacteria), the pathways of BMAA biosynthesis, and reliable methods of identification of BMAA. The main distinctive feature of our review is a detailed examination of the molecular mechanisms underlying the toxicity of BMAA to living cells. A brand new aspect, not previously discussed in any reviews, is the effect of BMAA on cyanobacterial cells. These recent studies, conducted using transcriptomics and proteomics, revealed potent regulatory effects of BMAA on the basic metabolism and cell development of these ancient photoautotrophic prokaryotes. Exogenous BMAA strongly influences cell differentiation and primary metabolic processes in cyanobacteria, such as nitrogen fixation, photosynthesis, carbon fixation, and various biosynthetic processes involving 2-oxoglutarate and glutamate. Cyanobacteria were found to be more sensitive to exogenous BMAA under nitrogen-limited growth conditions. We suggest a hypothesis that this toxic diaminoacid can be used by phytoplankton organisms as a possible allelopathic tool for controlling the population of cyanobacterial cells during a period of intense competition for nitrogen and other resources in various ecosystems.
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Hu Y, Jin X, Gao F, Lin T, Zhu H, Hou X, Yin Y, Kan S, Chen D. Selenium-enriched Bifidobacterium longum DD98 effectively ameliorates dextran sulfate sodium-induced ulcerative colitis in mice. Front Microbiol 2022; 13:955112. [PMID: 35992694 PMCID: PMC9389208 DOI: 10.3389/fmicb.2022.955112] [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: 05/28/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
The pathogenesis of ulcerative colitis (UC) is complicated with impaired intestinal epithelial barrier and imbalanced gut microbiota. Both selenium and probiotics have shown effects in regulating intestinal flora and ameliorating UC. The objective of this study is to investigate the alleviating effects of Selenium-enriched Bifidobacterium longum DD98 (Se-B. longum DD98) on dextran sulfate sodium (DSS)-induced colitis in mice and explore the underlying mechanism. After treatment of B. longum DD98, Se-B. longum DD98, and sulfasalazine for 3 weeks, the disease severity of UC mice was decreased, with colon lengthened and pathological phenotype improved. The expression of pro-inflammatory cytokines and oxidative stress parameters were also decreased. Thus, Se-B. longum DD98 showed a stronger effect on relieving the aforementioned symptoms caused by DSS-induced colitis. Exploration of the potential mechanism demonstrated that Se-B. longum DD98 showed higher activities to suppress the inflammatory response by inhibiting the activation of the toll-like receptor 4 (TLR4), compared to B. longum DD98 and sulfasalazine. Se-B. longum DD98 also significantly improved the intestinal barrier integrity by increasing the expression of tight junction proteins including ZO-1 and occludin. 16S rDNA sequencing analyses showed that Se-B. longum DD98 improved the diversity of the intestinal flora and promoted the abundance of health-benefiting taxa including Lachnospiraceae, Lactobacillaceae, and Prevotellaceae in family level. In conclusion, compared to B. longum DD98 and sulfasalazine, Se-B. longum DD98 showed stronger therapeutic effects on DSS-induced colitis in mice and might be a promising candidate for the treatment of UC.
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Affiliation(s)
- Yongjia Hu
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Xueli Jin
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Fei Gao
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Lin
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Hui Zhu
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao Hou
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Yin
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Shidong Kan
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Daijie Chen
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Daijie Chen,
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Picard M, Pochon X, Atalah J, Pearman JK, Rees A, Howarth JD, Moy CM, Vandergoes MJ, Hawes I, Khan S, Wood SA. Using metabarcoding and droplet digital PCR to investigate drivers of historical shifts in cyanobacteria from six contrasting lakes. Sci Rep 2022; 12:12810. [PMID: 35896561 PMCID: PMC9329365 DOI: 10.1038/s41598-022-14216-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 06/02/2022] [Indexed: 11/16/2022] Open
Abstract
The frequency and intensity of cyanobacterial blooms is increasing worldwide. Multiple factors are implicated, most of which are anthropogenic. New Zealand provides a useful location to study the impacts of human settlement on lake ecosystems. The first humans (Polynesians) arrived about 750 years ago. Following their settlement, there were marked landscape modifications which intensified after European settlement about 150 years ago. The aims of this study were to reconstruct cyanobacterial communities in six lakes over the last 1000 years and explore key drivers of change. Cyanobacterial environmental DNA was extracted from sediment cores and analysed using metabarcoding and droplet digital PCR. Cyanobacteria, including potentially toxic or bloom forming species, were already present in these lakes prior to human arrival, however their overall abundance was low. Total cyanobacteria abundance and richness increased in all lakes after European settlement but was very pronounced in four lakes, where bloom-forming taxa became dominant. These shifts occurred concomitant with land-use change. The catchment of one deteriorated lake is only moderately modified, thus the introduction of non-native fish is posited as the key factor driving this change. The paleolimnological approach used in this study has enabled new insights into timing and potential causes of changes in cyanobacterial communities.
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Affiliation(s)
- Maïlys Picard
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand. .,Department of Biological Sciences, School of Biological Sciences, University of Waikato, Hamilton, 3216, New Zealand.
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand.,Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth, 0941, New Zealand
| | - Javier Atalah
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand
| | - John K Pearman
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand
| | - Andrew Rees
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Jamie D Howarth
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Christopher M Moy
- Department of Zoology, University of Otago, 340 Great King Street, North Dunedin, Dunedin, 9016, New Zealand
| | | | - Ian Hawes
- Department of Biological Sciences, School of Biological Sciences, University of Waikato, Hamilton, 3216, New Zealand
| | - Samiullah Khan
- Department of Zoology, University of Otago, 340 Great King Street, North Dunedin, Dunedin, 9016, New Zealand
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand
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19
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Gutiérrez CF, Rodríguez-Romero N, Egan S, Holmes E, Sanabria J. Exploiting the Potential of Bioreactors for Creating Spatial Organization in the Soil Microbiome: A Strategy for Increasing Sustainable Agricultural Practices. Microorganisms 2022; 10:microorganisms10071464. [PMID: 35889183 PMCID: PMC9319577 DOI: 10.3390/microorganisms10071464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 02/04/2023] Open
Abstract
Industrial production of synthetic nitrogen fertilizers and their crop application have caused considerable environmental impacts. Some eco-friendly alternatives try to solve them but raise some restrictions. We tested a novel method to produce a nitrogen bioinoculant by enriching a soil microbial community in bioreactors supplying N2 by air pumping. The biomass enriched with diazotrophic bacteria was diluted and applied to N-depleted and sterilized soil of tomato plants. We estimated microbial composition and diversity by 16S rRNA metabarcoding from soil and bioreactors at different run times and during plant uprooting. Bioreactors promoted the N-fixing microbial community and revealed a hided diversity. One hundred twenty-four (124) operational taxonomic units (OTUs) were assigned to bacteria with a greater Shannon diversity during the reactor’s steady state. A total of 753 OTUs were found in the rhizospheres with higher biodiversity when the lowest concentration of bacteria was applied. The apparent bacterial abundance in the batch and continuous bioreactors suggested a more specific functional ecological organization. We demonstrate the usefulness of bioreactors to evidence hidden diversity in the soil when it passes through bioreactors. By obtaining the same growth of inoculated plants and the control with chemical synthesis fertilizers, we evidence the potential of the methodology that we have called directed bioprospecting to grow a complex nitrogen-fixing microbial community. The simplicity of the reactor’s operation makes its application promising for developing countries with low technological progress.
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Affiliation(s)
- Carlos Fernando Gutiérrez
- Environmental Microbiology and Biotechnology Laboratory, Engineering School of Environmental & Natural Resources, Engineering Faculty, Universidad del Valle, Meléndez Campus, Cali 76001, Colombia; (C.F.G.); (N.R.-R.)
| | - Nicolás Rodríguez-Romero
- Environmental Microbiology and Biotechnology Laboratory, Engineering School of Environmental & Natural Resources, Engineering Faculty, Universidad del Valle, Meléndez Campus, Cali 76001, Colombia; (C.F.G.); (N.R.-R.)
| | - Siobhon Egan
- Australian National Phenome Center, Murdoch University, Perth 6150, Australia; (S.E.); (E.H.)
| | - Elaine Holmes
- Australian National Phenome Center, Murdoch University, Perth 6150, Australia; (S.E.); (E.H.)
| | - Janeth Sanabria
- Environmental Microbiology and Biotechnology Laboratory, Engineering School of Environmental & Natural Resources, Engineering Faculty, Universidad del Valle, Meléndez Campus, Cali 76001, Colombia; (C.F.G.); (N.R.-R.)
- Australian National Phenome Center, Murdoch University, Perth 6150, Australia; (S.E.); (E.H.)
