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Haque A, Chowdhury A, Islam Bhuiyan MN, Bhowmik B, Afrin S, Sarkar R, Haque MM. Molecular characterization, antibiotic resistant pattern and biofilm forming potentiality of bacterial community associated with Ompok pabda fish farming in southwestern Bangladesh. Microb Pathog 2024; 194:106818. [PMID: 39047804 DOI: 10.1016/j.micpath.2024.106818] [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: 04/22/2024] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
Ompok pabda is gaining popularity in the aquaculture industry due to its increasing demand; however research on microbial diversity and antibiotic susceptibility remains limited. The present study was designed to identify the bacterial pathogens commonly found in the pabda farming system with their biofilm forming potential and antibiotic susceptibility. Different bacterial strains were isolated from water, sediments and gut, gill of pabda fish and the isolates were identified based on their morphological traits, biochemical and molecular analysis. Antibiotic susceptibilities, antibiotic resistance gene determination and biofilm formation capabilities were evaluated by disc diffusion method, PCR amplification and Microtiter plate (MTP) assay, respectively. The respective isolates of gill and gut of pabda aquaculture and their environments were: Exiguobacterium spp. (25 %), Enterococcus spp. (20 %), Bacillus spp. (10 %), Acinetobacter spp. (10 %), Enterobacter spp. (10 %), Aeromonas spp. (10 %), Lactococcus spp. (5 %), Klebsiella spp. (5 %) and Kurthia spp. (5 %). Antibiotic resistance frequencies were found to be relatively high, especially for trimethoprim (95 %), sulfafurazole (75 %), ampicillin (60 %), amoxicillin-clavulanic acid (55 %), and cephradine (50 %). 30 % isolates were categorized as DR bacteria followed by 30 % isolates were MDR bacteria and 40 % were classified as XDR bacteria. Moreover, 4 antibiotic resistant genes were detected with sul1 (30 %), dfrA1 (10 %), tetC (40 %), and qnrA (5 %) of isolates. Based on the microtiter plate method, 20 %, 25 %, and 30 % of isolates were found to produce strong, moderate, and weak biofilms, respectively. The findings suggest that biofilm forming bacterial strains found in O. pabda fish farm may be a potential source of numerous antibiotic-resistant bacteria. The study sheds new light on antibiotic resistance genes, which are typically inherited by bacteria and play an important role in developing effective treatments or control strategies.
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Affiliation(s)
- Afrina Haque
- Department of Zoology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Abhijit Chowdhury
- Institute of Food Science and Technology (IFST), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh; Central Analytical & Research Facilities (CARF), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh.
| | - Mohammad Nazrul Islam Bhuiyan
- Institute of Food Science and Technology (IFST), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Banasree Bhowmik
- Institute of Food Science and Technology (IFST), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Sadia Afrin
- Institute of Food Science and Technology (IFST), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Rajib Sarkar
- Institute of Food Science and Technology (IFST), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Md Mansurul Haque
- Department of Zoology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
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Pracser N, Voglauer EM, Thalguter S, Pietzka A, Selberherr E, Wagner M, Rychli K. Exploring the occurrence of Listeria in biofilms and deciphering the bacterial community in a frozen vegetable producing environment. Front Microbiol 2024; 15:1404002. [PMID: 39050638 PMCID: PMC11266072 DOI: 10.3389/fmicb.2024.1404002] [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: 03/20/2024] [Accepted: 06/24/2024] [Indexed: 07/27/2024] Open
Abstract
The establishment of Listeria (L.) monocytogenes within food processing environments constitutes a significant public health concern. This versatile bacterium demonstrates an exceptional capacity to endure challenging environmental conditions in the food processing environment, where contamination of food products regularly occurs. The diverse repertoire of stress resistance genes, the potential to colonize biofilms, and the support of a co-existing microbiota have been proposed as root causes for the survival of L. monocytogenes in food processing environments. In this study, 71 sites were sampled after cleaning and disinfection in a European frozen vegetable processing facility, where L. monocytogenes in-house clones persisted for years. L. monocytogenes and L. innocua were detected by a culture-dependent method at 14 sampling sites, primarily on conveyor belts and associated parts. The presence of biofilms, as determined by the quantification of bacterial load and the analysis of extracellular matrix components (carbohydrates, proteins, extracellular DNA) was confirmed at nine sites (12.7%). In two cases, L. innocua was detected in a biofilm. Furthermore, we explored the resident microbial community in the processing environment and on biofilm-positive sites, as well as the co-occurrence of bacterial taxa with Listeria by 16S rRNA gene sequencing. Pseudomonas, Acinetobacter, and Exiguobacterium dominated the microbial community of the processing environment. Using differential abundance analysis, amplicon sequence variants (ASVs) assigned to Enterobacterales (Enterobacter, Serratia, unclassified Enterobacteriaceae) and Carnobacterium were found to be significantly higher abundant in Listeria-positive samples. Several Pseudomonas ASVs were less abundant in Listeria-positive compared to Listeria-negative samples. Acinetobacter, Pseudomonas, Janthinobacterium, Brevundimonas, and Exiguobacterium were key players in the microbial community in biofilms, and Exiguobacterium and Janthinobacterium were more relatively abundant in biofilms. Further, the microbial composition varied between the different areas and the surface materials.
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Affiliation(s)
- Nadja Pracser
- FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
| | - Eva M. Voglauer
- FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
| | - Sarah Thalguter
- FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
| | - Ariane Pietzka
- Austrian National Reference Laboratory for Listeria monocytogenes, Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Graz, Austria
| | - Evelyne Selberherr
- Clinical Department for Farm Animals and Food System Science, Centre for Food Science and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Martin Wagner
- FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
- Clinical Department for Farm Animals and Food System Science, Centre for Food Science and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Kathrin Rychli
- Clinical Department for Farm Animals and Food System Science, Centre for Food Science and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
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Kothe CI, Rasmussen JA, Mak SST, Gilbert MTP, Evans J. Exploring the microbial diversity of novel misos with metagenomics. Food Microbiol 2024; 117:104372. [PMID: 37919016 DOI: 10.1016/j.fm.2023.104372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 11/04/2023]
Abstract
Interest in fermented foods, especially plant-based ones, has increased considerably in the last decade. Miso-a Japanese paste traditionally fermented with soybeans, salt, and kōji (Aspergillus oryzae grown on grains or beans)-has gained attention among chefs for its rich flavour and versatility. Some chefs have even been experimenting with making novel misos with untraditional substrates to create new flavours. Such novel fermented foods also offer new scientific opportunities. To explore the microbial diversity of these new traditional foods, we sampled six misos made by the team at a leading restaurant called Noma in Copenhagen (Denmark), using yellow peas (including a nixtamalised treatment), lupin seeds, Swedish Vreta peas, grey peas, and Gotland lentils as substrates. All misos were made with the same recipe and fermented for 3 months at 28 °C. Samples were collected at the end of fermentation for subsequent shotgun metagenomic sequencing and a genome-resolved metagenomic analysis. The taxonomic profile of the samples revealed the presence of kōji mould (A. oryzae) and Bacillus amyloliquefaciens in all misos. Various species of the genera Latilactobacillus, Lactiplantibacillus, Pediococcus and Staphylococcus were also detected. The Metagenome-Assembled Genomes (MAGs) revealed genomic sequences belonging to 12 different species and functional analyses of these MAGs were performed. Notably, we detected the presence of Exiguobacterium-the first reported instance of the genus in miso-and Average Nucleotide Identity (ANI) analyses suggest a potentially new species. We hope these results will improve the scientific literature on misos and contribute to developing novel fermented plant-based foods.
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Affiliation(s)
- Caroline Isabel Kothe
- Sustainable Food Innovation Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark.
| | - Jacob Agerbo Rasmussen
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Denmark
| | - Sarah S T Mak
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Denmark; University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Joshua Evans
- Sustainable Food Innovation Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark.
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Vishnivetskaya TA, Niedermeyer J, Guttierrez-Rodriguerz E, Baltzegar D, Parsons C, Kathariou S. Draft genome sequence of Exiguobacterium sp. from whole cantaloupe, with inhibition capacity against Listeria monocytogenes. Microbiol Resour Announc 2024; 13:e0085023. [PMID: 38095870 DOI: 10.1128/mra.00850-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/15/2023] [Indexed: 01/18/2024] Open
Abstract
We report the draft genome sequence of a novel species, Exiguobacterium sp., isolated from a freshly harvested and untreated cantaloupe in North Carolina. The strain Exiguobacterium wild type exhibited inhibitory activity against the foodborne pathogen Listeria monocytogenes, including strains of diverse serotypes and genotypes, both on agar media and in biofilms.
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Affiliation(s)
| | - Jeffrey Niedermeyer
- Department of Food Science, North Carolina State University , Raleigh, North Carolina, USA
| | | | - David Baltzegar
- Genomic Sciences Laboratory, North Carolina State University , Raleigh, North Carolina, USA
| | - Cameron Parsons
- Department of Food Science, North Carolina State University , Raleigh, North Carolina, USA
| | - Sophia Kathariou
- Department of Food Science, North Carolina State University , Raleigh, North Carolina, USA
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Shen L, Liu Y, Chen L, Lei T, Ren P, Ji M, Song W, Lin H, Su W, Wang S, Rooman M, Pucci F. Genomic basis of environmental adaptation in the widespread poly-extremophilic Exiguobacterium group. THE ISME JOURNAL 2024; 18:wrad020. [PMID: 38365240 PMCID: PMC10837837 DOI: 10.1093/ismejo/wrad020] [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: 11/19/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 02/18/2024]
Abstract
Delineating cohesive ecological units and determining the genetic basis for their environmental adaptation are among the most important objectives in microbiology. In the last decade, many studies have been devoted to characterizing the genetic diversity in microbial populations to address these issues. However, the impact of extreme environmental conditions, such as temperature and salinity, on microbial ecology and evolution remains unclear so far. In order to better understand the mechanisms of adaptation, we studied the (pan)genome of Exiguobacterium, a poly-extremophile bacterium able to grow in a wide range of environments, from permafrost to hot springs. To have the genome for all known Exiguobacterium type strains, we first sequenced those that were not yet available. Using a reverse-ecology approach, we showed how the integration of phylogenomic information, genomic features, gene and pathway enrichment data, regulatory element analyses, protein amino acid composition, and protein structure analyses of the entire Exiguobacterium pangenome allows to sharply delineate ecological units consisting of mesophilic, psychrophilic, halophilic-mesophilic, and halophilic-thermophilic ecotypes. This in-depth study clarified the genetic basis of the defined ecotypes and identified some key mechanisms driving the environmental adaptation to extreme environments. Our study points the way to organizing the vast microbial diversity into meaningful ecologically units, which, in turn, provides insight into how microbial communities adapt and respond to different environmental conditions in a changing world.
