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Zhang FQ, Liu J, Chen XJ. Comparative analysis of bacterial diversity in two hot springs in Hefei, China. Sci Rep 2023; 13:5832. [PMID: 37037855 PMCID: PMC10086057 DOI: 10.1038/s41598-023-32853-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 04/03/2023] [Indexed: 04/12/2023] Open
Abstract
Hot springs are extreme ecological environments of microbes. The study is the first comparative analysis of bacterial diversity of Tangchi and Bantang hot spring water samples collected in Hefei, China, which is conducive to the further development and utilization of microbial resources in hot springs. Illumina MiSeq system was utilized to sequence and analyze the bacterial 16S rRNA gene from hot spring water samples by bioinformatics, to probe into the bacterial abundance and diversity of two hot springs in Hefei. Results revealed that prevalent bacterial phyla in Tangchi hot spring were Bacillota and Aquificota, and the prevalent bacterial genus was Hydrogenobacter; prevalent phyla in Bantang hot spring were Pseudomonadota followed by Actinobacteriota, and prevalent genera were CL500-29_marine_group and Polynucleobacter. More species and higher evenness in Bantang hot spring than those in Tangchi hot spring. In MetaCyc pathway analysis, the major pathways of metabolism existed in the bacteria from the two hot springs were 'pyruvate fermentation to isobutanol (engineered)', 'acetylene degradation', 'carbon fixation pathways in prokaryotes', 'nitrate reduction I (denitrification)', 'methanogenesis from acetate', 'superpathway of glucose and xylose degradation', etc.
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Affiliation(s)
- Feng-Qin Zhang
- College of Chemistry and Material Engineering, Chaohu University, Chaohu, 238024, Anhui, China
| | - Jun Liu
- College of Biology and Food Engineering, Anhui Polytechnic University, Wuhu, 241000, Anhui, China
| | - Xiao-Ju Chen
- College of Chemistry and Material Engineering, Chaohu University, Chaohu, 238024, Anhui, China.
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Pin Viso ND, Rizzo PF, Young BJ, Gabioud E, Bres P, Riera NI, Merino L, Farber MD, Crespo DC. The Use of Raw Poultry Waste as Soil Amendment Under Field Conditions Caused a Loss of Bacterial Genetic Diversity Together with an Increment of Eutrophic Risk and Phytotoxic Effects. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02119-0. [PMID: 36197502 DOI: 10.1007/s00248-022-02119-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Poultry waste has been used as fertilizer to avoid soil degradation caused by the long-term application of chemical fertilizer. However, few studies have evaluated field conditions where livestock wastes have been used for extended periods of time. In this study, physicochemical parameters, metabarcoding of the 16S rRNA gene, and ecotoxicity indexes were used for the characterization of chicken manure and poultry litter to examine the effect of their application to agricultural soils for 10 years. Poultry wastes showed high concentrations of nutrients and increased electrical conductivity leading to phytotoxic effects on seeds. The bacterial communities were dominated by typical members of the gastrointestinal tract, noting the presence of pathogenic bacteria. Soils subjected to poultry manure applications showed statistically higher values of total and extractable phosphorous, increasing the risk of eutrophication. Moreover, while the soil bacterial community remained dominated by the ones related to the biogeochemical cycles of nutrients and plant growth promotion, losses of alpha diversity were observed on treated soils. Altogether, our work would contribute to understand the effects of common local agricultural practices and support the adoption of the waste treatment process in compliance with environmental sustainability guidelines.
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Affiliation(s)
- Natalia D Pin Viso
- Instituto de Agrobiotecnología y Biología Molecular, IABiMo, INTA-CONICET, Calle Las Cabañas y Los Reseros s/n, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, 1425, Ciudad Autónoma de Buenos Aires, Argentina
- Universidad Nacional de Hurlingham, Tte. Origone 151, 1688, Hurlingham, Buenos Aires, Argentina
| | - Pedro F Rizzo
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola (IMyZA), Calle Las Cabañas y Los Reseros S/N, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
| | - Brian J Young
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola (IMyZA), Calle Las Cabañas y Los Reseros S/N, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
| | - Emmanuel Gabioud
- Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Agropecuaria Paraná, Ruta 11 Km 12.5, 3101, Oro Verde, Entre Ríos, Argentina
| | - Patricia Bres
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola (IMyZA), Calle Las Cabañas y Los Reseros S/N, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
| | - Nicolás I Riera
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola (IMyZA), Calle Las Cabañas y Los Reseros S/N, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
| | - Lina Merino
- Universidad Nacional de Hurlingham, Tte. Origone 151, 1688, Hurlingham, Buenos Aires, Argentina
| | - Marisa D Farber
- Instituto de Agrobiotecnología y Biología Molecular, IABiMo, INTA-CONICET, Calle Las Cabañas y Los Reseros s/n, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, 1425, Ciudad Autónoma de Buenos Aires, Argentina.