- Correspondence:
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20
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Haryono MAS, Law YY, Arumugam K, Liew LCW, Nguyen TQN, Drautz-Moses DI, Schuster SC, Wuertz S, Williams RBH. Recovery of High Quality Metagenome-Assembled Genomes From Full-Scale Activated Sludge Microbial Communities in a Tropical Climate Using Longitudinal Metagenome Sampling. Front Microbiol 2022; 13:869135. [PMID: 35756038 PMCID: PMC9230771 DOI: 10.3389/fmicb.2022.869135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/05/2022] [Indexed: 01/23/2023] Open
Abstract
The analysis of metagenome data based on the recovery of draft genomes (so called metagenome-assembled genomes, or MAG) has assumed an increasingly central role in microbiome research in recent years. Microbial communities underpinning the operation of wastewater treatment plants are particularly challenging targets for MAG analysis due to their high ecological complexity, and remain important, albeit understudied, microbial communities that play ssa key role in mediating interactions between human and natural ecosystems. Here we consider strategies for recovery of MAG sequence from time series metagenome surveys of full-scale activated sludge microbial communities. We generate MAG catalogs from this set of data using several different strategies, including the use of multiple individual sample assemblies, two variations on multi-sample co-assembly and a recently published MAG recovery workflow using deep learning. We obtain a total of just under 9,100 draft genomes, which collapse to around 3,100 non-redundant genomic clusters. We examine the strengths and weaknesses of these approaches in relation to MAG yield and quality, showing that co-assembly may offer advantages over single-sample assembly in the case of metagenome data obtained from closely sampled longitudinal study designs. Around 1,000 MAGs were candidates for being considered high quality, based on single-copy marker gene occurrence statistics, however only 58 MAG formally meet the MIMAG criteria for being high quality draft genomes. These findings carry broader broader implications for performing genome-resolved metagenomics on highly complex communities, the design and implementation of genome recoverability strategies, MAG decontamination and the search for better binning methodology.
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Affiliation(s)
- Mindia A S Haryono
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Ying Yu Law
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Krithika Arumugam
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Larry C-W Liew
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Thi Quynh Ngoc Nguyen
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
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21
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Qiu G, Law Y, Zuniga-Montanez R, Deng X, Lu Y, Roy S, Thi SS, Hoon HY, Nguyen TQN, Eganathan K, Liu X, Nielsen PH, Williams RBH, Wuertz S. Global warming readiness: Feasibility of enhanced biological phosphorus removal at 35 °C. WATER RESEARCH 2022; 216:118301. [PMID: 35364353 DOI: 10.1016/j.watres.2022.118301] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 03/07/2022] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
Recent research has shown enhanced biological phosphorus removal (EBPR) from municipal wastewater at warmer temperatures around 30 °C to be achievable in both laboratory-scale reactors and full-scale treatment plants. In the context of a changing climate, the feasibility of EBPR at even higher temperatures is of interest. We operated two lab-scale EBPR sequencing batch reactors for > 300 days at 30 °C and 35 °C, respectively, and followed the dynamics of the communities of polyphosphate accumulating organisms (PAOs) and competing glycogen accumulating organisms (GAOs) using a combination of 16S rRNA gene metabarcoding, quantitative PCR and fluorescence in situ hybridization analyses. Stable and nearly complete phosphorus (P) removal was achieved at 30 °C; similarly, long term P removal was stable at 35 °C with effluent PO43-_P concentrations < 0.5 mg/L on half of all monitored days. Diverse and abundant Candidatus Accumulibacter amplicon sequence variants were closely related to those found in temperate environments, suggesting that EBPR at this temperature does not require a highly specialized PAO community. A slow-feeding strategy effectively limited the carbon uptake rates of GAOs, allowing PAOs to outcompete GAOs at both temperatures. Candidatus Competibacter was the main GAO, along with cluster III Defluviicoccus members. These organisms withstood the slow-feeding regime, suggesting that their bioenergetic characteristics of carbon uptake differ from those of their tetrad-forming relatives. Comparative cycle studies revealed higher carbon and P cycling activity of Ca. Accumulibacter when the temperature was increased from 30 °C to 35 °C, implying that the lowered P removal performance at 35 °C was not a direct effect of temperature, but a result of higher metabolic rates of carbon (and/or P) utilization of PAOs and GAOs, the resultant carbon deficiency, and escalated community competition. An increase in the TOC-to-PO43--P ratio (from 25:1 to 40:1) effectively eased the carbon deficiency and benefited PAOs. In general, a slow-feeding strategy and sufficiently high carbon input benefited a high and stable EBPR at 35 °C, representing basic conditions suitable for full-scale treatment plants experiencing higher water temperatures.
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Affiliation(s)
- Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore.
| | - Yingyu Law
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Rogelio Zuniga-Montanez
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore; Department of Civil and Environmental Engineering, University of California, One Shields Avenue, Davis, CA 95616, United States
| | - Xuhan Deng
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Yang Lu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Samarpita Roy
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Sara Swa Thi
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Hui Yi Hoon
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Thi Quynh Ngoc Nguyen
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Kaliyamoorthy Eganathan
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 119077, Singapore
| | - Xianghui Liu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Per H Nielsen
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore; Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg DK-9220, Denmark
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 119077, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore; Department of Civil and Environmental Engineering, University of California, One Shields Avenue, Davis, CA 95616, United States; School of Civil and Environmental Engineering, Nanyang Technological University, 639798, Singapore.
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22
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Chen L, Chen H, Hu Z, Tian Y, Wang C, Xie P, Deng X, Zhang Y, Tang X, Lin X, Li B, Wei C, Qiu G. Carbon uptake bioenergetics of PAOs and GAOs in full-scale enhanced biological phosphorus removal systems. WATER RESEARCH 2022; 216:118258. [PMID: 35320769 DOI: 10.1016/j.watres.2022.118258] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
This work analyzed, for the first time, the bioenergetics of PAOs and GAOs in full-scale wastewater treatment plants (WWTPs) for the uptake of different carbon sources. Fifteen samples were collected from five full-scale WWTPs. Predominance of different PAOs, i.e., Ca. Accumulibacter (0.00-0.49%), Tetrasphaera (0.37-3.94%), Microlunatus phosphovorus (0.01-0.18%), etc., and GAOs, i.e., Ca. Competibacter (0.08-5.39%), Defluviicoccus (0.05-5.34%), Micropruina (0.17-1.87%), etc., were shown by 16S rRNA gene amplicon sequencing. Despite the distinct PAO/GAO community compositions in different samples, proton motive force (PMF) was found as the key driving force (up to 90.1%) for the uptake of volatile fatty acids (VFAs, acetate and propionate) and amino acids (glutamate and aspartate) by both GAOs and PAOs at the community level, contrasting the previous understanding that Defluviicoccus have a low demand of PMF for acetate uptake. For the uptake of acetate or propionate, PAOs rarely activated F1, F0- ATPase (< 11.7%) or fumarate reductase (< 5.3%) for PMF generation; whereas, intensive involvements of these two pathways (up to 49.2% and 61.0%, respectively) were observed for GAOs, highlighting a major and community-level difference in their VFA uptake biogenetics in full-scale systems. However, different from VFAs, the uptake of glutamate and aspartate by both PAOs and GAOs commonly involved fumarate reductase and F1, F0-ATPase activities. Apart from these major and community-level differences, high level fine-scale micro-diversity in carbon uptake bioenergetics was observed within PAO and GAO lineages, probably resulting from their versatilities in employing different pathways for reducing power generation. Ca. Accumulibacter and Halomonas seemed to show higher dependency on the reverse operation of F1, F0-ATPase than other PAOs, likely due to the low involvement of glyoxylate shunt pathway. Unlike Tetrasphaera, but similar to Ca. Accumulibacter, Microlunatus phosphovorus took up glutamate and aspartate via the proton/glutamate-aspartate symporter driven by PMF. This feature was testified using a pure culture of Microlunatus phosphovorus stain NM-1. The major difference between PAOs and GAOs highlights the potential to selectively suppress GAOs for community regulation in EBPR systems. The finer-scale carbon uptake bioenergetics of PAOs or GAOs from different lineages benefits in understanding their interactions in community assembly in complex environment.
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Affiliation(s)
- Liping Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Hang Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Zekun Hu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Yucheng Tian
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Cenchao Wang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Peiran Xie
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Xuhan Deng
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Yushen Zhang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Xia Tang
- Guangzhou Sewage Purification Co., Ltd, Guangzhou 510006, China
| | - Xueran Lin
- Guangzhou Sewage Purification Co., Ltd, Guangzhou 510006, China
| | - Biqing Li
- Guangzhou Sewage Purification Co., Ltd, Guangzhou 510006, China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Key Laboratory of Pollution Control and Ecological Restoration in Industrial Clusters, Ministry of Education, Guangzhou 510006, China
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Key Laboratory of Pollution Control and Ecological Restoration in Industrial Clusters, Ministry of Education, Guangzhou 510006, China.