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Affiliation(s)
- Liang Shen
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, and Anhui Provincial Engineering Research Centre for Molecular Detection and Diagnostics, Anhui Normal University, Wuhu 241000, China
| | - Yongqin Liu
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Liangzhong Chen
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Tingting Lei
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Ping Ren
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Mukan Ji
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Weizhi Song
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, NSW 2052, Australia
| | - Hao Lin
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Wei Su
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Sheng Wang
- Shanghai Zelixir Biotech Company Ltd., Shanghai 200030, China
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels 1050, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Brussels 1050, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels 1050, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Brussels 1050, Belgium
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An J, Sun L, Liu M, Dai R, Ge G, Wang Z, Jia Y. Influences of Growth Stage and Ensiling Time on Fermentation Characteristics, Nitrite, and Bacterial Communities during Ensiling of Alfalfa. PLANTS (BASEL, SWITZERLAND) 2023; 13:84. [PMID: 38202392 PMCID: PMC10780930 DOI: 10.3390/plants13010084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/05/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024]
Abstract
This study examined the impacts of growth stage and ensiling duration on the fermentation characteristics, nitrite content, and bacterial communities during the ensiling of alfalfa. Harvested alfalfa was divided into two groups: vegetative growth stage (VG) and late budding stage (LB). The fresh alfalfa underwent wilting until reaching approximately 65% moisture content, followed by natural fermentation. The experiment followed a completely randomized design, with samples collected after the wilting of alfalfa raw materials (MR) and on days 1, 3, 5, 7, 15, 30, and 60 of fermentation. The growth stage significantly influenced the chemical composition of alfalfa, with crude protein content being significantly higher in the vegetative growth stage alfalfa compared to that in the late budding stage (p < 0.05). Soluble carbohydrates, neutral detergent fiber, and acid detergent fiber content were significantly lower in the vegetative growth stage compared to the late budding stage (p < 0.05). Nitrite content, nitrate content, nitrite reductase activity, and nitrate reductase activity were all significantly higher in the vegetative growth stage compared to the late budding stage (p < 0.05). In terms of fermentation parameters, silage from the late budding stage exhibited superior characteristics compared to that from the vegetative growth stage. Compared to the alfalfa silage during the vegetative growth stage, the late budding stage group exhibited a higher lactate content and lower pH level. Notably, butyric acid was only detected in the silage from the vegetative growth stage group. Throughout the ensiling process, nitrite content, nitrate levels, nitrite reductase activity, and nitrate reductase activity decreased in both treatment groups. The dominant lactic acid bacteria differed between the two groups, with Enterococcus being predominant in vegetative growth stage alfalfa silage, and Weissella being predominant in late budding stage silage, transitioning to Lactiplantibacillus in the later stages of fermentation. On the 3rd day of silage fermentation, the vegetative growth stage group exhibited the highest abundance of Enterococcus, which subsequently decreased to its lowest level on the 15th day. Correlation analysis revealed that lactic acid bacteria, including Limosilactobacillus, Levilactobacillus, Loigolactobacillus, Pediococcus, Lactiplantibacillus, and Weissella, played a key role in nitrite and nitrate degradation in alfalfa silage. The presence of nitrite may be linked to Erwinia, unclassified_o__Enterobacterales, Pantoea, Exiguobacterium, Enterobacter, and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium.
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Affiliation(s)
- Jiangbo An
- Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot 010019, China; (J.A.); (M.L.); (R.D.); (G.G.); (Z.W.)
- Key Laboratory of Grassland Resources, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010019, China
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Lin Sun
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China;
| | - Mingjian Liu
- Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot 010019, China; (J.A.); (M.L.); (R.D.); (G.G.); (Z.W.)
- Key Laboratory of Grassland Resources, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010019, China
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Rui Dai
- Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot 010019, China; (J.A.); (M.L.); (R.D.); (G.G.); (Z.W.)
- Key Laboratory of Grassland Resources, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010019, China
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Gentu Ge
- Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot 010019, China; (J.A.); (M.L.); (R.D.); (G.G.); (Z.W.)
- Key Laboratory of Grassland Resources, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010019, China
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Zhijun Wang
- Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot 010019, China; (J.A.); (M.L.); (R.D.); (G.G.); (Z.W.)
- Key Laboratory of Grassland Resources, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010019, China
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Yushan Jia
- Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot 010019, China; (J.A.); (M.L.); (R.D.); (G.G.); (Z.W.)
- Key Laboratory of Grassland Resources, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010019, China
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010019, China
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Sadeghi J, Chaganti SR, Johnson TB, Heath DD. Host species and habitat shape fish-associated bacterial communities: phylosymbiosis between fish and their microbiome. MICROBIOME 2023; 11:258. [PMID: 37981701 PMCID: PMC10658978 DOI: 10.1186/s40168-023-01697-6] [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: 07/13/2022] [Accepted: 10/11/2023] [Indexed: 11/21/2023]
Abstract
BACKGROUND While many studies have reported that the structure of the gut and skin microbiota is driven by both species-specific and habitat-specific factors, the relative importance of host-specific versus environmental factors in wild vertebrates remains poorly understood. The aim of this study was to determine the diversity and composition of fish skin, gut, and surrounding water bacterial communities (hereafter referred to as microbiota) and assess the extent to which host habitat and phylogeny predict microbiota similarity. Skin swabs and gut samples from 334 fish belonging to 17 species were sampled in three Laurentian Great Lakes (LGLs) habitats (Detroit River, Lake Erie, Lake Ontario). We also collected and filtered water samples at the time of fish collection. We analyzed bacterial community composition using 16S metabarcoding and tested for community variation. RESULTS We found that the water microbiota was distinct from the fish microbiota, although the skin microbiota more closely resembled the water microbiota. We also found that environmental (sample location), habitat, fish diet, and host species factors shape and promote divergence or convergence of the fish microbiota. Since host species significantly affected both gut and skin microbiota (separately from host species effects), we tested for phylosymbiosis using pairwise host species phylogenetic distance versus bacterial community dissimilarity. We found significant phylogenetic effects on bacterial community dissimilarity, consistent with phylosymbiosis for both the fish skin and gut microbiota, perhaps reflecting the longstanding co-evolutionary relationship between the host species and their microbiomes. CONCLUSIONS Analyzing the gut and skin mucus microbiota across diverse fish species in complex natural ecosystems such as the LGLs provides insights into the potential for habitat and species-specific effects on the microbiome, and ultimately the health, of the host. Video Abstract.
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Affiliation(s)
- Javad Sadeghi
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, N9B 3P4, Canada
| | - Subba Rao Chaganti
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, USA
| | - Timothy B Johnson
- Ontario Ministry of Natural Resources and Forestry, Glenora Fisheries Station, Picton, ON, Canada
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, N9B 3P4, Canada.
- Department of Integrative Biology, University of Windsor, Windsor, ON, Canada.
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Sun Y, Zhang Y, Hao X, Zhang X, Ma Y, Niu Z. A novel marine bacterium Exiguobacterium marinum a-1 isolated from in situ plastisphere for degradation of additive-free polypropylene. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 336:122390. [PMID: 37597737 DOI: 10.1016/j.envpol.2023.122390] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/21/2023]
Abstract
As the ecological niche most closely associated with polymers, microorganisms in the 'plastisphere' have great potential for plastics degradation. Microorganisms isolated from the 'plastisphere' could colonize and degrade commercial plastics containing different additives, but the observed weight loss and surface changes were most likely caused by releasing the additives rather than actual degradation of the plastics itself. Unlike commercial plastics that contain additives, whether marine microorganisms in the 'plastisphere' have adapted to additive-free plastics as a surface to colonize and potentially degrade is not yet known. Herein, a novel marine bacterium, Exiguobacterium marinum a-1, was successfully isolated from mature 'plastisphere' that had been deployed in situ for up to 20 months. Strain a-1 could use additive-free polypropylene (PP) films as its primary energy and carbon source. After strain a-1 was incubated with additive-free PP films for 80 days, the weight of films decreased by 9.2%. The ability of strain a-1 to rapidly form biofilms and effectively colonize the surface of additive-free PP films was confirmed by Scanning Electron Microscopy (SEM), as reflected by the increase in roughness and visible craters on the surface of additive-free PP films. Additionally, the functional groups of -CO, -C-H, and -OH were identified on the treated additive-free PP films according to Fourier Transform Infrared (FTIR). Genomic data from strain a-1 revealed a suite of key genes involved in biosurfactant synthesis, flagellar assembly, and cellular chemotaxis, contributing to its rapid biofilm formation on hydrophobic polymer surfaces. In particular, key enzymes that may be responsible for the degradation of additive-free PP films, such as glutathione peroxidase, cytochrome p450 and esterase were also recognized. This study highlights the potential of microorganisms present in the 'plastisphere' to metabolize plastic polymers and points to the intrinsic importance of the new strain a-1 in the mitigation of plastic pollution.
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Affiliation(s)
- Yueling Sun
- School of Marine Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Ying Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Xiaohan Hao
- School of Marine Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Xiaohan Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Yongzheng Ma
- School of Marine Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Zhiguang Niu
- School of Marine Science and Technology, Tianjin University, Tianjin, 300072, China; International Joint Institute of Tianjin University, Fuzhou, Fuzhou, 350205, China.
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Bendia AG, Moreira JCF, Ferreira JCN, Romano RG, Ferreira IGC, Franco DC, Evangelista H, Montone RC, Pellizari VH. Insights into Antarctic microbiomes: diversity patterns for terrestrial and marine habitats. AN ACAD BRAS CIENC 2023; 95:e20211442. [PMID: 37820122 DOI: 10.1590/0001-3765202320211442] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 08/27/2022] [Indexed: 10/13/2023] Open
Abstract
Microorganisms in Antarctica are recognized for having crucial roles in ecosystems functioning and biogeochemical cycles. To explore the diversity and composition of microbial communities through different terrestrial and marine Antarctic habitats, we analyze 16S rRNA sequence datasets from fumarole and marine sediments, soil, snow and seawater environments. We obtained measures of alpha- and beta-diversities, as well as we have identified the core microbiome and the indicator microbial taxa of a particular habitat. Our results showed a unique microbial community structure according to each habitat, including specific taxa composing each microbiome. Marine sediments harbored the highest microbial diversity among the analyzed habitats. In the fumarole sediments, the core microbiome was composed mainly of thermophiles and hyperthermophilic Archaea, while in the majority of soil samples Archaea was absent. In the seawater samples, the core microbiome was mainly composed by cultured and uncultured orders usually identified on Antarctic pelagic ecosystems. Snow samples exhibited common taxa previously described for habitats of the Antarctic Peninsula, which suggests long-distance dispersal processes occurring from the Peninsula to the Continent. This study contributes as a baseline for further efforts on evaluating the microbial responses to environmental conditions and future changes.
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Affiliation(s)
- Amanda G Bendia
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Julio Cezar F Moreira
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Juliana C N Ferreira
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Renato G Romano
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Ivan G C Ferreira
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Diego C Franco
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Heitor Evangelista
- Universidade do Estado do Rio de Janeiro (UERJ), Instituto de Biologia Roberto Alcantara Gomes, Maracanã, 20550-013 Rio de Janeiro, RJ, Brazil
| | - Rosalinda C Montone
- Universidade de São Paulo (USP), Departamento de Oceanografia Física, Química e Geológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Vivian Helena Pellizari
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
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10
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Makaranga A, Jutur PP. Dynamic metabolomic crosstalk between Chlorella saccharophila and its new symbiotic bacteria enhances lutein production in microalga without compromising its biomass. Enzyme Microb Technol 2023; 170:110291. [PMID: 37481992 DOI: 10.1016/j.enzmictec.2023.110291] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/29/2023] [Accepted: 07/16/2023] [Indexed: 07/25/2023]
Abstract
The microalgae Chlorella saccharophila UTEX247 was co-cultured with its symbiotic indigenous isolated bacterial strain, Exiguobacterium sp., to determine the possible effects of bacteria on microalgae growth and lutein productivity. Under optimal conditions, the lutein productivity of co-culture was 298.97 µg L-1 d-1, which was nearly 1.45-fold higher compared to monocultures i.e., 103.3 µg L-1 d-1. The highest lutein productivities were obtained in co-cultures, accompanied by a significant increase in cell biomass up to 0.84-fold. These conditions were analyzed using an untargeted metabolomics approach to identify metabolites enhancing valuable renewables, i.e., lutein, without compromising growth. Our qualitative metabolomic analysis identified nearly 30 (microalgae alone), 41 (bacteria alone), and 75 (co-cultures) metabolites, respectively. Among these, 46 metabolites were unique in the co-culture alone. The co-culture interactions significantly altered the role of metabolites such as thiamine precursors, reactive sugar anomers like furanose and branched-chain amino acids (BCAA). Nevertheless, the central metabolism cycle upregulation depicted increased availability of carbon skeletons, leading to increased cell biomass and pigments. In conclusion, the co-cultures induce the production of relevant metabolites which regulate growth and lutein simultaneously in C. saccharophila UTEX247, which paves the way for a new perspective in microalgal biorefineries.
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Affiliation(s)
- Abdalah Makaranga
- Omics of Algae Group and DBT-ICGEB Centre for Advanced Bioenergy Research, Industrial Biotechnology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Pannaga Pavan Jutur
- Omics of Algae Group and DBT-ICGEB Centre for Advanced Bioenergy Research, Industrial Biotechnology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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11
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Rincón-Rosales R, Rogel MA, Rincón-Molina CI, Guerrero G, Manzano-Gómez LA, López-López A, Rincón Molina FA, Martínez-Romero E. Complete genome sequence of Exiguobacterium profundum TSS-3 isolated from an extremely saline-alkaline spring located in Ixtapa, Chiapas-México. Microbiol Resour Announc 2023; 12:e0017123. [PMID: 37606375 PMCID: PMC10508092 DOI: 10.1128/mra.00171-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 07/14/2023] [Indexed: 08/23/2023] Open
Abstract
We report the complete genome sequence of Exiguobacterium profundum TSS-3, a strain isolated from the sediment of an extremely saline-alkaline spring located in Ixtapa, Chiapas-México (16° 47´ LN and 92° 54´ LO). Its genome is composed of a 2.8-Mb chromosome and a small 4.6-Kb plasmid.