- Universidad Nacional de Hurlingham, Tte. Origone 151, 1688, Hurlingham, Buenos Aires, Argentina.
| | - Diana C Crespo
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, 1425, Ciudad Autónoma de Buenos Aires, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola (IMyZA), Calle Las Cabañas y Los Reseros S/N, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
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Blandón LM, Marín MA, Quintero M, Jutinico-Shubach LM, Montoya-Giraldo M, Santos-Acevedo M, Gómez-León J. Diversity of cultivable bacteria from deep-sea sediments of the Colombian Caribbean and their potential in bioremediation. Antonie van Leeuwenhoek 2022; 115:421-431. [PMID: 35066712 DOI: 10.1007/s10482-021-01706-4] [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: 09/01/2021] [Accepted: 12/28/2021] [Indexed: 11/26/2022]
Abstract
The diversity of deep-sea cultivable bacteria was studied in seven sediment samples of the Colombian Caribbean. Three hundred and fifty two marine bacteria were isolated according to its distinct morphological character on the solid media, then DNA sequences of the 16S rRNA were amplified to identify the isolated strains. The identified bacterial were arranged in three phylogenetic groups, Firmicutes, Proteobacteria, and Actinobacteria, with 34 different OTUs defined at ≥ 97% of similarity and 70 OTUs at ≥ 98.65%, being the 51% Firmicutes, 34% Proteobacteria and 15% Actinobacteria. Bacillus and Fictibacillus were the dominant genera in Firmicutes, Halomonas and Pseudomonas in Proteobacteria and Streptomyces and Micromonospora in Actinobacteria. In addition, the strains were tested for biosurfactants and lipolytic enzymes production, with 120 biosurfactant producing strains (mainly Firmicutes) and, 56 lipolytic enzymes producing strains (Proteobacteria). This report contributes to the understanding of the diversity of the marine deep-sea cultivable bacteria from the Colombian Caribbean, and their potential application as bioremediation agents.
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Affiliation(s)
- Lina Marcela Blandón
- Marine Bioprospecting Line, Marine and Coastal Research Institute "José Benito Vives de Andréis"- INVEMAR, Calle 25 No. 2-55, Playa Salguero, Santa Marta D.T.C.H., Colombia
| | - Mario Alejandro Marín
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas - UNICAMP, Campinas, SP, 13083-970, Brazil
| | - Marynes Quintero
- Marine Bioprospecting Line, Marine and Coastal Research Institute "José Benito Vives de Andréis"- INVEMAR, Calle 25 No. 2-55, Playa Salguero, Santa Marta D.T.C.H., Colombia
| | - Laura Marcela Jutinico-Shubach
- Marine Bioprospecting Line, Marine and Coastal Research Institute "José Benito Vives de Andréis"- INVEMAR, Calle 25 No. 2-55, Playa Salguero, Santa Marta D.T.C.H., Colombia
| | - Manuela Montoya-Giraldo
- Marine Bioprospecting Line, Marine and Coastal Research Institute "José Benito Vives de Andréis"- INVEMAR, Calle 25 No. 2-55, Playa Salguero, Santa Marta D.T.C.H., Colombia
| | - Marisol Santos-Acevedo
- Marine Bioprospecting Line, Marine and Coastal Research Institute "José Benito Vives de Andréis"- INVEMAR, Calle 25 No. 2-55, Playa Salguero, Santa Marta D.T.C.H., Colombia
| | - Javier Gómez-León
- Marine Bioprospecting Line, Marine and Coastal Research Institute "José Benito Vives de Andréis"- INVEMAR, Calle 25 No. 2-55, Playa Salguero, Santa Marta D.T.C.H., Colombia.