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23
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A Cyanobacteria Enriched Layer of Shark Bay Stromatolites Reveals a New Acaryochloris Strain Living in Near Infrared Light. Microorganisms 2022; 10:microorganisms10051035. [PMID: 35630477 PMCID: PMC9144716 DOI: 10.3390/microorganisms10051035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 12/04/2022] Open
Abstract
The genus Acaryochloris is unique among phototrophic organisms due to the dominance of chlorophyll d in its photosynthetic reaction centres and light-harvesting proteins. This allows Acaryochloris to capture light energy for photosynthesis over an extended spectrum of up to ~760 nm in the near infra-red (NIR) spectrum. Acaryochloris sp. has been reported in a variety of ecological niches, ranging from polar to tropical shallow aquatic sites. Here, we report a new Acarychloris strain isolated from an NIR-enriched stratified microbial layer 4–6 mm under the surface of stromatolite mats located in the Hamelin Pool of Shark Bay, Western Australia. Pigment analysis by spectrometry/fluorometry, flow cytometry and spectral confocal microscopy identifies unique patterns in pigment content that likely reflect niche adaption. For example, unlike the original A. marina species (type strain MBIC11017), this new strain, Acarychloris LARK001, shows little change in the chlorophyll d/a ratio in response to changes in light wavelength, displays a different Fv/Fm response and lacks detectable levels of phycocyanin. Indeed, 16S rRNA analysis supports the identity of the A. marina LARK001 strain as close to but distinct from from the A. marina HICR111A strain first isolated from Heron Island and previously found on the Great Barrier Reef under coral rubble on the reef flat. Taken together, A. marina LARK001 is a new cyanobacterial strain adapted to the stromatolite mats in Shark Bay.
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24
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Monitoring Bacterial Community Dynamics in a Drinking Water Treatment Plant: An Integrative Approach Using Metabarcoding and Microbial Indicators in Large Water Volumes. WATER 2022. [DOI: 10.3390/w14091435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Monitoring bacterial communities in a drinking water treatment plant (DWTP) may help to understand their regular operations. Bacterial community dynamics in an advanced full-scale DWTP were analyzed by 16S rRNA metabarcoding, and microbial water quality indicators were determined at nine different stages of potabilization: river water and groundwater intake, decantation, sand filtration, ozonization, carbon filtration, reverse osmosis, mixing chamber and post-chlorination drinking water. The microbial content of large water volumes (up to 1100 L) was concentrated by hollow fiber ultrafiltration. Around 10 million reads were obtained and grouped into 10,039 amplicon sequence variants. Metabarcoding analysis showed high bacterial diversity at all treatment stages and above all in groundwater intake, followed by carbon filtration and mixing chamber samples. Shifts in bacterial communities occurred downstream of ozonization, carbon filtration, and, more drastically, chlorination. Proteobacteria and Bacteroidota predominated in river water and throughout the process, but in the final drinking water, the strong selective pressure of chlorination reduced diversity and was clearly dominated by Cyanobacteria. Significant seasonal variation in species distribution was observed in decantation and carbon filtration samples. Some amplicon sequence variants related to potentially pathogenic genera were found in the DWTP. However, they were either not detected in the final water or in very low abundance (<2%), and all EU Directive quality standards were fully met. A combination of culture and high-throughput sequencing techniques may help DWTP managers to detect shifts in microbiome, allowing for a more in-depth assessment of operational performance.
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25
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Cano-Díaz C, Maestre FT, Wang J, Li J, Singh BK, Ochoa V, Gozalo B, Delgado-Baquerizo M. Effects of vegetation on soil cyanobacterial communities through time and space. THE NEW PHYTOLOGIST 2022; 234:435-448. [PMID: 35088410 DOI: 10.1111/nph.17996] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Photoautotrophic soil cyanobacteria play essential ecological roles and are known to exhibit large changes in their diversity and abundance throughout early succession. However, much less is known about how and why soil cyanobacterial communities change as soil develops over centuries and millennia, and the effects that vegetation have on such communities. We combined an extensive field survey, including 16 global soil chronosequences across contrasting ecosystems (from deserts to tropical forests), with molecular analyses to investigate how the diversity and abundance of photosynthetic and nonphotosynthetic soil cyanobacteria are affected by vegetation change during soil development, over time periods from hundreds to thousands of years. We show that, in most chronosequences, the abundance, species richness and community composition of soil cyanobacteria are relatively stable as soil develops (from centuries to millennia). Regardless of soil age, forest chronosequences were consistently dominated by nonphotosynthetic cyanobacteria (Vampirovibrionia), while grasslands and shrublands were dominated by photosynthetic cyanobacteria. Chronosequences undergoing drastic vegetation shifts (e.g. transitions from grasslands to forests) experienced significant changes in the composition of soil cyanobacterial communities. Our results advance our understanding of the ecology of cyanobacterial classes, and of the understudied nonphotosynthetic cyanobacteria in particular, and highlight the key role of vegetation as a major driver of their temporal dynamics as soil develops.
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Affiliation(s)
- Concha Cano-Díaz
- Departamento de Biología, Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, Móstoles, 28933, Spain
- CISAS - Centre for Research and Development in Agrifood Systems and Sustainability, Instituto Politécnico de Viana do Castelo, Viana do Castelo, Portugal
| | - Fernando T Maestre
- Instituto Multidisciplinar para el Estudio del Medio "Ramon Margalef", Universidad de Alicante, Edificio Nuevos Institutos, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, 03690, Spain
- Departamento de Ecología, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, Alicante, 03690, Spain
| | - Juntao Wang
- Global Centre for Land Based Innovation, University of Western Sydney, Penrith, NSW, 2751, Australia
- Hawkesbury Institute for the Environment, University of Western Sydney, Penrith, NSW, 2751, Australia
| | - Jing Li
- Global Centre for Land Based Innovation, University of Western Sydney, Penrith, NSW, 2751, Australia
- Hawkesbury Institute for the Environment, University of Western Sydney, Penrith, NSW, 2751, Australia
- Beijing Key Laboratory of Wetland Ecological Function and Restoration, Institute of Wetland Research, Chinese Academy of Forestry, Beijing, 100091, China
| | - Brajesh K Singh
- Global Centre for Land Based Innovation, University of Western Sydney, Penrith, NSW, 2751, Australia
- Hawkesbury Institute for the Environment, University of Western Sydney, Penrith, NSW, 2751, Australia
| | - Victoria Ochoa
- Instituto Multidisciplinar para el Estudio del Medio "Ramon Margalef", Universidad de Alicante, Edificio Nuevos Institutos, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, 03690, Spain
| | - Beatriz Gozalo
- Instituto Multidisciplinar para el Estudio del Medio "Ramon Margalef", Universidad de Alicante, Edificio Nuevos Institutos, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, 03690, Spain
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, Sevilla, E-41012, Spain
- Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, Sevilla, 41013, Spain
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26
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Hu C, Rzymski P. Non-Photosynthetic Melainabacteria (Cyanobacteria) in Human Gut: Characteristics and Association with Health. Life (Basel) 2022; 12:life12040476. [PMID: 35454968 PMCID: PMC9029806 DOI: 10.3390/life12040476] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 01/13/2023] Open
Abstract
Gut microorganisms are comprised of thousands of species and play an important role in the host’s metabolism, overall health status, and risk of disease. Recently, the discovery of non-photosynthetic cyanobacteria (class “Melainabacteria”) in the human and animal gut triggered a broad interest in studying cyanobacteria’s evolution, physiology, and ecological relevance of the Melainabacteria members. In the present paper, we review the general characteristics of Melainabacteria, their phylogeny, distribution, and ecology. The potential link between these microorganisms and human health is also discussed based on available human-microbiome studies. Their abundance tends to increase in patients with selected neurodegenerative, gastrointestinal, hepatic, metabolic, and respiratory diseases. However, the available evidence is correlative and requires further longitudinal studies. Although the research on Melainabacteria in the human gut is still in its infancy, elucidation of their role appears important in better understanding microbiome–human health interactions. Further studies aiming to identify particular gut cyanobacteria species, culture them in vitro, and characterize them on the molecular, biochemical, and physiological levels are encouraged.
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Affiliation(s)
- Chenlin Hu
- College of Pharmacy, University of Houston, Houston, TX 77204, USA
- Correspondence: (C.H.); (P.R.)
| | - Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806 Poznan, Poland
- Integrated Science Association (ISA), Universal Scientific Education and Research Network (USERN), 60-806 Poznań, Poland
- Correspondence: (C.H.); (P.R.)