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Affiliation(s)
- Reiner Rincón-Rosales
- Departamento de Ingeniería Química y Bioquímica, Tecnológico Nacional de México / Instituto Tecnológico de Tuxtla Gutiérrez, Tuxtla Gutiérrez, Chiapas, Mexico
| | - Marco A. Rogel
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Clara Ivette Rincón-Molina
- Departamento de Ingeniería Química y Bioquímica, Tecnológico Nacional de México / Instituto Tecnológico de Tuxtla Gutiérrez, Tuxtla Gutiérrez, Chiapas, Mexico
| | - Gabriela Guerrero
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | | - Aline López-López
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Francisco A. Rincón Molina
- Departamento de Ingeniería Química y Bioquímica, Tecnológico Nacional de México / Instituto Tecnológico de Tuxtla Gutiérrez, Tuxtla Gutiérrez, Chiapas, Mexico
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12
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Huang Y, Tang J, Zhang B, Long ZE, Ni H, Fu X, Zou L. Influencing factors and mechanism of Cr(VI) reduction by facultative anaerobic Exiguobacterium sp. PY14. Front Microbiol 2023; 14:1242410. [PMID: 37637125 PMCID: PMC10449125 DOI: 10.3389/fmicb.2023.1242410] [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: 06/19/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023] Open
Abstract
Microbial reduction is an effective way to deal with hexavalent chromium [Cr(VI)] contamination in the environment, which can significantly mitigate the biotoxicity and migration of this pollutant. The present study investigated the influence of environmental factors on aqueous Cr(VI) removal by a newly isolated facultative anaerobic bacterium, Exiguobacterium sp. PY14, and revealed the reduction mechanism. This strain with a minimum inhibitory concentration of 400 mg/L showed the strongest Cr(VI) removal capacity at pH 8.0 because of its basophilic nature, which was obviously depressed by increasing the Cr(VI) initial concentration under both aerobic and anaerobic conditions. In contrast, the removal rate constant for 50 mg/L of Cr(VI) under anaerobic conditions (1.82 × 10-2 h-1) was 3.3 times that under aerobic conditions. The co-existence of Fe(III) and Cu(II) significantly promoted the removal of Cr(VI), while Ag(I), Pb(II), Zn(II), and Cd(II) inhibited it. Electron-shuttling organics such as riboflavin, humic acid, and anthraquinone-2,6-disulfonate promoted the Cr(VI) removal to varying degrees, and the enhancement was more significant under anaerobic conditions. The removal of aqueous Cr(VI) by strain PY14 was demonstrated to be due to cytoplasmic rather than extracellular reduction by analyzing the contributions of different cell components, and the end products existed in the aqueous solution in the form of organo-Cr(III) complexes. Several possible genes involved in Cr(VI) metabolism, including chrR and chrA that encode well-known Chr family proteins responsible for chromate reduction and transport, respectively, were identified in the genome of PY14, which further clarified the Cr(VI) reduction pathway of this strain. The research progress in the influence of crucial environmental factors and biological reduction mechanisms will help promote the potential application of Exiguobacterium sp. PY14 with high adaptability to environmental stress in Cr(VI) removal in the actual environment.
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Affiliation(s)
- Yunhong Huang
- Nanchang Key Laboratory of Microbial Resources Exploitation and Utilization from Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, China
| | - Jie Tang
- Nanchang Key Laboratory of Microbial Resources Exploitation and Utilization from Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, China
| | - Bei Zhang
- College of Art and Design, Jiangxi Institute of Fashion Technology, Nanchang, China
| | - Zhong-Er Long
- Nanchang Key Laboratory of Microbial Resources Exploitation and Utilization from Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, China
| | - Haiyan Ni
- Nanchang Key Laboratory of Microbial Resources Exploitation and Utilization from Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, China
| | - Xueqin Fu
- Nanchang Key Laboratory of Microbial Resources Exploitation and Utilization from Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, China
| | - Long Zou
- Nanchang Key Laboratory of Microbial Resources Exploitation and Utilization from Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, China
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13
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Sieler MJ, Al-Samarrie CE, Kasschau KD, Varga ZM, Kent ML, Sharpton TJ. Disentangling the link between zebrafish diet, gut microbiome succession, and Mycobacterium chelonae infection. Anim Microbiome 2023; 5:38. [PMID: 37563644 PMCID: PMC10413624 DOI: 10.1186/s42523-023-00254-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 06/21/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND Despite the long-established importance of zebrafish (Danio rerio) as a model organism and their increasing use in microbiome-targeted studies, relatively little is known about how husbandry practices involving diet impact the zebrafish gut microbiome. Given the microbiome's important role in mediating host physiology and the potential for diet to drive variation in microbiome composition, we sought to clarify how three different dietary formulations that are commonly used in zebrafish facilities impact the gut microbiome. We compared the composition of gut microbiomes in approximately 60 AB line adult (129- and 214-day-old) zebrafish fed each diet throughout their lifespan. RESULTS Our analysis finds that diet has a substantial impact on the composition of the gut microbiome in adult fish, and that diet also impacts the developmental variation in the gut microbiome. We further evaluated how 214-day-old fish microbiome compositions respond to exposure of a common laboratory pathogen, Mycobacterium chelonae, and whether these responses differ as a function of diet. Our analysis finds that diet determines the manner in which the zebrafish gut microbiome responds to M. chelonae exposure, especially for moderate and low abundance taxa. Moreover, histopathological analysis finds that male fish fed different diets are differentially infected by M. chelonae. CONCLUSIONS Overall, our results indicate that diet drives the successional development of the gut microbiome as well as its sensitivity to exogenous exposure. Consequently, investigators should carefully consider the role of diet in their microbiome zebrafish investigations, especially when integrating results across studies that vary by diet.
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Affiliation(s)
- Michael J Sieler
- Department of Microbiology, Oregon State University, Corvallis, OR, 97330, USA
| | | | - Kristin D Kasschau
- Department of Microbiology, Oregon State University, Corvallis, OR, 97330, USA
| | - Zoltan M Varga
- Zebrafish International Resource Center, University of Oregon, Eugene, OR, 97330, USA
| | - Michael L Kent
- Department of Microbiology, Oregon State University, Corvallis, OR, 97330, USA
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, 97330, USA
- Zebrafish International Resource Center, University of Oregon, Eugene, OR, 97330, USA
| | - Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR, 97330, USA.
- Department of Statistics, Oregon State University, Corvallis, OR, 97330, USA.
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14
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López-Sánchez R, Hernández-Oaxaca D, Escobar-Zepeda A, Ramos Cerrillo B, López-Munguía A, Segovia L. Analysing the dynamics of the bacterial community in pozol, a Mexican fermented corn dough. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001355. [PMID: 37410634 PMCID: PMC10433422 DOI: 10.1099/mic.0.001355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/13/2023] [Indexed: 07/08/2023]
Abstract
Pozol is a traditional prehispanic Mexican beverage made from fermented nixtamal dough; it is still part of everyday life in many communities due to its nutritional properties. It is the product of spontaneous fermentation and has a complex microbiota composed primarily of lactic acid bacteria (LAB). Although this is a beverage that has been used for centuries, the microbial processes that participate in this fermented beverage are not well understood. We fermented corn dough to produce pozol and sampled it at four key times to follow the community and metabolic changes (0, 9 24 and 48 h) by shotgun metagenomic sequencing to determine structural changes in the bacterial community, as well as metabolic genes used for substrate fermentation, nutritional properties and product safety. We found a core of 25 abundant genera throughout the 4 key fermentation times, with the genus Streptococcus being the most prevalent throughout fermentation. We also performed an analysis focused on metagenomic assembled genomes (MAGs) to identify species from the most abundant genera. Genes involving starch, plant cell wall (PCW), fructan and sucrose degradation were found throughout fermentation and in MAGs, indicating the metabolic potential of the pozol microbiota to degrade these carbohydrates. Complete metabolic modules responsible for amino acid and vitamin biosynthesis increased considerably during fermentation, and were also found to be abundant in MAG, highlighting the bacterial contribution to the well-known nutritional properties attributed to pozol. Further, clusters of genes containing CAZymes (CGCs) and essential amino acids and vitamins were found in the reconstructed MAGs for abundant species in pozol. The results of this study contribute to our understanding of the metabolic role of micro-organisms in the transformation of corn to produce this traditional beverage and their contribution to the nutritional impact that pozol has had for centuries in the traditional cuisine of southeast Mexico.
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Affiliation(s)
- Rafael López-Sánchez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, CP 62210, Mexico
| | - Diana Hernández-Oaxaca
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, CP 62210, Mexico
| | | | - Blanca Ramos Cerrillo
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, CP 62210, Mexico
| | - Agustin López-Munguía
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, CP 62210, Mexico
| | - Lorenzo Segovia
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, CP 62210, Mexico
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15
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Purohit A, Pawar L, Yadav SK. Structural and functional insights of a cold-adaptive β-glucosidase with very high glucose tolerance from Microbacterium sp. CIAB417. Enzyme Microb Technol 2023; 169:110284. [PMID: 37406591 DOI: 10.1016/j.enzmictec.2023.110284] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/07/2023]
Abstract
A gene glu1 (WP_243232135.1) coding for β-glucosidase from the genome of Microbacterium sp. CIAB417 was characterized for its cold adaptive nature and tolerance to high levels of glucose and ethanol. The phylogenetic analysis suggested the close association of glu1 with a similar gene from a mesophilic bacterium Microbacterium indicum. The purified recombinant GLU1 displayed its optimal activity and stability at pH 5 and temperature 30ᴼC. Additionally, the presence of L3 loop in GLU1 suggested its cold adaptive nature. The glucose tolerant Gate keeper residues (Leu 174 & Trp 169) with a distance of ∼ 6.953 Å between them was also predicted in GLU1. The GLU1 enzyme showed ≥ 95% and ≥ 40% relative activity in the presence of 5 M glucose and 20% ethanol. The Vmax, Km, and Kcat values of GLU1 for cellobiose substrate were observed to be 45.22 U/mg, 3.5 mM, and 41.0157 s-1, respectively. The GLU1 was found to be highly efficient in hydrolysis of celloologosaccharides (C2-C5), lactose and safranal picrocrocin into glucose. Hence, cold adaptive GLU1 with very high glucose and ethanol tolerance could be very useful in bio-refinery, dairy, and flavor industries.
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Affiliation(s)
- Anjali Purohit
- Biotechnology and Synthetic Biology, Center of Innovative and Applied Bioprocessing (CIAB), Knowledge City, Sector-81, Mohali 140306, Punjab, India
| | - Lata Pawar
- Biotechnology and Synthetic Biology, Center of Innovative and Applied Bioprocessing (CIAB), Knowledge City, Sector-81, Mohali 140306, Punjab, India
| | - Sudesh Kumar Yadav
- Biotechnology and Synthetic Biology, Center of Innovative and Applied Bioprocessing (CIAB), Knowledge City, Sector-81, Mohali 140306, Punjab, India; Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, India.
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16
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Yuan D, Wang L, Wang H, Miao R, Wang Y, Jin H, Tan L, Wei C, Hu Q, Gong Y. Application of microalgae Scenedesmus acuminatus enhances water quality in rice-crayfish culture. Front Bioeng Biotechnol 2023; 11:1143622. [PMID: 37214297 PMCID: PMC10192885 DOI: 10.3389/fbioe.2023.1143622] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Improper management of aquatic environments substantially restricts the development of the aquaculture industry. The industrialisation of the crayfish Procambarus clarkii, for example, is currently being limited by poor water quality. Research suggests that microalgal biotechnology has a great potential for water quality regulation. However, the ecological effects of microalgal applications on aquatic communities in aquaculture systems remain largely unknown. In the present study, 5 L Scenedesmus acuminatus GT-2 culture (biomass 120 g L-1) was added to an approximately 1,000 m2 rice-crayfish culture to examine the response of aquatic ecosystems to microalgal application. The total nitrogen content decreased significantly as a result of microalgal addition. Moreover, the microalgal addition changed the bacterial community structure directionally and produced more nitrate reducing and aerobic bacteria. The effect of microalgal addition on plankton community structure was not obvious, except for a significant difference in Spirogyra growth which was inhibited by 81.0% under microalgal addition. Furthermore, the network of microorganisms in culture systems with the added microalga had higher interconnectivity and was more complex, which indicating microalgal application enhance the stability of aquaculture systems. The application of microalgae was found to have the greatest effect on the 6th day of the experiment, as supported by both environmental and biological evidence. These findings can provide valuable guidance for the practical application of microalgae in aquaculture systems.