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Bacterial diversity changes in agricultural soils influenced by poultry litter fertilization. Braz J Microbiol 2021; 52:675-686. [PMID: 33590447 DOI: 10.1007/s42770-021-00437-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 02/02/2021] [Indexed: 01/28/2023] Open
Abstract
Poultry litter is widely applied as agricultural fertilizer and can affect the soil microbiome through nutrient overload and antibiotic contamination. In this study, we assessed changes in soil bacterial diversity using high-throughput sequencing approaches. Four samples in triplicate were studied: soils with short- and long-term fertilization by poultry litter (S1 = 10 months and S2 = 30 years, respectively), a soil inside a poultry shed (S3), and a forest soil used as control (S0). Samples S0, S1, and S2 revealed a relatively high richness, with confirmed operational taxonomic units (OTUs) in the three replicates of each sample ranging from 1243 to 1279, while richness in S3 was about three times lower (466). The most abundant phyla were Proteobacteria, Bacteroidetes, and Actinobacteria. Acidobacteria, Planctomycetes, and Verrucomicrobia were also abundant but highly diminished in S3, while Firmicutes was less abundant in S0. Changes in bacterial communities were very evident at the genera level. The genera Gaiella, Rhodoplanes, Solirubacter, and Sphingomonas were predominant in S0 but strongly decreased in the other soils. Pedobacter and Devosia were the most abundant in S1 and were diminished in S2, while Herbiconiux, Brevundimonas, Proteiniphilum, and Petrimonas were abundant in S2. The most abundant genera in S3 were Deinococcus, Truepera, Rhodanobacter, and Castellaniella. A predictive analysis of the metabolic functions with Tax4Fun2 software suggested the potential presence of enzymes associated with antibiotic resistance as well as with denitrification pathways, indicating that the S3 soil is a potential source of nitrous oxide, a powerful greenhouse gas.
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Misra P, Maji D, Awasthi A, Pandey SS, Yadav A, Pandey A, Saikia D, Babu CSV, Kalra A. Vulnerability of Soil Microbiome to Monocropping of Medicinal and Aromatic Plants and Its Restoration Through Intercropping and Organic Amendments. Front Microbiol 2019; 10:2604. [PMID: 31803153 PMCID: PMC6877478 DOI: 10.3389/fmicb.2019.02604] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 10/28/2019] [Indexed: 12/22/2022] Open
Abstract
Cultivation of medicinal and aromatic plants (MAPs) is persistently increasing due to excessive demands of naturals. Agricultural land and its microbial diversity are primarily adapted to conventional crops, and introduction of MAP and their continuous monocropping may disturb the ecological stability of soil microbiome. Here, the effect of cultivation of MAPs on soil microbial diversity was studied. The aim of the study is to examine the effects of cultivation of MAPs on the possible shift in soil microbial diversity and to restore such impacts by using organic amendments or intercropping. Terminal restriction fragments polymorphism (TRFLP) and next-generation sequencing (NGS) studies showed that of the various selected MAPs, maximal modulation in the soil microbial diversity patterns was noticed in fields of Mentha arvensis and Artemisia annua, and the traces of essential oil/phytochemicals were detected in bulk and rhizospheric soil. In both Artemisia- and Mentha-cultivated soil, the total operating taxonomic unit (OTU) declined in both bulk and rhizospheric soil in comparison to control (Zea mays), but the bacterial richness of Mentha soil was slightly higher than that of control. However, cultivation of Mentha improved the evenness of the microbial community. The inclusion of crops like Sesbania and Chlorophytum and the application of vermicompost (VC) enhanced the microbial richness and evenness, thereby restoring the soil microbial state shift and resulting in higher productivity in the continuously Mentha cropped field. Our study concludes that long-term cultivation of some MAPs may affect the richness but promote the evenness of microbial diversity. The state shift could be restored to some extent, and crop productivity could be enhanced by the inclusion of selected crops and organic manures in cropping systems.