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27
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Begmatov S, Dorofeev AG, Kadnikov VV, Beletsky AV, Pimenov NV, Ravin NV, Mardanov AV. The structure of microbial communities of activated sludge of large-scale wastewater treatment plants in the city of Moscow. Sci Rep 2022; 12:3458. [PMID: 35236881 PMCID: PMC8891259 DOI: 10.1038/s41598-022-07132-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 02/03/2022] [Indexed: 12/21/2022] Open
Abstract
Microbial communities in wastewater treatment plants (WWTPs) play a key role in water purification. Microbial communities of activated sludge (AS) vary extensively based on plant operating technology, influent characteristics and WWTP capacity. In this study we performed 16S rRNA gene profiling of AS at nine large-scale WWTPs responsible for the treatment of municipal sewage from the city of Moscow, Russia. Two plants employed conventional aerobic process, one plant—nitrification/denitrification technology, and six plants were operated with the University of Cape Town (UCT) anaerobic/anoxic/oxic process. Microbial communities were impacted by the technology and dominated by the Proteobacteria, Bacteroidota and Actinobacteriota. WWTPs employing the UCT process enabled efficient removal of not only organic matter, but also nitrogen and phosphorus, consistently with the high content of ammonia-oxidizing Nitrosomonas sp. and phosphate-accumulating bacteria. The latter group was represented by Candidatus Accumulibacter, Tetrasphaera sp. and denitrifiers. Co-occurrence network analysis provided information on key hub microorganisms in AS, which may be targeted for manipulating the AS stability and performance. Comparison of AS communities from WWTPs in Moscow and worldwide revealed that Moscow samples clustered together indicating that influent characteristics, related to social, cultural and environmental factors, could be more important than a plant operating technology.
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Affiliation(s)
- Shahjahon Begmatov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, Moscow, Russia, 119071
| | - Alexander G Dorofeev
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33‑2, Moscow, Russia, 119071
| | - Vitaly V Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, Moscow, Russia, 119071
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, Moscow, Russia, 119071
| | - Nikolai V Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33‑2, Moscow, Russia, 119071
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, Moscow, Russia, 119071.
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, Moscow, Russia, 119071.
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Tamburini FB, Maghini D, Oduaran OH, Brewster R, Hulley MR, Sahibdeen V, Norris SA, Tollman S, Kahn K, Wagner RG, Wade AN, Wafawanaka F, Gómez-Olivé FX, Twine R, Lombard Z, Hazelhurst S, Bhatt AS. Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa. Nat Commun 2022; 13:926. [PMID: 35194028 PMCID: PMC8863827 DOI: 10.1038/s41467-021-27917-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/25/2021] [Indexed: 12/15/2022] Open
Abstract
Human gut microbiome research focuses on populations living in high-income countries and to a lesser extent, non-urban agriculturalist and hunter-gatherer societies. The scarcity of research between these extremes limits our understanding of how the gut microbiota relates to health and disease in the majority of the world's population. Here, we evaluate gut microbiome composition in transitioning South African populations using short- and long-read sequencing. We analyze stool from adult females living in rural Bushbuckridge (n = 118) or urban Soweto (n = 51) and find that these microbiomes are taxonomically intermediate between those of individuals living in high-income countries and traditional communities. We demonstrate that reference collections are incomplete for characterizing microbiomes of individuals living outside high-income countries, yielding artificially low beta diversity measurements, and generate complete genomes of undescribed taxa, including Treponema, Lentisphaerae, and Succinatimonas. Our results suggest that the gut microbiome of South Africans does not conform to a simple "western-nonwestern" axis and contains undescribed microbial diversity.
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Affiliation(s)
| | - Dylan Maghini
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Ovokeraye H Oduaran
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Ryan Brewster
- School of Medicine, Stanford University, Stanford, CA, USA
| | - Michaella R Hulley
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, School of Pathology, Faculty of Health Sciences, National Health Laboratory Service & University of the Witwatersrand, Johannesburg, South Africa
| | - Venesa Sahibdeen
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, National Health Laboratory Service & University of the Witwatersrand, Johannesburg, South Africa
| | - Shane A Norris
- SAMRC Developmental Pathways for Health Research Unit, Department of Paediatrics, University of the Witwatersrand, Johannesburg, South Africa.,School of Human Development and Health, University of Southampton, Southampton, UK
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,INDEPTH Network, East Legon, Accra, Ghana
| | - Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,INDEPTH Network, East Legon, Accra, Ghana
| | - Ryan G Wagner
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,INDEPTH Network, East Legon, Accra, Ghana
| | - Alisha N Wade
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Floidy Wafawanaka
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - F Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,INDEPTH Network, East Legon, Accra, Ghana
| | - Rhian Twine
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zané Lombard
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, National Health Laboratory Service & University of the Witwatersrand, Johannesburg, South Africa
| | | | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa. .,School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa.
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA. .,School of Medicine, Stanford University, Stanford, CA, USA. .,Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA.
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29
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Pardesi B, Roberton AM, Lee KC, Angert ER, Rosendale DI, Boycheva S, White WL, Clements KD. Distinct microbiota composition and fermentation products indicate functional compartmentalization in the hindgut of a marine herbivorous fish. Mol Ecol 2022; 31:2494-2509. [PMID: 35152505 PMCID: PMC9306998 DOI: 10.1111/mec.16394] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 11/28/2022]
Abstract
Many marine herbivorous fishes harbour diverse microbial communities in the hindgut that can play important roles in host health and nutrition. Kyphosus sydneyanus is a temperate marine herbivorous fish that feeds predominantly on brown seaweeds. We employed 16S rRNA gene amplicon sequencing and gas chromatography to characterize microbial communities and their metabolites in different hindgut regions of six K. sydneyanus. Measurements were confined to three distal sections of the intestine, labelled III, IV and V from anterior to posterior. A total of 625 operational taxonomic units from 20 phyla and 123 genera were obtained. Bacteroidota, Firmicutes and Proteobacteria were the major phyla in mean relative abundance, which varied along the gut. Firmicutes (76%) was the most dominant group in section III, whereas Bacteroidota (69.3%) dominated section V. Total short‐chain fatty acid (SCFA) concentration was highest in sections IV and V, confirming active fermentation in these two most distal sections. The abundance of Bacteroidota correlated with propionate concentration in section V, while Firmicutes positively correlated with formate in sections III and IV. Acetate levels were highest in sections IV and V, which correlated with abundance of Bacteroidota. Despite differences in gut microbial community composition, SCFA profiles were consistent between individual fish in the different hindgut regions of K. sydneyanus, although proportions of SCFAs differed among gut sections. These findings demonstrate functional compartmentalization of the hindgut microbial community, highlighting the need for regional sampling when interpreting overall microbiome function. These results support previous work suggesting that hindgut microbiota in marine herbivorous fish are important to nutrition in some host species by converting dietary carbohydrates into metabolically useful SCFAs.
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Affiliation(s)
- Bikiran Pardesi
- School of Biological Sciences University of Auckland Auckland New Zealand
| | | | - Kevin C. Lee
- Faculty of Health and Environmental Sciences Auckland University of Technology Auckland New Zealand
| | - Esther R. Angert
- Department of Microbiology Cornell University Ithaca NY 14853 USA
| | - Douglas I. Rosendale
- Plant & Food Research Ltd Palmerston North New Zealand
- Anagenix Ltd Parnell, Auckland 1052 New Zealand
| | - Svetlana Boycheva
- School of Biological Sciences University of Auckland Auckland New Zealand
- Biotelliga, Parnell, Auckland 1052 New Zealand
| | - William Lindsey White
- School of Science Faculty of Health and Environmental Sciences Auckland University of Technology Auckland New Zealand
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30
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Gene-environment-gut interactions in Huntington's disease mice are associated with environmental modulation of the gut microbiome. iScience 2022; 25:103687. [PMID: 35059604 PMCID: PMC8760441 DOI: 10.1016/j.isci.2021.103687] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/14/2021] [Accepted: 12/21/2021] [Indexed: 12/14/2022] Open
Abstract
Gut dysbiosis in Huntington's disease (HD) has recently been reported using microbiome profiling in R6/1 HD mice and replicated in clinical HD. In HD mice, environmental enrichment (EE) and exercise (EX) were shown to have therapeutic impacts on the brain and associated symptoms. We hypothesize that these housing interventions modulate the gut microbiome, configuring one of the mechanisms that mediate their therapeutic effects observed in HD. We exposed R6/1 mice to a protocol of either EE or EX, relative to standard-housed control conditions, before the onset of gut dysbiosis and motor deficits. We characterized gut structure and function, as well as gut microbiome profiling using 16S rRNA sequencing. Multivariate analysis identified specific orders, namely Bacteroidales, Lachnospirales and Oscillospirales, as the main bacterial signatures that discriminate between housing conditions. Our findings suggest a promising role for the gut microbiome in mediating the effects of EE and EX exposures, and possibly other environmental interventions, in HD mice. Gastrointestinal structure and motility are intact at an early stage in a HD mouse model There is sexual dimorphism in the presentation of the HD gut dysbiosis phenotype Bacteroidales, Lachnospirales and Oscillospirales bacteria are affected by experience Environmental enrichment and exercise may modulate HD via the microbiota-gut-brain axis
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31
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Oren A, Garrity GM. CANDIDATUS LIST No. 3. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2022; 72. [PMID: 35100104 DOI: 10.1099/ijsem.0.005186] [Citation(s) in RCA: 251] [Impact Index Per Article: 125.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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32
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Cao RR, He P, Lei SF. Novel microbiota-related gene set enrichment analysis identified osteoporosis associated gut microbiota from autoimmune diseases. J Bone Miner Metab 2021; 39:984-996. [PMID: 34338852 DOI: 10.1007/s00774-021-01247-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/21/2021] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Gut microbiota is now considered to be a hidden organ that interacts bidirectionally with cellular responses in numerous organs belonged to the immune, bone, and nervous systems. Here, we aimed to investigate the relationships between gut microbiota and complex diseases by utilizing multiple publicly available genome-wide association. MATERIALS AND METHODS We applied a novel microbiota-related gene set enrichment analysis approach to detect the associations between gut microbiota and complex diseases by processing genome-wide association studies (GWASs) data sets of six autoimmune diseases (including celiac disease (CeD), inflammatory bowel diseases (IBD), multiple sclerosis (MS), primary biliary cirrhosis (PBC), type 1 diabetes (T1D) and primary sclerosing cholangitis (PSC)) and osteoporosis (OP). RESULTS The family Oxalobacteraceae and genus Candidatus_Soleaferrea were found to be correlated with all of the six autoimmune diseases (FDR adjusted P < 0.05). Moreover, we observed that the six autoimmune diseases except PBC shared 3 overlapping features (including family Peptostreptococcaceae, order Gastranaerophilales and genus Romboutsia). For all of the six autoimmune diseases and BMDs (LS-BMD and TB-BMD), an association signal was observed for genus Candidatus_Soleaferrea (FDR adjusted P < 0.05). Notably, FA / FN-BMD shared the maximum number of overlapping microbial features (e.g., genus Ruminococcaceae_UCG009, Erysipelatoclostridium and Ruminococcaceae_UCG013). CONCLUSION Our study found that part of the gut microbiota could be novel regulators of BMDs and autoimmune diseases via the effects of its metabolites and may lead to a better understanding of the role played by gut microbiota in the communication of the microbiota-skeletal/immune-gut axis.