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Affiliation(s)
- Danni Yuan
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Lan Wang
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Hongxia Wang
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Rongli Miao
- Hydrobiological Data Analysis Center, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yulu Wang
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Hu Jin
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Lu Tan
- Systems Ecology and Watershed Ecology Center for Freshwater Ecology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chaojun Wei
- Hydrobiological Data Analysis Center, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Qiang Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yingchun Gong
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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17
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Barghoth MG, Desouky SE, Radwan AA, Shah MP, Salem SS. Characterizations of highly efficient moderately halophilic toluene degrading exiguobacterium mexicanum M7 strain isolated from Egyptian saline sediments. Biotechnol Genet Eng Rev 2023:1-19. [PMID: 36861663 DOI: 10.1080/02648725.2023.2184053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/15/2023] [Indexed: 03/03/2023]
Abstract
Toluene and other monoaromatic compounds are released into the environment particularly saline habitats due to the inappropriate disposal methods of petroleum products. Studying the bio-removal strategy is required to clean up these hazardous hydrocarbons that threaten all ecosystem life using halophilic bacteria with higher biodegradation efficiency of monoaromatic compounds as a sole carbon and energy source. Therefore, sixteen pure halophilic bacterial isolates were obtained from saline soil of Wadi An Natrun, Egypt, which have the ability to degrade toluene and consume it as the only source of carbon and energy. Amongst these isolates, isolate M7 exhibited the best growth with considerable properties. This isolate was selected as the most potent strain and identified based on phenotypic and genotypic characterizations. The strain M7 was belonging to Exiguobacterium genus and founded to be closely matched to the Exiguobacterium mexicanum with a similarity of 99%. Using toluene as sole carbon source, strain M7 showed good growth at a wide range temperature degree (20-40ºC), pH (5-9), and salt concentrations (2.5-10%, w/v) with optimal growth conditions at 35ºC, pH 8, and 5%, respectively. The biodegradation ratio of toluene was estimated at above optimal conditions and analyzed using Purge-Trap GC-MS. The results showed that strain M7 has the potentiality to degraded 88.32% of toluene within greatly short time (48 h). The current study findings support the potential ability to use strain M7 as a biotechnological tool in many applications such as effluent treatment and toluene waste management.
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Affiliation(s)
- Mohammed G Barghoth
- Department of Botany and Microbiology, Faculty of Science (Boys), Al-Azhar University, Nasr, Cairo, Egypt
| | - Said E Desouky
- Department of Botany and Microbiology, Faculty of Science (Boys), Al-Azhar University, Nasr, Cairo, Egypt
| | - Ahmed A Radwan
- Department of Botany and Microbiology, Faculty of Science (Boys), Al-Azhar University, Nasr, Cairo, Egypt
| | - Maulin P Shah
- Industrial Waste Water Research Lab, Enviro Technology Ltd, Ankleshwar, Gujarat, India
| | - Salem S Salem
- Department of Botany and Microbiology, Faculty of Science (Boys), Al-Azhar University, Nasr, Cairo, Egypt
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18
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Sieler M, Al-Samarrie C, Kasschau K, Varga Z, Kent M, Sharpton T. Common laboratory diets differentially influence zebrafish gut microbiome's successional development and sensitivity to pathogen exposure. RESEARCH SQUARE 2023:rs.3.rs-2530939. [PMID: 36778316 PMCID: PMC9915791 DOI: 10.21203/rs.3.rs-2530939/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Background Despite the long-established importance of zebrafish (Danio rerio) as a model organism and their increasing use in microbiome-targeted studies, relatively little is known about how husbandry practices involving diet impact the zebrafish gut microbiome. Given the microbiome's important role in mediating host physiology and the potential for diet to drive variation in microbiome composition, we sought to clarify how three different dietary formulations that are commonly used in zebrafish facilities impact the gut microbiome. We compared the composition of gut microbiomes in approximately 60 AB line adult (4- and 7-month-old) zebrafish fed each diet throughout their lifespan. Results Our analysis finds that diet has a substantial impact on the composition of the gut microbiome in adult fish, and that diet also impacts the developmental variation in the gut microbiome. We further evaluated whether the 7-month-old fish microbiome compositions that result from dietary variation are differentially sensitive to infection by a common laboratory pathogen, Mycobacterium chelonae. Our analysis finds that the gut microbiome's sensitivity to M. chelonae infection varies as a function of diet, especially for moderate and low abundance taxa. Conclusions Overall, our results indicate that diet drives the successional development of the gut microbiome as well as its sensitivity to exogenous exposure. Consequently, investigators should carefully consider the role of diet in their microbiome zebrafish investigations, especially when integrating results across studies that vary by diet.
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19
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Zhao Z, Oury BM, Xia L, Qin Z, Pan X, Qian J, Luo F, Wu Y, Liu L, Wang W. The ecological response and distribution characteristics of microorganisms and polycyclic aromatic hydrocarbons in a retired coal gas plant post-thermal remediation site. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159314. [PMID: 36220477 DOI: 10.1016/j.scitotenv.2022.159314] [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: 07/15/2022] [Revised: 09/16/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Thermal remediation is one of the most common approaches of removing organic pollutants in the retired contamination sites. However, little is known about the performance of bacterial community characteristics after in situ thermal remediation. In this study, the ecological response and spatial distributional characteristics of microorganisms and polycyclic aromatic hydrocarbons (PAHs) were investigated using a high throughput sequencing method in a retired coal gas plant site after in situ thermal remediation in Nanjing, China. Combination of Venn, clustering-correlation heatmap and two - factor correlation network analysis revealed that, microbial communities were obviously affected and classified by soil depths, temperature, and contamination level, respectively. The common and endemic microorganisms of each group were identified. The relative abundances of Thermaerobacter, Calditerricola, Brevibacillus, Ralstonia and Rhodococcus (aerobic bacteria) gradually declined with the increase of soil depth, while those of Bacillus, Fictibacillus, Paenibacillus, Rheinheimera presented opposite tendency. Some thermophilic degradation bacteria of PAHs, including Thermaerobacter, Calditerricola, Bacillus, Rhodococcus, unclassified_p__Firmicutes, Arthrobacter and Deinococcus, were identified and increased in the abundance at heavily polluted sites. Additionally, Proteobacteria, Bacteroidota, Deinococcota, Chloroflexi, Acidobacteriota, and Actinobacteriota showed negative response to the increase of soil depth, temperature and pollution level, while Firmicutes presented a positive response. This implied that Firmicutes has better stress resistance and adaptability to thermal remediation condition. The key environmental factors affecting microorganism composition and distribution were Temperature, Total nitrogen, Oxidation-Reduction Potential, Organic matters, and PAHs concentrations, which explains the dominant driving mechanism of soil depth, temperature, and contamination level on microbial characteristics in thermal remediation site. Our study could contribute to a better understanding of the resilience and adaptation mechanisms of microbial community at the contaminated site after the in situ thermal remediation.
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Affiliation(s)
- Zhenhua Zhao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA.
| | - Barry Mody Oury
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Liling Xia
- Nanjing Vocational University of Industry Technology, Nanjing 210016, China.
| | - Zhirui Qin
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Xiangyu Pan
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Jichan Qian
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Fangzhou Luo
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Yong Wu
- Nanjing Qingzhan Environmental Engineering CO. Ltd, China
| | - Luqi Liu
- SUMEC Complete Equipment & Engineering CO. LTD, Nanjing 210018, China
| | - Wei Wang
- SUMEC Complete Equipment & Engineering CO. LTD, Nanjing 210018, China
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20
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Soleimanifar M, Jayasuriya A, Adams MP, Rodriguez-Freire L. Leaching composition and associated microbial community of recycled concrete aggregate (RCA). JOURNAL OF HAZARDOUS MATERIALS 2023; 442:130048. [PMID: 36182880 DOI: 10.1016/j.jhazmat.2022.130048] [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: 10/08/2021] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Recycled concrete aggregate (RCA) has been used as an alternative sustainable material in the construction industry, but RCA long-term environmental impacts are unknown. In this study, the bacterial enrichment potential to reduce the alkalinity of two different types of RCA was examined, from laboratory-produced concrete and from a stockpile of demolished concrete that had been in service in transportation applications. Washed and un-washed lab and field RCA were biostimulated by being exposed to ATCC® Medium 661 in batch experiments. pH, metal composition and microbial community changes in the leachates were monitored over time. Results show that initial pH of field RCA leachate could be decreased to less concerning values, as low as 8, but concentrations of some metals in the leachate exceeded groundwater quality standards. However, the biostimulated RCA released lower metal concentration and was more resistant to pH increases than non-biostimulated RCA during a long-term leaching experiment with DI water. The microbial community was enriched on anaerobic, halotolerant and alkaliphile microorganisms, resistant to extreme environmental conditions. The outcome of this research suggests a baseline for field RCA pretreatment before field application, using a biostimulation method that would generate a less environmentally detrimental runoff.
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Affiliation(s)
- Maedeh Soleimanifar
- Department of Civil & Environmental Engineering, New Jersey Institute of Technology, 07102 Newark, NJ, United States
| | - Anuruddha Jayasuriya
- Department of Civil & Environmental Engineering, New Jersey Institute of Technology, 07102 Newark, NJ, United States
| | - Matthew P Adams
- Department of Civil & Environmental Engineering, New Jersey Institute of Technology, 07102 Newark, NJ, United States
| | - Lucia Rodriguez-Freire
- Department of Civil & Environmental Engineering, New Jersey Institute of Technology, 07102 Newark, NJ, United States; School of Engineering, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, United Kingdom.
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21
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Mills M, Lee S, Mollenkopf D, Wittum T, Sullivan SMP, Lee J. Comparison of environmental microbiomes in an antibiotic resistance-polluted urban river highlights periphyton and fish gut communities as reservoirs of concern. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158042. [PMID: 35973543 DOI: 10.1016/j.scitotenv.2022.158042] [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: 05/27/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Natural waterways near urban areas are heavily impacted by anthropogenic activities, including their microbial communities. A contaminant of growing public health concern in rivers is antibiotic resistant genes (ARGs), which can spread between neighboring bacteria and increase the potential for transmission of AR bacteria to animals and humans. To identify the matrices of most concern for AR, we compared ARG burdens and microbial community structures between sample types from the Scioto River Watershed, Ohio, the United States, from 2017 to 2018. Five environmental matrices (water, sediment, periphyton, detritus, and fish gut) were collected from 26 river sites. Due to our focus on clinically relevant ARGs, three carbapenem resistance genes (blaKPC, blaNDM, and blaOXA-48) were quantified via DropletDigital™ PCR. At a subset of nine urbanized sites, we conducted16S rRNA gene sequencing and functional gene predictions. Carbapenem resistance genes were quantified from all matrices, with blaKPC being the most detected (88 % of samples), followed by blaNDM (64 %) and blaOXA-48 (23 %). Fish gut samples showed higher concentrations of blaKPC and blaNDM than any other matrix, indicating potential ARG bioaccumulation, and risk of broader dissemination through aquatic and nearshore food webs. Periphyton had higher concentrations of blaNDM than water, sediment, or detritus. Microbial community analysis identified differences by sample type in community diversity and structure. Sediment samples had the most diverse microbial communities, and detritus, the least. Spearman correlations did not reveal significant relationships between the concentrations of the monitored ARGs and microbial community diversity. However, several differentially abundant taxa and microbial functions were identified by sample type that is definitive of these matrices' roles in the river ecosystem and habitat type. In summary, the fish gut and periphyton are a concern as AR reservoirs due to their relatively high concentration of carbapenem resistance genes, diverse microbial communities, and natural functions that promote AR.