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Affiliation(s)
- Pooja Misra
- Microbial Technology Department, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow, India
- Academy of Scientific and Innovative Research, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow, India
| | - Deepamala Maji
- Microbial Technology Department, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow, India
| | - Ashutosh Awasthi
- Microbial Technology Department, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow, India
| | - Shiv Shanker Pandey
- Microbial Technology Department, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow, India
| | - Anju Yadav
- Analytical Chemistry Department, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow, India
| | - Alok Pandey
- Microbial Technology Department, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow, India
| | - Dharmendra Saikia
- Department of Molecular Bioprospection, Council of Scientific and Industrial Research, Lucknow, India
| | - C. S. Vivek Babu
- Academy of Scientific and Innovative Research, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow, India
- Central Institute of Medicinal and Aromatic Plants, Research Centre, Council of Scientific and Industrial Research, Bengaluru, India
| | - Alok Kalra
- Microbial Technology Department, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow, India
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Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y, Takai K, Sievert SM, Simon J, Campbell BJ, Hanson TE, Woyke T, Klotz MG, Hugenholtz P. Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.). Front Microbiol 2017; 8:682. [PMID: 28484436 PMCID: PMC5401914 DOI: 10.3389/fmicb.2017.00682] [Citation(s) in RCA: 218] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 04/04/2017] [Indexed: 12/25/2022] Open
Abstract
The Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria. In order to address this issue, we investigated the phylogenetic placement of this class in the bacterial domain using 16S and 23S rRNA genes, as well as 120 single-copy marker proteins. Single- and concatenated-marker trees were created using a data set of 4,170 bacterial representatives, including 98 Epsilonproteobacteria. Phylogenies were inferred under a variety of tree building methods, with sequential jackknifing of outgroup phyla to ensure robustness of phylogenetic affiliations under differing combinations of bacterial genomes. Based on the assessment of nearly 300 phylogenetic tree topologies, we conclude that the continued inclusion of Epsilonproteobacteria within the Proteobacteria is not warranted, and that this group should be reassigned to a novel phylum for which we propose the name Epsilonbacteraeota (phyl. nov.). We further recommend the reclassification of the order Desulfurellales (Deltaproteobacteria) to a novel class within this phylum and a number of subordinate changes to ensure consistency with the genome-based phylogeny. Phylogenomic analysis of 658 genomes belonging to the newly proposed Epsilonbacteraeota suggests that the ancestor of this phylum was an autotrophic, motile, thermophilic chemolithotroph that likely assimilated nitrogen from ammonium taken up from the environment or generated from environmental nitrate and nitrite by employing a variety of functional redox modules. The emergence of chemoorganoheterotrophic lifestyles in several Epsilonbacteraeota families is the result of multiple independent losses of various ancestral chemolithoautotrophic pathways. Our proposed reclassification of this group resolves an important anomaly in bacterial systematics and ensures that the taxonomy of Proteobacteria remains robust, specifically as genome-based taxonomies become more common.
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Affiliation(s)
- David W. Waite
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St LuciaQLD, Australia
| | - Inka Vanwonterghem
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St LuciaQLD, Australia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St LuciaQLD, Australia
| | - Donovan H. Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St LuciaQLD, Australia
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, KingstonRI, USA
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and TechnologyYokosuka, Japan
| | - Stefan M. Sievert
- Department of Biology, Woods Hole Oceanographic Institution, Woods HoleMA, USA
| | - Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität DarmstadtDarmstadt, Germany
| | - Barbara J. Campbell
- Department of Biological Sciences, Life Science Facility, Clemson University, ClemsonSC, USA
| | - Thomas E. Hanson
- School of Marine Science and Policy, College of Earth, Ocean, and Environment, Delaware Biotechnology Institute, University of Delaware, NewarkDE, USA
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut CreekCA, USA
| | - Martin G. Klotz
- Department of Biology and School of Earth and Environmental Sciences, Queens College of the City University of New York, New YorkNY, USA
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen UniversityXiamen, China
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St LuciaQLD, Australia
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Emelyanov VV. Mitochondrial connection to the origin of the eukaryotic cell. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:1599-618. [PMID: 12694174 DOI: 10.1046/j.1432-1033.2003.03499.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Phylogenetic evidence is presented that primitively amitochondriate eukaryotes containing the nucleus, cytoskeleton, and endomembrane system may have never existed. Instead, the primary host for the mitochondrial progenitor may have been a chimeric prokaryote, created by fusion between an archaebacterium and a eubacterium, in which eubacterial energy metabolism (glycolysis and fermentation) was retained. A Rickettsia-like intracellular symbiont, suggested to be the last common ancestor of the family Rickettsiaceae and mitochondria, may have penetrated such a host (pro-eukaryote), surrounded by a single membrane, due to tightly membrane-associated phospholipase activity, as do present-day rickettsiae. The relatively rapid evolutionary conversion of the invader into an organelle may have occurred in a safe milieu via numerous, often dramatic, changes involving both partners, which resulted in successful coupling of the host glycolysis and the symbiont respiration. Establishment of a potent energy-generating organelle made it possible, through rapid dramatic changes, to develop genuine eukaryotic elements. Such sequential, or converging, global events could fill the gap between prokaryotes and eukaryotes known as major evolutionary discontinuity.
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