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Affiliation(s)
- Rong-Rong Cao
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, Jiangsu, 215123, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Department of Epidemiology, School of Public Health, Medical College of Soochow University, 199 Renai Road, Suzhou, Jiangsu, 215123, People's Republic of China
| | - Pei He
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, Jiangsu, 215123, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Department of Epidemiology, School of Public Health, Medical College of Soochow University, 199 Renai Road, Suzhou, Jiangsu, 215123, People's Republic of China
| | - Shu-Feng Lei
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, Jiangsu, 215123, People's Republic of China.
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Department of Epidemiology, School of Public Health, Medical College of Soochow University, 199 Renai Road, Suzhou, Jiangsu, 215123, People's Republic of China.
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33
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Liu R, Shi J, Shultz S, Guo D, Liu D. Fecal Bacterial Community of Allopatric Przewalski's Gazelles and Their Sympatric Relatives. Front Microbiol 2021; 12:737042. [PMID: 34630362 PMCID: PMC8499116 DOI: 10.3389/fmicb.2021.737042] [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: 07/06/2021] [Accepted: 08/26/2021] [Indexed: 01/07/2023] Open
Abstract
Mammal gastrointestinal tracts harbor diverse bacterial communities that play important roles in digestion, development, behavior, and immune function. Although, there is an increasing understanding of the factors that affect microbial community composition in laboratory populations, the impact of environment and host community composition on microbiomes in wild populations is less understood. Given that the composition of bacterial communities can be shaped by ecological factors, particularly exposure to the microbiome of other individuals, inter-specific interactions should impact on microbiome community composition. Here, we evaluated inter-population and inter-specific similarity in the fecal microbiota of Przewalski's gazelle (Procapra przewalskii), an endangered endemic ruminant around Qinghai Lake in China. We compared the fecal bacterial communities of three Przewalski's gazelle populations, with those of two sympatric ruminants, Tibetan gazelle (Procapra picticaudata) and Tibetan sheep (Ovis aries). The fecal bacterial community richness (Chao1, ACE) did not vary across the three Przewalski's gazelle populations, nor did the composition vary between species. In contrast, the managed Przewalski's gazelle population had higher bacterial diversity (Shannon and Simpson) and was more similar to its sympatric Tibetan sheep in beta diversity than the wild Przewalski's gazelle populations. These results suggest that ecological factors like host community composition or diet affect Przewalski's gazelle's gastrointestinal bacterial community. The role of bacterial community composition in maintaining gastrointestinal health should be assessed to improve conservation management of endangered Przewalski's gazelle. More broadly, captive breeding and reintroduction efforts may be impeded, where captive management results in dysbiosis and introduction of pathogenic bacteria. In free ranging populations, where wildlife and livestock co-occur, infection by domestic pathogens and diseases may be an underappreciated threat to wild animals.
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Affiliation(s)
- Ruoshuang Liu
- School of Environment, Beijing Normal University, Beijing, China
| | - Jianbin Shi
- School of Environment, Beijing Normal University, Beijing, China
| | - Susanne Shultz
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, United Kingdom
| | - Dongsheng Guo
- Key Laboratory of Biodiversity Sciences and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Dingzhen Liu
- Key Laboratory of Biodiversity Sciences and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
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34
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Ferretti MV, Hussien RA, Ballicora MA, Iglesias AA, Figueroa CM, Asencion Diez MD. The ADP-glucose pyrophosphorylase from Melainabacteria: a comparative study between photosynthetic and non-photosynthetic bacterial sources. Biochimie 2021; 192:30-37. [PMID: 34560201 DOI: 10.1016/j.biochi.2021.09.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/11/2021] [Accepted: 09/20/2021] [Indexed: 11/18/2022]
Abstract
Until recently, the cyanobacterial phylum only included oxygenic photosynthesizer members. The discovery of Melainabacteria as a group of supposed non-photosynthetic cyanobacteria asked to revisit such scenario. From metagenomic data, we were able to identify sequences encoding putative ADP-glucose pyrophosphorylases (ADP-GlcPPase) from free-living and intestinal Melainabacteria. The respective genes were de novo synthesized and over-expressed in Escherichia coli. The purified recombinant proteins from both Melainabacteria species were active as ADP-GlcPPases, exhibiting Vmax values of 2.3 (free-living) and 7.1 U/mg (intestinal). The enzymes showed similar S0.5 values (∼0.3 mM) for ATP, while the one from the intestinal source exhibited a 6-fold higher affinity toward glucose-1P. Both recombinant ADP-GlcPPases were sensitive to glucose-6P activation (A0.5 ∼0.3 mM) and Pi and ADP inhibition (I0.5 between 0.2 and 3 mM). Interestingly, the enzymes from Melainabacteria were insensitive to 3-phosphoglycerate, which is the principal activator of ADP-GlcPPases from photosynthetic cyanobacteria. As far as we know, this is the first biochemical characterization of an active enzyme from Melainabacteria. This work contributes to a better understanding of the evolution of allosteric regulation in the ADP-GlcPPase family, which is critical for synthesizing the main reserve polysaccharide in prokaryotes (glycogen) and plants (starch). In addition, our results offer further information to discussions regarding the phylogenetic position of Melainabacteria.
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Affiliation(s)
- María V Ferretti
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina
| | - Rania A Hussien
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, USA; Department of Chemistry, Al Baha University, Al Baha, Saudi Arabia
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, USA
| | - Alberto A Iglesias
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina
| | - Carlos M Figueroa
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina
| | - Matías D Asencion Diez
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina.
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35
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Roush D, Giraldo-Silva A, Garcia-Pichel F. Cydrasil 3, a curated 16S rRNA gene reference package and web app for cyanobacterial phylogenetic placement. Sci Data 2021; 8:230. [PMID: 34475414 PMCID: PMC8413452 DOI: 10.1038/s41597-021-01015-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 08/06/2021] [Indexed: 02/01/2023] Open
Abstract
Cyanobacteria are a widespread and important bacterial phylum, responsible for a significant portion of global carbon and nitrogen fixation. Unfortunately, reliable and accurate automated classification of cyanobacterial 16S rRNA gene sequences is muddled by conflicting systematic frameworks, inconsistent taxonomic definitions (including the phylum itself), and database errors. To address this, we introduce Cydrasil 3 ( https://www.cydrasil.org ), a curated 16S rRNA gene reference package, database, and web application designed to provide a full phylogenetic perspective for cyanobacterial systematics and routine identification. Cydrasil 3 contains over 1300 manually curated sequences longer than 1100 base pairs and can be used for phylogenetic placement or as a reference sequence set for de novo phylogenetic reconstructions. The web application (utilizing PaPaRA and EPA-ng) can place thousands of sequences into the reference tree and has detailed instructions on how to analyze results. While the Cydrasil web application offers no taxonomic assignments, it instead provides phylogenetic placement, as well as a searchable database with curation notes and metadata, and a mechanism for community feedback.