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Affiliation(s)
- Molly Mills
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA; Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Seungjun Lee
- Department of Food Science and Nutrition, Pukyong National University, Busan, Republic of Korea
| | - Dixie Mollenkopf
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, USA
| | - Thomas Wittum
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA
| | - S Mažeika Patricio Sullivan
- Schiermeier Olentangy River Wetland Research Park, School of Environment and Natural Resources, The Ohio State University, Columbus, OH 43210, USA
| | - Jiyoung Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA; Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA; Department of Food Science & Technology, The Ohio State University, Columbus, OH, USA.
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22
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Krumbeck JA, Turner DD, Diesel A, Hoffman AR, Heatley JJ. Skin microbiota of quaker parrots (Myiopsitta monachus) with normal feathering or feather loss via next-generation sequencing technology. J Exot Pet Med 2022. [DOI: 10.1053/j.jepm.2022.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Chen JS, Tsai HC, Hsu YL, Nagarajan V, Su HY, Hussain B, Hsu BM. Comprehensive assessment of bacterial communities and their functional profiles in the Huang Gang Creek in the Tatun Volcano Group basin, Taiwan using 16S rRNA amplicon sequencing. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 234:113375. [PMID: 35278991 DOI: 10.1016/j.ecoenv.2022.113375] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
The microbial characteristics of water bodies located in the outflow of hot springs may affect the water quality parameters of the associated river ecosystem. Using 16S rRNA amplicon sequencing, we investigated the bacterial diversity and functional profiles of the Huang Gang (HG) Creek, located in the trace metal-rich, acid-sulfate thermal springs zone of the Tatun Volcano Group (TVG). Biofilms and water samples were collected from the upstream, midstream, and geothermal valleys and downstream of the creek. The results showed that the biofilm and water samples had distinct bacterial diversity and abundance profiles. Acidophilic sulfur-oxidizing bacteria were found to be more abundant in water samples, whereas aquatic photosynthetic bacterial communities were dominant in biofilms. The water samples were contaminated with Legionella and Chlamydiae, which could contaminate the nearby river and cause clinical infections in humans. The upstream samples were highly unique and displayed higher diversity than the other sites. Moderate thermo-acidophiles were dominant in the upstream and midstream regions, whereas the geothermal valley and downstream samples were abundant in thermo-acidophiles. In addition, functional profiling revealed higher expression of sulfur, arsenic, and iron-related functions in water and lead-related functions in the biofilms of the creek. As described in previous studies, the hydrochemical properties of the HG Creek were influenced by the TVG hot springs. Our findings indicated that the hydrochemical properties of the HG Creek were highly correlated with the bacterial diversity and functional potential of running water as compared to biofilms.
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Affiliation(s)
- Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, Kaohsiung, Taiwan
| | - Hsin-Chi Tsai
- Department of Psychiatry, School of Medicine, Tzu Chi University, Hualien, Taiwan; Department of Psychiatry, Tzu-Chi General Hospital, Hualien, Taiwan
| | - Yu-Ling Hsu
- Department of Nuclear Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan
| | - Viji Nagarajan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Hung-Yuan Su
- Department of Emergency Medicine, E-Da Hospital and I-Shou University, Kaohsiung, Taiwan; School of Chinese Medicine for Post Baccalaureate, I-Shou University, Kaohsiung, Taiwan
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan.
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24
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Elsheshtawy A, Clokie BGJ, Albalat A, Beveridge A, Hamza A, Ibrahim A, MacKenzie S. Characterization of External Mucosal Microbiomes of Nile Tilapia and Grey Mullet Co-cultured in Semi-Intensive Pond Systems. Front Microbiol 2021; 12:773860. [PMID: 34966368 PMCID: PMC8710667 DOI: 10.3389/fmicb.2021.773860] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/10/2021] [Indexed: 11/13/2022] Open
Abstract
The external mucosal surfaces of the fish harbor complex microbial communities, which may play pivotal roles in the physiological, metabolic, and immunological status of the host. Currently, little is known about the composition and role of these communities, whether they are species and/or tissue specific and whether they reflect their surrounding environment. Co-culture of fish, a common practice in semi-intensive aquaculture, where different fish species cohabit in the same contained environment, is an easily accessible and informative model toward understanding such interactions. This study provides the first in-depth characterization of gill and skin microbiomes in co-cultured Nile tilapia (Oreochromis niloticus) and grey mullet (Mugil capito) in semi-intensive pond systems in Egypt using 16S rRNA gene-based amplicon sequencing. Results showed that the microbiome composition of the external surfaces of both species and pond water was dominated by the following bacterial phyla: Proteobacteria, Fusobacteriota, Firmicutes, Planctomycetota, Verrucomicrobiota, Bacteroidota, and Actinobacteriota. However, water microbial communities had the highest abundance and richness and significantly diverged from the external microbiome of both species; thus, the external autochthonous communities are not a passive reflection of their allochthonous communities. The autochthonous bacterial communities of the skin were distinct from those of the gill in both species, indicating that the external microbiome is likely organ specific. However, gill autochthonous communities were clearly species specific, whereas skin communities showed higher commonalities between both species. Core microbiome analysis identified the presence of shared core taxa between both species and pond water in addition to organ-specific taxa within and between the core community of each species. These core taxa included possibly beneficial genera such as Uncultured Pirellulaceae, Exiguobacterium, and Cetobacterium and opportunistic potential pathogens such as Aeromonas, Plesiomonas, and Vibrio. This study provides the first in-depth mapping of bacterial communities in this semi-intensive system that in turn provides a foundation for further studies toward enhancing the health and welfare of these cultured fish and ensuring sustainability.
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Affiliation(s)
- Ahmed Elsheshtawy
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom.,Faculty of Aquatic and Fisheries Sciences, Kafrelsheikh University, Kafr El Sheikh, Egypt
| | | | - Amaya Albalat
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Allan Beveridge
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Ahmad Hamza
- AQUAVET for Fish Nutrition and Health Solutions, Kafr El Sheikh, Egypt
| | | | - Simon MacKenzie
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
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25
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Genetic and Comparative Genome Analysis of Exiguobacterium aurantiacum SW-20, a Petroleum-Degrading Bacteria with Salt Tolerance and Heavy Metal-Tolerance Isolated from Produced Water of Changqing Oilfield, China. Microorganisms 2021; 10:microorganisms10010066. [PMID: 35056515 PMCID: PMC8779447 DOI: 10.3390/microorganisms10010066] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 12/30/2022] Open
Abstract
The genome of Exiguobacterium aurantiacum SW-20 (E. aurantiacum SW-20), a salt-tolerant microorganism with petroleum hydrocarbon-degrading ability isolated from the Changqing Oilfield, was sequenced and analyzed. Genomic data mining even comparative transcriptomics revealed that some genes existed in SW-20 might be related to the salt tolerance. Besides, genes related to petroleum hydrocarbon degradation discovered in genomic clusters were also found in the genome, indicating that these genes have a certain potential in the bioremediation of petroleum pollutants. Multiple natural product biosynthesis gene clusters were detected, which was critical for survival in the extreme conditions. Transcriptomic studies revealed that some genes were significantly up-regulated as salinity increased, implying that these genes might be related to the salt tolerance of SW-20 when living in a high salt environment. In our study, gene clusters including salt tolerance, heavy metal tolerance and alkane degradation were all compared. When the same functional gene clusters from different strains, it was discovered that the gene composition differed. Comparative genomics and in-depth analysis provided insights into the physiological features and adaptation strategies of E. aurantiacum SW-20 in the oilfield environment. Our research increased the understanding of niches adaption of SW-20 at genomic level.
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26
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Simultaneous preconcentrations of Cu(II), Ni(II), and Pb(II) by SPE using E. profundum loaded onto Amberlite XAD-4. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106758] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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27
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López MC, Galán B, Carmona M, Navarro Llorens JM, Peretó J, Porcar M, Getino L, Olivera ER, Luengo JM, Castro L, García JL. Xerotolerance: A New Property in Exiguobacterium Genus. Microorganisms 2021; 9:2455. [PMID: 34946057 PMCID: PMC8706201 DOI: 10.3390/microorganisms9122455] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 11/16/2022] Open
Abstract
The highly xerotolerant bacterium classified as Exiguobacterium sp. Helios isolated from a solar panel in Spain showed a close relationship to Exiguobacterium sibiricum 255-15 isolated from Siberian permafrost. Xerotolerance has not been previously described as a characteristic of the extremely diverse Exiguobacterium genus, but both strains Helios and 255-15 showed higher xerotolerance than that described in the reference xerotolerant model strain Deinococcus radiodurans. Significant changes observed in the cell morphology after their desiccation suggests that the structure of cellular surface plays an important role in xerotolerance. Apart from its remarkable resistance to desiccation, Exiguobacterium sp. Helios strain shows several polyextremophilic characteristics that make it a promising chassis for biotechnological applications. Exiguobacterium sp. Helios cells produce nanoparticles of selenium in the presence of selenite linked to its resistance mechanism. Using the Lactobacillus plasmid pRCR12 that harbors a cherry marker, we have developed a transformation protocol for Exiguobacterium sp. Helios strain, being the first time that a bacterium of Exiguobacterium genus has been genetically modified. The comparison of Exiguobacterium sp. Helios and E. sibiricum 255-15 genomes revealed several interesting similarities and differences. Both strains contain a complete set of competence-related DNA transformation genes, suggesting that they might have natural competence, and an incomplete set of genes involved in sporulation; moreover, these strains not produce spores, suggesting that these genes might be involved in xerotolerance.
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Affiliation(s)
- María Castillo López
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; (M.C.L.); (B.G.); (M.C.)
- Department of Biochemistry and Molecular Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Av. Complutense s/n, 28040 Madrid, Spain;
| | - Beatriz Galán
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; (M.C.L.); (B.G.); (M.C.)
| | - Manuel Carmona
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; (M.C.L.); (B.G.); (M.C.)
| | - Juana María Navarro Llorens
- Department of Biochemistry and Molecular Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Av. Complutense s/n, 28040 Madrid, Spain;
| | - Juli Peretó
- Program for Applied Systems Biology and Synthetic Biology, Instituto de Biología Integrativa de Sistemas (I2SYSBIO) (UV-CSIC), Carrer del Catedràtic Agustín Escardino Benlloch s/n, 46980 Paterna, Spain; (J.P.); (M.P.)
- Department of Biochemistry and Molecular Biology, University of Valencia, 46100 Burjassot, Spain
| | - Manuel Porcar
- Program for Applied Systems Biology and Synthetic Biology, Instituto de Biología Integrativa de Sistemas (I2SYSBIO) (UV-CSIC), Carrer del Catedràtic Agustín Escardino Benlloch s/n, 46980 Paterna, Spain; (J.P.); (M.P.)
| | - Luis Getino
- Department of Molecular Biology, Facultades de Veterinaria y Biología, Universidad de León, 24007 León, Spain; (L.G.); (E.R.O.); (J.M.L.)
| | - Elías R. Olivera
- Department of Molecular Biology, Facultades de Veterinaria y Biología, Universidad de León, 24007 León, Spain; (L.G.); (E.R.O.); (J.M.L.)
| | - José M. Luengo
- Department of Molecular Biology, Facultades de Veterinaria y Biología, Universidad de León, 24007 León, Spain; (L.G.); (E.R.O.); (J.M.L.)
| | - Laura Castro
- Department of Applied Mathematics, Materials Science and Engineering and Electronic Technology, School of Experimental Sciences and Technology, Rey Juan Carlos University, 28933 Móstoles, Spain;
| | - José Luís García
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; (M.C.L.); (B.G.); (M.C.)
- Program for Applied Systems Biology and Synthetic Biology, Instituto de Biología Integrativa de Sistemas (I2SYSBIO) (UV-CSIC), Carrer del Catedràtic Agustín Escardino Benlloch s/n, 46980 Paterna, Spain; (J.P.); (M.P.)
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28
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Delegan Y, Kocharovskaya Y, Bogun A, Sizova A, Solomentsev V, Iminova L, Lyakhovchenko N, Zinovieva A, Goyanov M, Solyanikova I. Characterization and genomic analysis of Exiguobacterium alkaliphilum B-3531D, an efficient crude oil degrading strain. ACTA ACUST UNITED AC 2021; 32:e00678. [PMID: 34660213 PMCID: PMC8502702 DOI: 10.1016/j.btre.2021.e00678] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/06/2021] [Accepted: 09/16/2021] [Indexed: 12/01/2022]
Abstract
B-3531D is the first E. alkaliphilum strain with fully assembled genome. It is the first E. alkaliphilum strain with the ability to utilize crude oil. Strain utilized 34.5% of crude oil for 14 days at 28 °C and a salinity of 11%.