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Affiliation(s)
- Daniel Roush
- School of Life Sciences, Arizona State University, 85282, Tempe, Arizona, USA.,Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, 85281, Tempe, Arizona, USA
| | - Ana Giraldo-Silva
- School of Life Sciences, Arizona State University, 85282, Tempe, Arizona, USA.,Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, 85281, Tempe, Arizona, USA
| | - Ferran Garcia-Pichel
- School of Life Sciences, Arizona State University, 85282, Tempe, Arizona, USA. .,Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, 85281, Tempe, Arizona, USA.
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Characterizing the Uncultivated Microbial Minority: towards Understanding the Roles of the Rare Biosphere in Microbial Communities. mSystems 2021; 6:e0077321. [PMID: 34427533 PMCID: PMC8407377 DOI: 10.1128/msystems.00773-21] [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] [Indexed: 11/24/2022] Open
Abstract
Microbial communities are frequently numerically dominated by just a few species. Often, the long “tail” of the rank-abundance plots of microbial communities constitutes the so-called “rare biosphere,” microorganisms that are highly diverse but are typically found in low abundance in these communities. Their presence in microbial communities has only recently become apparent with advances in high-throughput sequencing technologies. Despite their low numbers, they are thought to play important roles in their communities and may function as potential members to keep the communities intact and resilient. Their phylogenetic diversity also means that they are important subjects for better understanding the interplay between microbial diversity and evolution. I propose that more efforts should be put into characterizing these poorly understood and mostly unknown microbial lineages that hold vast potentials for our understanding of microbial diversity, ecology, and evolution of life on this planet.
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Abstract
The ancestors of cyanobacteria generated Earth's first biogenic molecular oxygen, but how they dealt with oxidative stress remains unconstrained. Here we investigate when superoxide dismutase enzymes (SODs) capable of removing superoxide free radicals evolved and estimate when Cyanobacteria originated. Our Bayesian molecular clocks, calibrated with microfossils, predict that stem Cyanobacteria arose 3300-3600 million years ago. Shortly afterwards, we find phylogenetic evidence that ancestral cyanobacteria used SODs with copper and zinc cofactors (CuZnSOD) during the Archaean. By the Paleoproterozoic, they became genetically capable of using iron, nickel, and manganese as cofactors (FeSOD, NiSOD, and MnSOD respectively). The evolution of NiSOD is particularly intriguing because it corresponds with cyanobacteria's invasion of the open ocean. Our analyses of metalloenzymes dealing with reactive oxygen species (ROS) now demonstrate that marine geochemical records alone may not predict patterns of metal usage by phototrophs from freshwater and terrestrial habitats.
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Accessing Dietary Effects on the Rumen Microbiome: Different Sequencing Methods Tell Different Stories. Vet Sci 2021; 8:vetsci8070138. [PMID: 34357930 PMCID: PMC8310016 DOI: 10.3390/vetsci8070138] [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: 06/08/2021] [Revised: 07/02/2021] [Accepted: 07/14/2021] [Indexed: 12/29/2022] Open
Abstract
The current study employed both amplicon and shotgun sequencing to examine and compare the rumen microbiome in Angus bulls fed with either a backgrounding diet (BCK) or finishing diet (HG), to assess if both methods produce comparable results. Rumen digesta samples from 16 bulls were subjected for microbial profiling. Distinctive microbial profiles were revealed by the two methods, indicating that choice of sequencing approach may be a critical facet in studies of the rumen microbiome. Shotgun-sequencing identified the presence of 303 bacterial genera and 171 archaeal species, several of which exhibited differential abundance. Amplicon-sequencing identified 48 bacterial genera, 4 archaeal species, and 9 protozoal species. Among them, 20 bacterial genera and 5 protozoal species were differentially abundant between the two diets. Overall, amplicon-sequencing showed a more drastic diet-derived effect on the ruminal microbial profile compared to shotgun-sequencing. While both methods detected dietary differences at various taxonomic levels, few consistent patterns were evident. Opposite results were seen for the phyla Firmicutes and Bacteroidetes, and the genus Selenomonas. This study showcases the importance of sequencing platform choice and suggests a need for integrative methods that allow robust comparisons of microbial data drawn from various omic approaches, allowing for comprehensive comparisons across studies.
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Hugenholtz P, Chuvochina M, Oren A, Parks DH, Soo RM. Prokaryotic taxonomy and nomenclature in the age of big sequence data. THE ISME JOURNAL 2021; 15:1879-1892. [PMID: 33824426 PMCID: PMC8245423 DOI: 10.1038/s41396-021-00941-x] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 02/01/2023]
Abstract
The classification of life forms into a hierarchical system (taxonomy) and the application of names to this hierarchy (nomenclature) is at a turning point in microbiology. The unprecedented availability of genome sequences means that a taxonomy can be built upon a comprehensive evolutionary framework, a longstanding goal of taxonomists. However, there is resistance to adopting a single framework to preserve taxonomic freedom, and ever increasing numbers of genomes derived from uncultured prokaryotes threaten to overwhelm current nomenclatural practices, which are based on characterised isolates. The challenge ahead then is to reach a consensus on the taxonomic framework and to adapt and scale the existing nomenclatural code, or create a new code, to systematically incorporate uncultured taxa into the chosen framework.
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Affiliation(s)
- Philip Hugenholtz
- grid.1003.20000 0000 9320 7537Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD Australia
| | - Maria Chuvochina
- grid.1003.20000 0000 9320 7537Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD Australia
| | - Aharon Oren
- grid.9619.70000 0004 1937 0538Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Edmond J. Safra campus, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Donovan H. Parks
- grid.1003.20000 0000 9320 7537Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD Australia
| | - Rochelle M. Soo
- grid.1003.20000 0000 9320 7537Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD Australia
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40
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Tran PQ, Bachand SC, McIntyre PB, Kraemer BM, Vadeboncoeur Y, Kimirei IA, Tamatamah R, McMahon KD, Anantharaman K. Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika. THE ISME JOURNAL 2021; 15:1971-1986. [PMID: 33564113 PMCID: PMC8245535 DOI: 10.1038/s41396-021-00898-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/22/2020] [Accepted: 01/18/2021] [Indexed: 01/31/2023]
Abstract
Lake Tanganyika (LT) is the largest tropical freshwater lake, and the largest body of anoxic freshwater on Earth's surface. LT's mixed oxygenated surface waters float atop a permanently anoxic layer and host rich animal biodiversity. However, little is known about microorganisms inhabiting LT's 1470 meter deep water column and their contributions to nutrient cycling, which affect ecosystem-level function and productivity. Here, we applied genome-resolved metagenomics and environmental analyses to link specific taxa to key biogeochemical processes across a vertical depth gradient in LT. We reconstructed 523 unique metagenome-assembled genomes (MAGs) from 34 bacterial and archaeal phyla, including many rarely observed in freshwater lakes. We identified sharp contrasts in community composition and metabolic potential with an abundance of typical freshwater taxa in oxygenated mixed upper layers, and Archaea and uncultured Candidate Phyla in deep anoxic waters. Genomic capacity for nitrogen and sulfur cycling was abundant in MAGs recovered from anoxic waters, highlighting microbial contributions to the productive surface layers via recycling of upwelled nutrients, and greenhouse gases such as nitrous oxide. Overall, our study provides a blueprint for incorporation of aquatic microbial genomics in the representation of tropical freshwater lakes, especially in the context of ongoing climate change, which is predicted to bring increased stratification and anoxia to freshwater lakes.
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Affiliation(s)
- Patricia Q Tran
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Samantha C Bachand
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Peter B McIntyre
- Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, USA
| | - Benjamin M Kraemer
- Department of Ecosystem Research, Leibniz Institute for Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | | | - Ismael A Kimirei
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | | | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
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41
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Phylogeny and Evolutionary History of Respiratory Complex I Proteins in Melainabacteria. Genes (Basel) 2021; 12:genes12060929. [PMID: 34207155 PMCID: PMC8235220 DOI: 10.3390/genes12060929] [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: 11/12/2020] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 12/13/2022] Open
Abstract
The evolution of oxygenic photosynthesis was one of the most transformative evolutionary events in Earth's history, leading eventually to the oxygenation of Earth's atmosphere and, consequently, the evolution of aerobic respiration. Previous work has shown that the terminal electron acceptors (complex IV) of aerobic respiration likely evolved after the evolution of oxygenic photosynthesis. However, complex I of the respiratory complex chain can be involved in anaerobic processes and, therefore, may have pre-dated the evolution of oxygenic photosynthesis. If so, aerobic respiration may have built upon respiratory chains that pre-date the rise of oxygen in Earth's atmosphere. The Melainabacteria provide a unique opportunity to examine this hypothesis because they contain genes for aerobic respiration but likely diverged from the Cyanobacteria before the evolution of oxygenic photosynthesis. Here, we examine the phylogenies of translated complex I sequences from 44 recently published Melainabacteria metagenome assembled genomes and genomes from other Melainabacteria, Cyanobacteria, and other bacterial groups to examine the evolutionary history of complex I. We find that complex I appears to have been present in the common ancestor of Melainabacteria and Cyanobacteria, supporting the idea that aerobic respiration built upon respiratory chains that pre-date the evolution of oxygenic photosynthesis and the rise of oxygen.