The aim of the work was to carry out the physiological, biochemical and genetic characterization of the Exiguobacterium alkaliphilum B-3531D strain. This strain is promising for use in the field of environmental biotechnology, since it has a pronounced ability to utilize crude oil and individual hydrocarbons in a wide temperature range. The genome of the strain was sequenced and completely assembled, it consists of a 2,903,369 bp circular chromosome and two circular plasmids, namely, pE73 (73,590 bp) and pE52 (52,125 bp). When cultivated in a mineral medium containing 2% of crude oil, the strain utilized 50% within 30 days of the experiment. In simulated seawater with the same oil content, the loss of hydrocarbons was 45% over the same period. For the first time we observed in an E. alkaliphilum strain the ability to efficiently utilize crude oil, including with an increased content of sodium chloride in the cultivation medium.
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Affiliation(s)
- Yanina Delegan
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of Russian Academy of Sciences, Pushchino, Moscow Oblast, 142290, Russian Federation
| | - Yulia Kocharovskaya
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of Russian Academy of Sciences, Pushchino, Moscow Oblast, 142290, Russian Federation.,Pushchino State Institute of Natural Science, Pushchino, Moscow Oblast, 142290, Russian Federation
| | - Alexander Bogun
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, 142279, Russian Federation
| | - Angelika Sizova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, 142279, Russian Federation
| | - Viktor Solomentsev
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, 142279, Russian Federation
| | - Leila Iminova
- Pushchino State Institute of Natural Science, Pushchino, Moscow Oblast, 142290, Russian Federation
| | | | - Alina Zinovieva
- Belgorod State University, Belgorod, 308015, Russian Federation
| | - Mikhail Goyanov
- Belgorod State University, Belgorod, 308015, Russian Federation
| | - Inna Solyanikova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of Russian Academy of Sciences, Pushchino, Moscow Oblast, 142290, Russian Federation.,Belgorod State University, Belgorod, 308015, Russian Federation
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29
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Zhu J, Lua AC. Antibacterial ultrafiltration membrane with silver nanoparticle impregnation by interfacial polymerization for ballast water. JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1002/pol.20210365] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jianhua Zhu
- School of Mechanical and Aerospace Engineering Nanyang Technological University Singapore Singapore
| | - Aik Chong Lua
- School of Mechanical and Aerospace Engineering Nanyang Technological University Singapore Singapore
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30
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Gusman VP, Medić DD, Trudić AD, Banović PZ, Nikolić NM. First Isolation of Exiguobacterium aurantiacum in Serbia. Pol J Microbiol 2021; 70:405-407. [PMID: 34584535 PMCID: PMC8458997 DOI: 10.33073/pjm-2021-037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/16/2021] [Accepted: 07/28/2021] [Indexed: 11/21/2022] Open
Abstract
Exiguobacterium aurantiacum is isolated from a variety of environmental samples but rarely from patients. The aim of the study was to represent isolation of unusual bacterial strains that could cause infection in patients. Final identification was performed using matrix-assisted description/ionization time-of-flight mass spectrometry (MALDI-TOF). Two isolates strains of E. aurantiacum were isolated, one isolate from distilled water used during surgical treatment and the second one from a patient with bacteremia after radical prostatectomy, both sensitive to all tested antimicrobials. Environmental strains could cause infection, especially in immunocompromised patients; therefore, rare bacteria testing is required, in which identification special assistance is provided by an automated system MALDI-TOF.
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Affiliation(s)
- Vera P Gusman
- Department of Microbiology, Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia.,Institute of Public Health of Vojvodina, Novi Sad, Serbia
| | - Deana D Medić
- Department of Microbiology, Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia.,Institute of Public Health of Vojvodina, Novi Sad, Serbia
| | - Anika Dj Trudić
- Department of Microbiology, Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia.,Institute for Pulmonary Diseases of Vojvodina, Sremska Kamenica, Serbia
| | - Pavle Z Banović
- Department of Microbiology, Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia.,Pasteur Institute of Novi Sad, Novi Sad, Serbia
| | - Nataša M Nikolić
- Department of Microbiology, Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia.,Institute of Public Health of Vojvodina, Novi Sad, Serbia
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31
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Dimov SG. The unusual microbiota of the traditional Bulgarian dairy product Krokmach – A pilot metagenomics study. INT J DAIRY TECHNOL 2021. [DOI: 10.1111/1471-0307.12809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Svetoslav G Dimov
- Department of Genetics Faculty of Biology Sofia University “St. Kliment Ohridski” 8, Dragan Tzankov blvd. Sofia 1164 Bulgaria
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32
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Zhang D, Zhu Z, Li Y, Li X, Guan Z, Zheng J. Comparative Genomics of Exiguobacterium Reveals What Makes a Cosmopolitan Bacterium. mSystems 2021; 6:e0038321. [PMID: 34282940 PMCID: PMC8407118 DOI: 10.1128/msystems.00383-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/28/2021] [Indexed: 11/20/2022] Open
Abstract
Although the strategies used by bacteria to adapt to specific environmental conditions are widely reported, fewer studies have addressed how microbes with a cosmopolitan distribution can survive in diverse ecosystems. Exiguobacterium is a versatile genus whose members are commonly found in various habitats. To better understand the mechanisms underlying the universality of Exiguobacterium, we collected 105 strains from diverse environments and performed large-scale metabolic and adaptive ability tests. We found that most Exiguobacterium members have the capacity to survive under wide ranges of temperature, salinity, and pH. According to phylogenetic and average nucleotide identity analyses, we identified 27 putative species and classified two genetic groups: groups I and II. Comparative genomic analysis revealed that the Exiguobacterium members utilize a variety of complex polysaccharides and proteins to support survival in diverse environments and also employ a number of chaperonins and transporters for this purpose. We observed that the group I species can be found in more diverse terrestrial environments and have a larger genome size than the group II species. Our analyses revealed that the expansion of transporter families drove genomic expansion in group I strains, and we identified 25 transporter families, many of which are involved in the transport of important substrates and resistance to environmental stresses and are enriched in group I strains. This study provides important insights into both the overall general genetic basis for the cosmopolitan distribution of a bacterial genus and the evolutionary and adaptive strategies of Exiguobacterium. IMPORTANCE The wide distribution characteristics of Exiguobacterium make it a valuable model for studying the adaptive strategies of bacteria that can survive in multiple habitats. In this study, we reveal that members of the Exiguobacterium genus have a cosmopolitan distribution and share an extensive adaptability that enables them to survive in various environments. The capacities shared by Exiguobacterium members, such as their diverse means of polysaccharide utilization and environmental-stress resistance, provide an important basis for their cosmopolitan distribution. Furthermore, the selective expansion of transporter families has been a main driving force for genomic evolution in Exiguobacterium. Our findings improve our understanding of the adaptive and evolutionary mechanisms of cosmopolitan bacteria and the vital genomic traits that can facilitate niche adaptation.
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Affiliation(s)
- Dechao Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Zhaolu Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Yangjie Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xudong Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Ziyu Guan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
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Liu F, Li Y, He W, Wang W, Zheng J, Zhang D. Exiguobacterium algae sp. nov. and Exiguobacterium qingdaonense sp. nov., two novel moderately halotolerant bacteria isolated from the coastal algae. Antonie van Leeuwenhoek 2021; 114:1399-1406. [PMID: 34251527 DOI: 10.1007/s10482-021-01594-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/16/2021] [Indexed: 10/20/2022]
Abstract
Two Gram-stain-positive, facultatively anaerobic, rod-shaped bacterial strains, S126T and S82T, were isolated from coastal algae of China. Strains S126T and S82T are halotolerant and could grow in the presence of 0-13% NaCl and 0-14% NaCl, respectively. The two strains shared 98.9% 16S rRNA gene sequence similarity with each other and 93.4-99.8% similarity with type strains of Exiguobacterium species. The major fatty acids (> 10%) of strains S126T and S82T were iso-C17:0, iso-C13:0, anteiso-C13:0 and iso-C15:0. The predominant quinones of strains S126T and S82T were MK-7 and MK-8. The polar lipid profiles of strain S126T and S82T contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The cell-wall peptidoglycans of both strains S126T and S82T were of the A3α L-Lys-Gly type. The average nucleotide identity (ANI) and average nucleotide index (AAI) between strains S126T and S82T and type strains of Exiguobacterium species were all below the thresholds to discriminate bacterial species, indicating that they constitute two novel species in the genus Exiguobacterium. Based on polyphasic taxonomy characterization and genomic aspects, the names Exiguobacterium algae sp. nov. and Exiguobacterium qingdaonense sp. nov. are proposed for the two novel species, with type strains being S126T (= CGMCC 1.17116T = KCTC 43079 T) and S82T (= CGMCC 1.17115T = KCTC 43078T), respectively.
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Affiliation(s)
- Fangming Liu
- First Institute of Oceanography (FIO), Ministry of Natural Resources (MNR) of China, Qingdao, 266061, China
| | - Yangjie Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Wenxuan He
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenqi Wang
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266237, China
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Dechao Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.
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Tedesco P, Palma Esposito F, Masino A, Vitale GA, Tortorella E, Poli A, Nicolaus B, van Zyl LJ, Trindade M, de Pascale D. Isolation and Characterization of Strain Exiguobacterium sp. KRL4, a Producer of Bioactive Secondary Metabolites from a Tibetan Glacier. Microorganisms 2021; 9:microorganisms9050890. [PMID: 33919419 PMCID: PMC8143284 DOI: 10.3390/microorganisms9050890] [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: 03/31/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 11/16/2022] Open
Abstract
Extremophilic microorganisms represent a unique source of novel natural products. Among them, cold adapted bacteria and particularly alpine microorganisms are still underexplored. Here, we describe the isolation and characterization of a novel Gram-positive, aerobic rod-shaped alpine bacterium (KRL4), isolated from sediments from the Karuola glacier in Tibet, China. Complete phenotypic analysis was performed revealing the great adaptability of the strain to a wide range of temperatures (5-40 °C), pHs (5.5-8.5), and salinities (0-15% w/v NaCl). Genome sequencing identified KRL4 as a member of the placeholder genus Exiguobacterium_A and annotation revealed that only half of the protein-encoding genes (1522 of 3079) could be assigned a putative function. An analysis of the secondary metabolite clusters revealed the presence of two uncharacterized phytoene synthase containing pathways and a novel siderophore pathway. Biological assays confirmed that the strain produces molecules with antioxidant and siderophore activities. Furthermore, intracellular extracts showed nematocidal activity towards C. elegans, suggesting that strain KRL4 is a source of anthelmintic compounds.
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Affiliation(s)
- Pietro Tedesco
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 80131 Naples, Italy; (P.T.); (F.P.E.); (A.M.); (G.A.V.); (E.T.)
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80122 Naples, Italy
| | - Fortunato Palma Esposito
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 80131 Naples, Italy; (P.T.); (F.P.E.); (A.M.); (G.A.V.); (E.T.)
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80122 Naples, Italy
| | - Antonio Masino
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 80131 Naples, Italy; (P.T.); (F.P.E.); (A.M.); (G.A.V.); (E.T.)
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy
| | - Giovanni Andrea Vitale
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 80131 Naples, Italy; (P.T.); (F.P.E.); (A.M.); (G.A.V.); (E.T.)
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80122 Naples, Italy
| | - Emiliana Tortorella
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 80131 Naples, Italy; (P.T.); (F.P.E.); (A.M.); (G.A.V.); (E.T.)
| | - Annarita Poli
- Institute of Biomolecular Chemistry, National Research Council, Pozzuoli, 80078 Naples, Italy; (A.P.); (B.N.)
| | - Barbara Nicolaus
- Institute of Biomolecular Chemistry, National Research Council, Pozzuoli, 80078 Naples, Italy; (A.P.); (B.N.)
| | - Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Bellville, 7535 Cape Town, South Africa; (L.J.v.Z.); (M.T.)
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Bellville, 7535 Cape Town, South Africa; (L.J.v.Z.); (M.T.)
| | - Donatella de Pascale
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 80131 Naples, Italy; (P.T.); (F.P.E.); (A.M.); (G.A.V.); (E.T.)