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42
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Ahmad AA, Zhang JB, Liang Z, Yang C, Kalwar Q, Shah T, Du M, Muhammad I, Zheng J, Yan P, Ding XZ, Long R. Dynamics of rumen bacterial composition of yak ( Bos grunniens) in response to dietary supplements during the cold season. PeerJ 2021; 9:e11520. [PMID: 34178446 PMCID: PMC8216167 DOI: 10.7717/peerj.11520] [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: 08/28/2020] [Accepted: 05/05/2021] [Indexed: 11/20/2022] Open
Abstract
This study aimed to explore the rumen bacterial community of yak in response to dietary supplements during the cold season. In addition, the rumen fermentation products were also analyzed. Twenty-one female domestic yaks were randomly divided into three groups i.e., pure grazing (GG) group, grazing plus oats hay supplement (OG) group, and grazing plus concentrate supplement group (CG). Rumen contents were collected after 90 days to assess rumen fermentation parameters and bacterial community. The GC group presented higher concentrations of ammonia nitrogen (P < 0.001), and total volatile fatty acids (TVFA) (P < 0.001), and lower rumen pH (P < 0.001) compared to other experimental groups. The CG group displayed higher proportions of propionate, butyrate, isobutyrate, and isovalerate while lower A/P ratio compared to other experimental groups. Shannon, Chao1, and ACE values were significantly lower in the OG group compared to GG and CG groups. Anosim test showed significant differences in bacterial community structure between groups but the PCA plot was not very informative to see these differences. Bacteroidetes, Proteobacteria, and Firmicutes were the three dominant phyla in all groups. The genera Oscillospira was more abundant in GG and OG groups. Higher relative abundance of Ruminococcus and Clostridium was observed in the GG group, while Ruminobacter, Corynebacterium, and Selenomonas were more abundant in the CG group. These findings will help in improving our understanding of rumen bacteria in yaks in response to changes in diet.
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Affiliation(s)
- Anum Ali Ahmad
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jian Bo Zhang
- Key Laboratory of yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Zeyi Liang
- Key Laboratory of yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chao Yang
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan, Provincial Engineering Research Center for Healthy Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Qudratullah Kalwar
- Key Laboratory of yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Tariq Shah
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Mei Du
- Key Laboratory of yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ishaq Muhammad
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Juanshan Zheng
- Key Laboratory of yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ping Yan
- Key Laboratory of yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xue-Zhi Ding
- Key Laboratory of yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ruijun Long
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China
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43
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Oliver T, Sánchez-Baracaldo P, Larkum AW, Rutherford AW, Cardona T. Time-resolved comparative molecular evolution of oxygenic photosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2021; 1862:148400. [PMID: 33617856 PMCID: PMC8047818 DOI: 10.1016/j.bbabio.2021.148400] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 02/01/2021] [Accepted: 02/12/2021] [Indexed: 12/15/2022]
Abstract
Oxygenic photosynthesis starts with the oxidation of water to O2, a light-driven reaction catalysed by photosystem II. Cyanobacteria are the only prokaryotes capable of water oxidation and therefore, it is assumed that the origin of oxygenic photosynthesis is a late innovation relative to the origin of life and bioenergetics. However, when exactly water oxidation originated remains an unanswered question. Here we use phylogenetic analysis to study a gene duplication event that is unique to photosystem II: the duplication that led to the evolution of the core antenna subunits CP43 and CP47. We compare the changes in the rates of evolution of this duplication with those of some of the oldest well-described events in the history of life: namely, the duplication leading to the Alpha and Beta subunits of the catalytic head of ATP synthase, and the divergence of archaeal and bacterial RNA polymerases and ribosomes. We also compare it with more recent events such as the duplication of Cyanobacteria-specific FtsH metalloprotease subunits and the radiation leading to Margulisbacteria, Sericytochromatia, Vampirovibrionia, and other clades containing anoxygenic phototrophs. We demonstrate that the ancestral core duplication of photosystem II exhibits patterns in the rates of protein evolution through geological time that are nearly identical to those of the ATP synthase, RNA polymerase, or the ribosome. Furthermore, we use ancestral sequence reconstruction in combination with comparative structural biology of photosystem subunits, to provide additional evidence supporting the premise that water oxidation had originated before the ancestral core duplications. Our work suggests that photosynthetic water oxidation originated closer to the origin of life and bioenergetics than can be documented based on phylogenetic or phylogenomic species trees alone.
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Affiliation(s)
- Thomas Oliver
- Department of Life Sciences, Imperial College London, London, UK
| | | | | | | | - Tanai Cardona
- Department of Life Sciences, Imperial College London, London, UK.
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44
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Zaouri N, Cheng H, Khairunnisa F, Alahmed A, Blilou I, Hong PY. A type dependent effect of treated wastewater matrix on seed germination and food production. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 769:144573. [PMID: 33477041 DOI: 10.1016/j.scitotenv.2020.144573] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/05/2020] [Accepted: 12/13/2020] [Indexed: 06/12/2023]
Abstract
Municipal wastewater treated by membrane bioreactor, either aerobically (AeMBR) or anaerobically (AnMBR), can be reused to irrigate crops. However, post-AeMBR and post-AnMBR effluent have different water quality that may impact crop growth and yield. This study aims to assess for differences in water quality from both AeMBR and AnMBR, and determine if the type of treated wastewater matrix would impact seed germination and crop yield. Compared to post-AeMBR and control, post-AnMBR effluent had a negative impact on seed germination for both tomatoes and lettuces. The use of post-AnMBR but not post-AeMBR effluent also resulted in a higher number of unripe tomato fruits at the time of harvesting. However, when post-AnMBR effluent was diluted to 25% and 75% v/v with tap water, higher lettuce biomass was harvested compared to the same concentrations of post-AeMBR effluent and control. The observed differences in germination and yield were likely due to differences in the concentrations of heavy metals (e.g. Zn) and steroids or phytohormones (e.g. testosterone, gibberellic acid) present in both post-MBR effluents. This study demonstrated that the type of treated wastewater generated from different upstream treatment technologies can potentially impact crop yield based on the crop type. By understanding how the type of treated wastewater affect downstream agricultural activities, changes in management practices can be made accordingly.
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Affiliation(s)
- Noor Zaouri
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia
| | - Hong Cheng
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia; Center of Excellence for NEOM Research, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia
| | - Fatin Khairunnisa
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia; Life Sciences Undergraduate Program, Department of Biological Sciences, National University of Singapore, 117558, Singapore
| | - Abdulelah Alahmed
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia
| | - Ikram Blilou
- Center of Desert Agriculture, Laboratory of Cell and Developmental Biology, Division of Biological and Environmental Science, and Engineering, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia
| | - Pei-Ying Hong
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia; Center of Excellence for NEOM Research, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia.
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45
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Cyanobiont genetic diversity and host specificity of cyanobiont-bearing dinoflagellate Ornithocercus in temperate coastal waters. Sci Rep 2021; 11:9458. [PMID: 33947914 PMCID: PMC8097063 DOI: 10.1038/s41598-021-89072-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/23/2021] [Indexed: 11/17/2022] Open
Abstract
Cyanobacteria are ubiquitous in marine environments and play an important role as primary producers. Some cyanobacteria, the so-called cyanobionts (cyanobacterial symbionts), have a symbiotic relationship with unicellular organisms. Among these relationships, in particular, the nature (e.g., genetic diversity, host or cyanobiont specificity, and cyanobiont seasonality) of the cyanobiont-dinoflagellate host consortia remains poorly understood. In this study, 16S rDNA of cyanobionts in 138 single host cells isolated over four seasons from temperate waters were sequenced using the MiSeq platform. Genetic analysis of cyanobionts from the dinoflagellate host Ornithocercus revealed that three genetic types of Synechococcales cyanobionts occurred in a wide range of water temperatures (11–24 °C), and their distribution seemed to be closely associated with variations in salinity. Furthermore, a certain degree of host (or cyanobiont) specificity in cyanobionts (or the host) among Ornithocercus species as well as among other dinophysoid species (i.e. Amphisolenia, Citharistes, and Histioneis), was observed. In addition to the Synechococcales cyanobionts, this study identified OTU sequences affiliated with Vampirovibrionales and Chroococcidiopsidales in some Ornithocercus cells, suggesting that Ornithocercus species are an additional habitat for these bacterial groups.
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46
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Boden JS, Grego M, Bolhuis H, Sánchez-Baracaldo P. Draft genome sequences of three filamentous cyanobacteria isolated from brackish habitats. J Genomics 2021; 9:20-25. [PMID: 33613774 PMCID: PMC7893532 DOI: 10.7150/jgen.53678] [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: 09/24/2020] [Accepted: 01/27/2021] [Indexed: 11/20/2022] Open
Abstract
Brackish cyanobacterial genome sequences are relatively rare. Here, we report the 5.5 Mbp, 5.8 Mbp and 6.1 Mbp draft genomes of Spirulina sp. CCY15215, Leptolyngbya sp. CCY15150 and Halomicronema sp. CCY15110 isolated from coastal microbial mats on the North Sea beach of the island of Schiermonnikoog in the Netherlands. Large scale phylogenomic analyses reveal that Spirulina sp. CCY15215 is a large cell diameter cyanobacterium, whereas Leptolyngbya sp. CCY15150 and Halomicronema sp. CCY15110 are the first reported brackish genomes belonging to the LPP clade consisting primarily of Leptolyngbya, Plectonema and Phormidium spp. Further genome mining divulges that all new draft genomes contain, ggpS and ggpP, the genes responsible for synthesising glucosylglycerol (GG), a compatible solute found in moderately salt-tolerant cyanobacteria.
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Affiliation(s)
- Joanne Sarah Boden
- School of Geographical Sciences, Faculty of Science, University of Bristol, Bristol, BS8 1SS, United Kingdom
| | - Michele Grego
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, and Utrecht University, Den Hoorn, the Netherlands
| | - Henk Bolhuis
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, and Utrecht University, Den Hoorn, the Netherlands
| | - Patricia Sánchez-Baracaldo
- School of Geographical Sciences, Faculty of Science, University of Bristol, Bristol, BS8 1SS, United Kingdom
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47
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Roy S, Guanglei Q, Zuniga-Montanez R, Williams RB, Wuertz S. Recent advances in understanding the ecophysiology of enhanced biological phosphorus removal. Curr Opin Biotechnol 2021; 67:166-174. [PMID: 33582603 DOI: 10.1016/j.copbio.2021.01.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 01/02/2023]
Abstract
Enhanced biological phosphorus removal (EBPR) is an efficient, cost-effective, and sustainable method for removing excess phosphorus from wastewater. Polyphosphate accumulating organisms (PAOs) exhibit a unique physiology alternating between anaerobic conditions for uptake of carbon substrates and aerobic or anoxic conditions for phosphorus uptake. The implementation of high-throughput sequencing technologies and advanced molecular tools along with biochemical characterization has provided many new perspectives on the EBPR process. These approaches have helped identify a wide range of carbon substrates and electron acceptors utilized by PAOs that in turn influence interactions with microbial community members and determine overall phosphorus removal efficiency. In this review, we systematically discuss the microbial diversity and metabolic response to a range of environmental conditions and process control strategies in EBPR.
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Affiliation(s)
- Samarpita Roy
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore 119077, Singapore
| | - Qiu Guanglei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Rogelio Zuniga-Montanez
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; Department of Civil and Environmental Engineering, University of California, One Shields Avenue, Davis, CA 95616, United States
| | - Rohan Bh Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore 119077, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; Department of Civil and Environmental Engineering, University of California, One Shields Avenue, Davis, CA 95616, United States; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore.
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48
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Aoki M, Miyashita Y, Tran PT, Okuno Y, Watari T, Yamaguchi T. Enrichment of marine manganese-oxidizing microorganisms using polycaprolactone as a solid organic substrate. Biotechnol Lett 2021; 43:813-823. [PMID: 33496920 DOI: 10.1007/s10529-021-03088-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 01/13/2021] [Indexed: 11/29/2022]
Abstract
OBJECTIVE Heterotrophic manganese (Mn)-oxidizing microorganisms responsible for biogenic manganese oxide (Bio-MnOx) production are fastidious. Their enrichment is not easily accomplished by merely adding a soluble organic substrate to non-sterile mixed cultures. The objective of this study was to evaluate polycaprolactone (PCL), an aliphatic polyester, as an effective solid organic substrate for the enrichment of marine Mn-oxidizing microorganisms. RESULTS We successfully obtained marine microbial enrichment with the capacity for dissolved Mn removal and MnOx production using PCL as a solid organic substrate. The removal of dissolved Mn by the Mn-oxidizing enrichment culture followed first-order kinetics with a rate constant of 0.014 h-1. 16S rRNA gene amplicon sequencing analysis revealed that the Mn-oxidizing enrichment culture was highly dominated by operational taxonomic units related to the bacterial phyla Cyanobacteria, Planctomycetes, and Proteobacteria. CONCLUSIONS Our data demonstrate that PCL can serve as a potential substrate to enrich Mn-oxidizing microorganisms with the ability to produce MnOx under marine conditions.
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Affiliation(s)
- Masataka Aoki
- Department of Civil Engineering, National Institute of Technology, Wakayama College, 77 Noshima, Nada, Gobo, Wakayama, 644-0023, Japan.
| | - Yukina Miyashita
- Department of Civil Engineering, National Institute of Technology, Wakayama College, 77 Noshima, Nada, Gobo, Wakayama, 644-0023, Japan
| | - P Thao Tran
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Yoshiharu Okuno
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Wakayama College, Gobo, Wakayama, Japan
| | - Takahiro Watari
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Niigata, Japan.,Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
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49
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Galperin MY, Wolf YI, Makarova KS, Vera Alvarez R, Landsman D, Koonin EV. COG database update: focus on microbial diversity, model organisms, and widespread pathogens. Nucleic Acids Res 2021; 49:D274-D281. [PMID: 33167031 DOI: 10.1093/nar/gkaa1018] [Citation(s) in RCA: 342] [Impact Index Per Article: 114.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/20/2022] Open
Abstract
The Clusters of Orthologous Genes (COG) database, also referred to as the Clusters of Orthologous Groups of proteins, was created in 1997 and went through several rounds of updates, most recently, in 2014. The current update, available at https://www.ncbi.nlm.nih.gov/research/COG, substantially expands the scope of the database to include complete genomes of 1187 bacteria and 122 archaea, typically, with a single genome per genus. In addition, the current version of the COGs includes the following new features: (i) the recently deprecated NCBI's gene index (gi) numbers for the encoded proteins are replaced with stable RefSeq or GenBank\ENA\DDBJ coding sequence (CDS) accession numbers; (ii) COG annotations are updated for >200 newly characterized protein families with corresponding references and PDB links, where available; (iii) lists of COGs grouped by pathways and functional systems are added; (iv) 266 new COGs for proteins involved in CRISPR-Cas immunity, sporulation in Firmicutes and photosynthesis in cyanobacteria are included; and (v) the database is made available as a web page, in addition to FTP. The current release includes 4877 COGs. Future plans include further expansion of the COG collection by adding archaeal COGs (arCOGs), splitting the COGs containing multiple paralogs, and continued refinement of COG annotations.
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Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Roberto Vera Alvarez
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
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50
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Ares Á, Brisbin MM, Sato KN, Martín JP, Iinuma Y, Mitarai S. Extreme storms cause rapid but short-lived shifts in nearshore subtropical bacterial communities. Environ Microbiol 2021; 22:4571-4588. [PMID: 33448616 DOI: 10.1111/1462-2920.15178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/27/2020] [Accepted: 07/24/2020] [Indexed: 01/04/2023]
Abstract
Climate change scenarios predict tropical cyclones will increase in both frequency and intensity, which will escalate the amount of terrestrial run-off and mechanical disruption affecting coastal ecosystems. Bacteria are key contributors to ecosystem functioning, but relatively little is known about how they respond to extreme storm events, particularly in nearshore subtropical regions. In this study, we combine field observations and mesocosm experiments to assess bacterial community dynamics and changes in physicochemical properties during early- and late-season tropical cyclones affecting Okinawa, Japan. Storms caused large and fast influxes of freshwater and terrestrial sediment - locally known as red soil pollution - and caused moderate increases of macronutrients, especially SiO2 and PO4 3-, with up to 25 and 0.5 μM respectively. We detected shifts in relative abundances of marine and terrestrially derived bacteria, including putative coral and human pathogens, during storm events. Soil input alone did not substantially affect marine bacterial communities in mesocosms, indicating that other components of run-off or other storm effects likely exert a larger influence on bacterial communities. The storm effects were short-lived and bacterial communities quickly recovered following both storm events. The early- and late-season storms caused different physicochemical and bacterial community changes, demonstrating the context-dependency of extreme storm responses in a subtropical coastal ecosystem.
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Affiliation(s)
- Ángela Ares
- Marine Biophysics Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
| | - Margaret Mars Brisbin
- Marine Biophysics Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
| | - Kirk N Sato
- Marine Biophysics Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan.,Friday Harbor Laboratories, University of Washington, WA, USA
| | - Juan P Martín
- Marine Biophysics Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
| | - Yoshiteru Iinuma
- Instrumental Analysis Section, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
| | - Satoshi Mitarai
- Marine Biophysics Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
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