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80122 Naples, Italy
- Correspondence:
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Ahmad T, Gupta G, Sharma A, Kaur B, El-Sheikh MA, Alyemeni MN. Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake. PLoS One 2021; 16:e0248116. [PMID: 33764980 PMCID: PMC7993826 DOI: 10.1371/journal.pone.0248116] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/21/2021] [Indexed: 11/23/2022] Open
Abstract
Freshwater lakes present an ecological border between humans and a variety of host organisms. The present study was designed to evaluate the microbiota composition and distribution in Dal Lake at Srinagar, India. The non-chimeric sequence reads were classified taxonomically into 49 phyla, 114 classes, 185 orders, 244 families and 384 genera. Proteobacteria was found to be the most abundant bacterial phylum in all the four samples. The highest number of observed species was found to be 3097 in sample taken from least populated area during summer (LPS) whereas the summer sample from highly populated area (HPS) was found most diverse among all as indicated by taxonomic diversity analysis. The QIIME output files were used for PICRUSt analysis to assign functional attributes. The samples exhibited a significant difference in their microbial community composition and structure. Comparative analysis of functional pathways indicated that the anthropogenic activities in populated areas and higher summer temperature, both decrease functional potential of the Lake microbiota. This is probably the first study to demonstrate the comparative taxonomic diversity and functional composition of an urban freshwater lake amid its highly populated and least populated areas during two extreme seasons (winter and summer).
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Affiliation(s)
- Tawseef Ahmad
- Department of Biotechnology, Punjabi University Patiala, Punjabi, India
| | - Gaganjot Gupta
- Department of Biotechnology, Punjabi University Patiala, Punjabi, India
| | - Anshula Sharma
- Department of Biotechnology, Punjabi University Patiala, Punjabi, India
| | - Baljinder Kaur
- Department of Biotechnology, Punjabi University Patiala, Punjabi, India
- * E-mail: (BK); (MNA)
| | - Mohamed A. El-Sheikh
- Botany and Microbiology Department, Faculty of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Nasser Alyemeni
- Botany and Microbiology Department, Faculty of Science, King Saud University, Riyadh, Saudi Arabia
- * E-mail: (BK); (MNA)
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Yasin MT, Ali Y, Ahmad K, Ghani A, Amanat K, Basheir MM, Faheem M, Hussain S, Ahmad B, Hussain A, Bokhari SAI. Alkaline lipase production by novel meso-tolerant psychrophilic Exiguobacterium sp. strain (AMBL-20) isolated from glacier of northeastern Pakistan. Arch Microbiol 2020; 203:1309-1320. [PMID: 33325000 DOI: 10.1007/s00203-020-02133-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 11/15/2020] [Accepted: 11/19/2020] [Indexed: 11/30/2022]
Abstract
Lipase is an important commercial enzyme with unique and versatile biotechnological applications. This study was conducted to biosynthesize and characterizes alkaliphilic lipase by Exiguobacterium sp. strain AMBL-20T isolated from the glacial water samples of the northeastern (Gilgit-Baltistan) region of Pakistan. The isolated bacterium was identified as Exiguobaterium sp. strain AMBL-20T on the basis of morphological, biochemical, and phylogenetic analysis of 16S rRNA sequences with GenBank accession number MW229267. The bacterial strain was further screened for its lipolytic activity, biosynthesis, and characterization by different parameters with the aim of maximizing lipase activity. Results showed that 2% Olive oil, 0.2% peptone at 25 °C, pH 8, and 24 h of incubation time found optimal for maximum lipase production. The lipase enzyme was partially purified by ammonium sulphate precipitation and its activity was standardized at pH 8 under 30 °C temperature. The enzyme showed functional stability over a range of temperature and pH. Hence, extracellular alkaliphilic lipase from Exiguobacterium sp. is a potential candidate with extraordinary industrial applications, particularly in bio-detergent formulations.
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Affiliation(s)
- Muhammad Talha Yasin
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Yasir Ali
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Khurshid Ahmad
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Abdul Ghani
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Kinza Amanat
- Department of Microbiology, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Muhammad Mudassir Basheir
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Muhammad Faheem
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Saddam Hussain
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Bashir Ahmad
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Adil Hussain
- Department of Biotechnology, University of Okara, Okara, 56130, Pakistan
| | - Syed Ali Imran Bokhari
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
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Srivastava AK, Srivastava R, Sharma A, Bharati AP, Tiwari PK, Singh AK, Srivastava AK, Chakdar H, Kashyap PL, Saxena AK. Pan-genome analysis of Exiguobacterium reveals species delineation and genomic similarity with Exiguobacterium profundum PHM 11. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:639-650. [PMID: 32996243 DOI: 10.1111/1758-2229.12890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
The stint of the bacterial species is convoluting, but the new algorithms to calculate genome-to-genome distance (GGD) and DNA-DNA hybridization (DDH) for comparative genome analysis have rejuvenated the exploration of species and sub-species characterization. The present study reports the first whole genome sequence of Exiguobacterium profundum PHM11. PHM11 genome consist of ~ 2.92 Mb comprising 48 contigs, 47.93% G + C content. Functional annotations revealed a total of 3033 protein coding genes and 33 non-protein coding genes. Out of these, only 2316 could be characterized and others reported as hypothetical proteins. The comparative analysis of predicted proteome of PHM11 with five other Exiguobacterium sp. identified 3806 clusters, out of which the PHM11 shared a total of 2723 clusters having 1664 common clusters, 131 singletons and 928 distributed between five species. The pan-genome analysis of 70 different genomic sequences of Exigubacterium strains devoid of a species taxon was done on the basis of GGD and the DDH which identified eight genomes analogous to the PHM11 at species level and may be characterized as E. profundum. The ANI value and phylogenetic tree analysis also support the same. The results regarding pan-genome analysis provide a convincing insight for delineation of these eight strains to species.
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Affiliation(s)
- Alok Kumar Srivastava
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, UP, 275103, India
| | - Ruchi Srivastava
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, UP, 275103, India
| | - Anjney Sharma
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, UP, 275103, India
| | - Akhilendra Pratap Bharati
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, UP, 275103, India
| | - Praveen Kumar Tiwari
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, UP, 275103, India
| | - Alok Kumar Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, UP, 275103, India
| | - Anchal Kumar Srivastava
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, UP, 275103, India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, UP, 275103, India
| | - Prem Lal Kashyap
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, UP, 275103, India
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Hu A, Gao C, Lu Z, Lu F, Kong L, Bie X. Detection of Exiguobacterium spp. and E. acetylicum on fresh-cut leafy vegetables by a multiplex PCR assay. J Microbiol Methods 2020; 180:106100. [PMID: 33249127 DOI: 10.1016/j.mimet.2020.106100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 11/16/2022]
Abstract
AIMS To identify the main spoilage bacterium on fresh-cut leafy vegetables and establish a multiplex PCR assay. METHODS AND RESULTS Based on physiological-biochemical, molecular identification, and artificial contamination tests, the main bacterium to spoil fresh-cut leafy vegetables was identified as Exiguobacterium spp. and Exiguobacterium acetylicum. Comparative genomics showed that P401_RS0117025 and oxi_50,582,462 genes are specific to Exiguobacterium spp. and E. acetylicum. Based on this, three pairs of primer sets to EaG-291, EaS-2B, and Ea16S-12 genes were designed and used to develop a multiplex PCR assay, which exhibited 100% specificity among 16 Exiguobacterium and 10 non-Exiguobacterium strains. Finally, 84 fresh-cut leafy vegetable samples were analyzed by multiplex PCR assay and standard physiological-biochemical experiments, the results showed multiplex PCR assay reached a detection rate of 96%. CONCLUSIONS The main spoilage bacterium was identified as Exiguobacterium spp. and E. acetylicum on fresh-cut leafy vegetables based on the novel specific genes explored in this study. SIGNIFICANCE AND IMPACT OF STUDY A rapid, specific, and sensitive PCR assay was developed for the detection of Exiguobacterium spp. and E. acetylicum.
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Affiliation(s)
- Antuo Hu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China.
| | - Cancan Gao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China.
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China.
| | - Liangyu Kong
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xiaomei Bie
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China.
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Culot A, Grosset N, Bruey Q, Auzou M, Giard JC, Favard B, Wakatsuki A, Baron S, Frouel S, Techer C, Gautier M. Isolation of Harveyi clade Vibrio spp. collected in aquaculture farms: How can the identification issue be addressed? J Microbiol Methods 2020; 180:106106. [PMID: 33248180 DOI: 10.1016/j.mimet.2020.106106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/14/2020] [Accepted: 11/14/2020] [Indexed: 10/22/2022]
Abstract
Aquaculture is a fast growing industry with its development hampered by bacterial diseases. Vibriosis caused by Harveyi clade strains is known for causing heavy loss especially in shrimp aquaculture farms. For farm treatment and pathogen spread management, veterinarians and researchers need reliable bacterial identification tools. A range of identification methods have been presented for Vibrio spp. in recent literature but little feedback on their performance have been made available to this day. This study aims at comparing Vibrio spp. identification methods and providing guidance on their use. Fifty farms were sampled and bacterial colonies were isolated using specific culture media before microscopic analysis and genomic profiling using ERIC-PCR. A preliminary identification step was carried out using MALDI-ToF mass spectrometry. Four methods were compared for strain identification on 14 newly isolated Harveyi clade Vibrio spp. strains: whole genome sequencing (digital DNA DNA Hybridization (dDDH)), 5 MLSA schemes, ferric uptake regulation (fur) and lecithin-dependent haemolysin (ldh) single gene based identification methods. Apart from dDDH which is a reference method, no technique could identify all the isolates to the species level. The other tested techniques allowed a faster, cheaper but sub genus clade identification which can be interesting when absolute precision is not required. In this regard, MALDI-ToF and fur based identification seemed especially promising.
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Affiliation(s)
- Antoine Culot
- Microbiology Laboratory, Institut National de Recherche en Agriculture, Alimentation et Environnement, (INRAE), UMR 1253 Science and, Technology of Milk and Eggs (STLO), Rennes, France; Mixscience SAS, Bruz, France.
| | - Noel Grosset
- Microbiology Laboratory, Institut National de Recherche en Agriculture, Alimentation et Environnement, (INRAE), UMR 1253 Science and, Technology of Milk and Eggs (STLO), Rennes, France
| | | | - Michel Auzou
- Service Microbiologie, Centre Hospitalier Universitaire de Caen, Caen, France
| | | | | | | | - Sandrine Baron
- Laboratoire de Ploufragan-Plouzane-Niort, ANSES, Ploufragan, France
| | | | | | - Michel Gautier
- Microbiology Laboratory, Institut National de Recherche en Agriculture, Alimentation et Environnement, (INRAE), UMR 1253 Science and, Technology of Milk and Eggs (STLO), Rennes, France.
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Brockmann M, Aupperle-Lellbach H, Gentil M, Heusinger A, Müller E, Marschang RE, Pees M. Challenges in microbiological identification of aerobic bacteria isolated from the skin of reptiles. PLoS One 2020; 15:e0240085. [PMID: 33075077 PMCID: PMC7571677 DOI: 10.1371/journal.pone.0240085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/19/2020] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Bacterial pathogens are often involved in dermatitis in reptiles. Exact identification of reptile-specific but otherwise uncommon bacterial species may be challenging. However, identification is crucial to evaluate the importance of the detected bacterial species. OBJECTIVE The aim of this study was to assess the number of aerobic bacterial isolates cultured from skin-derived samples of reptiles which were not reliably identified by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS), and to determine their identity. MATERIAL AND METHODS Routine bacterial diagnostics were performed on 235 skin samples, and 417 bacterial isolates were analysed by MALDI-TOF MS. The isolates were grouped into categories based on their first score: category I (≥ 2.00), category II (≥ 1.70 and < 2.00), and category III (< 1.70). Isolates from category III were further investigated by 16S rRNA gene sequencing and the following criteria were applied: query cover 100%, e-value rounded to 0.0 and sequence identity (%) > 98.00% for genus identification, and > 99.00% for species identification. RESULTS The majority of bacterial isolates were in category I (85.1%) or category II (8.4%). In category III (6.5%) results achieved at first by MALDI-TOF MS corresponded to the results of the molecular analysis in 8.0% of isolates at the species level and in 24.0% at the genus level. Bacterial isolates classified as category III were heterogenic in genus (e.g. Chryseobacterium, Devriesea, Pseudomonas, Staphylococcus, Uruburuella), and some have only been described in reptiles so far. CONCLUSIONS Most of the aerobic bacterial isolates cultured from reptile skin achieved high scores by MALDI-TOF MS. However, in the majority of category III isolates MALDI-TOF MS results were different from those of the molecular analysis. This strengthens the need to carefully examine low-scored results for plausibility and to be familiar with the occurrence and morphology of relevant reptile-specific bacterial species (e.g. Devriesea agamarum) as well as with the limits of the database used.
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MESH Headings
- Animals
- Bacteria, Aerobic/chemistry
- Bacteria, Aerobic/genetics
- Bacteria, Aerobic/isolation & purification
- Gram-Negative Bacteria/genetics
- Gram-Negative Bacteria/isolation & purification
- Gram-Negative Bacteria/metabolism
- Gram-Positive Bacteria/genetics
- Gram-Positive Bacteria/isolation & purification
- Gram-Positive Bacteria/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Reptiles/microbiology
- Skin/microbiology
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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Affiliation(s)
| | | | | | | | | | | | - Michael Pees
- Clinic for Birds and Reptiles, University of Leipzig, Leipzig, Germany
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Lavrentyeva EV, Banzaraktsaeva TG, Radnagurueva AA, Buryukhaev SP, Dambaev VB, Baturina OA, Kozyreva LP, Barkhutova DD. Microbial Community of Umkhei Thermal Lake (Baikal Rift Zone) in the Groundwater Discharge Zone. CONTEMP PROBL ECOL+ 2020. [DOI: 10.1134/s1995425519060088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Picon A, Del Olmo A, Nuñez M. Bacterial diversity in six species of fresh edible seaweeds submitted to high pressure processing and long-term refrigerated storage. Food Microbiol 2020; 94:103646. [PMID: 33279071 DOI: 10.1016/j.fm.2020.103646] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 02/06/2023]
Abstract
Seaweeds are highly perishable foods due to their richness in nutrients. High pressure processing (HPP) has been applied for extending the shelf life of fresh seaweeds but there is no information on the effect of HPP on the bacterial diversity of seaweeds. The culturable bacteria of six species of fresh edible seaweeds (green seaweeds Codium fragile and Ulva lactuca, brown seaweeds Himanthalia elongata, Laminaria ochroleuca and Undaria pinnatifida, and red seaweed Chondrus crispus) were investigated and compared to those of HPP-treated (400 and 600 MPa for 5 min) seaweeds, at the start and end of their refrigerated storage period. A total of 523 and 506 bacterial isolates were respectively retrieved from untreated and HPP-treated seaweeds. Isolates from untreated seaweeds belonged to 18 orders, 35 families, 71 genera and 135 species whereas isolates from HPP-treated seaweeds belonged to 13 orders, 23 families, 43 genera and 103 species. HPP treatment significantly reduced the number of isolates belonging to 6 families and greatly increased the number of Bacillaceae isolates. At the end of storage, decreases in bacterial diversity at the genus and species level were observed for untreated as well as for HPP-treated seaweeds.
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Affiliation(s)
- Antonia Picon
- INIA, Departamento de Tecnología de Alimentos, Carretera de La Coruña Km 7, 28040, Madrid, Spain.
| | - Ana Del Olmo
- INIA, Departamento de Tecnología de Alimentos, Carretera de La Coruña Km 7, 28040, Madrid, Spain
| | - Manuel Nuñez
- INIA, Departamento de Tecnología de Alimentos, Carretera de La Coruña Km 7, 28040, Madrid, Spain
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Congestri R, Savio S, Farrotti S, Amati A, Krasojevic K, Perini N, Costa F, Migliore L. Developing a microbial consortium for removing nutrients in dishwasher wastewater: towards a biofilter for its up-cycling. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2020; 82:1142-1154. [PMID: 33055404 DOI: 10.2166/wst.2020.325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Microbial consortia are effective biofilters to treat wastewaters, allowing for resource recovery and water remediation. To reuse and save water in the domestic cycle, we assembled a suspended biofilm, a 'biofilter' to treat dishwasher wastewater. Bacterial monocultures of both photo- and heterotrophs were assembled in an increasingly complex fashion to test their nutrient stripping capacity. This 'biofilter' is the core of an integrated system (Zero Mile System) devoted to reusing and upcycling of reconditioned wastewater, partly in subsequent dishwasher cycles and partly into a vertical garden for plant food cultivation. The biofilter was assembled based on a strain of the photosynthetic, filamentous cyanobacterium Trichormus variabilis, selected to produce an oxygen evolving scaffold, and three heterotrophic aerobic bacterial isolates coming from the dishwasher wastewater itself: Acinetobacter, Exiguobacterium and Pseudomonas spp. The consortium was constructed starting with 16 isolates tested one-to-one with T. variabilis and then selecting the heterotrophic microbes up to a final one-to-three consortium, which included two dominant and a rare component of the wastewater community. This consortium thrives in the wastewater much better than T. variabilis alone, efficiently stripping N and P in short time, a pivotal step for the reuse and saving of water in household appliances.
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Affiliation(s)
- R Congestri
- Department of Biology, University of Rome 'Tor Vergata', Via della Ricerca Scientifica, Rome 00133, Italy E-mail:
| | - S Savio
- Department of Biology, University of Rome 'Tor Vergata', Via della Ricerca Scientifica, Rome 00133, Italy E-mail:
| | - S Farrotti
- Department of Biology, University of Rome 'Tor Vergata', Via della Ricerca Scientifica, Rome 00133, Italy E-mail:
| | - A Amati
- Department of Biology, University of Rome 'Tor Vergata', Via della Ricerca Scientifica, Rome 00133, Italy E-mail: ; Department of Design, Polytechnic University of Milan, Via Durando 38/A, Milan 20158, Italy
| | - K Krasojevic
- Department of Biology, University of Rome 'Tor Vergata', Via della Ricerca Scientifica, Rome 00133, Italy E-mail: ; Department of Design, Polytechnic University of Milan, Via Durando 38/A, Milan 20158, Italy
| | - N Perini
- Department of Biology, University of Rome 'Tor Vergata', Via della Ricerca Scientifica, Rome 00133, Italy E-mail:
| | - F Costa
- Department of Design, Polytechnic University of Milan, Via Durando 38/A, Milan 20158, Italy
| | - L Migliore
- Department of Biology, University of Rome 'Tor Vergata', Via della Ricerca Scientifica, Rome 00133, Italy E-mail:
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44
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Cao Y, Zhang B, Zhu Z, Song X, Cai Q, Chen B, Dong G, Ye X. Microbial eco-physiological strategies for salinity-mediated crude oil biodegradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 727:138723. [PMID: 32334234 DOI: 10.1016/j.scitotenv.2020.138723] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/13/2020] [Accepted: 04/13/2020] [Indexed: 05/26/2023]
Abstract
Salinity variability strongly affects the behaviors of oil degrading bacteria for spilled oil biodegradation in the marine environment. However, limited studies explored the strategies of microbes on salinity-mediated crude oil biodegradation. In this study, a halotolerant bio-emulsifier producer, Exiguobacterium sp. N41P, was examined as a model strain for Alaska North Slope (ANS) crude oil (0.5%, v/v) biodegradation. Results indicated that Exiguobacterium sp. N41P could tolerant a wide range of salinity (0-120 g/L NaCl) and achieve the highest degradation efficiency under the salinity of 15 g/L NaCl due to the highest biofilm formation ability. Moreover, increased salinity induced decreased cell surface hydrophobicity and a migration of microbial growth from oil phase to aqueous phase, leading to limited bio-emulsifier productivity and depressed degradation of insoluble long-chain n-alkanes while enhancing the degradation of relative soluble naphthalene. Research findings illustrated the microbial eco-physiological mechanism for spilled oil biodegradation under diverse salinities and advanced the understanding of sophisticated marine crude oil biodegradation process.
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Affiliation(s)
- Yiqi Cao
- The Northern Region Persistent Organic Pollution (NRPOP) Control Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B 3X5, Canada
| | - Baiyu Zhang
- The Northern Region Persistent Organic Pollution (NRPOP) Control Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B 3X5, Canada.
| | - Zhiwen Zhu
- The Northern Region Persistent Organic Pollution (NRPOP) Control Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B 3X5, Canada
| | - Xing Song
- The Northern Region Persistent Organic Pollution (NRPOP) Control Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B 3X5, Canada
| | - Qinhong Cai
- The Northern Region Persistent Organic Pollution (NRPOP) Control Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B 3X5, Canada
| | - Bing Chen
- The Northern Region Persistent Organic Pollution (NRPOP) Control Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B 3X5, Canada
| | - Guihua Dong
- The Northern Region Persistent Organic Pollution (NRPOP) Control Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B 3X5, Canada
| | - Xudong Ye
- The Northern Region Persistent Organic Pollution (NRPOP) Control Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B 3X5, Canada
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45
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Castro-Severyn J, Pardo-Esté C, Mendez KN, Morales N, Marquez SL, Molina F, Remonsellez F, Castro-Nallar E, Saavedra CP. Genomic Variation and Arsenic Tolerance Emerged as Niche Specific Adaptations by Different Exiguobacterium Strains Isolated From the Extreme Salar de Huasco Environment in Chilean - Altiplano. Front Microbiol 2020; 11:1632. [PMID: 32760381 PMCID: PMC7374977 DOI: 10.3389/fmicb.2020.01632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/23/2020] [Indexed: 12/17/2022] Open
Abstract
Polyextremophilic bacteria can thrive in environments with multiple stressors such as the Salar de Huasco (SH). Microbial communities in SH are exposed to low atmospheric pressure, high UV radiation, wide temperature ranges, salinity gradient and the presence of toxic compounds such as arsenic (As). In this work we focus on arsenic stress as one of the main adverse factors in SH and bacteria that belong to the Exiguobacterium genus due to their plasticity and ubiquity. Therefore, our aim was to shed light on the effect of niche conditions pressure (particularly arsenic), on the adaptation and divergence (at genotypic and phenotypic levels) of Exiguobacterium strains from five different SH sites. Also, to capture greater diversity in this genus, we use as outgroup five As(III) sensitive strains isolated from Easter Island (Chile) and The Great Salt Lake (United States). For this, samples were obtained from five different SH sites under an arsenic gradient (9 to 321 mg/kg: sediment) and isolated and sequenced the genomes of 14 Exiguobacterium strains, which had different arsenic tolerance levels. Then, we used comparative genomic analysis to assess the genomic divergence of these strains and their association with phenotypic differences such as arsenic tolerance levels and the ability to resist poly-stress. Phylogenetic analysis showed that SH strains share a common ancestor. Consequently, populations were separated and structured in different SH microenvironments, giving rise to multiple coexisting lineages. Hence, this genotypic variability is also evidenced by the COG (Clusters of Orthologous Groups) composition and the size of their accessory genomes. Interestingly, these observations correlate with physiological traits such as growth patterns, gene expression, and enzyme activity related to arsenic response and/or tolerance. Therefore, Exiguobacterium strains from SH are adapted to physiologically overcome the contrasting environmental conditions, like the arsenic present in their habitat.
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Affiliation(s)
- Juan Castro-Severyn
- Laboratorio de Microbiología Aplicada y Extremófilos, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile.,Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Coral Pardo-Esté
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Katterinne N Mendez
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Naiyulin Morales
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Sebastián L Marquez
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Franck Molina
- Sys2Diag CNRS/Alcediag, CNRS UMR 3145, Montpellier, France
| | - Francisco Remonsellez
- Laboratorio de Microbiología Aplicada y Extremófilos, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile.,Centro de Investigación Tecnológica del Agua en el Desierto-CEITSAZA, Universidad Católica del Norte, Antofagasta, Chile
| | - Eduardo Castro-Nallar
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Claudia P Saavedra
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
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46
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Lei J, Zheng M, Wang L, Yin G, Lou Y, Shi L. Complete genome sequence of Exiguobacterium mexicanum A-EM, isolated from seafloor hydrothermal vents in Atlantic Ocean. Mar Genomics 2020; 55:100801. [PMID: 32620456 DOI: 10.1016/j.margen.2020.100801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 06/03/2020] [Accepted: 06/18/2020] [Indexed: 11/28/2022]
Abstract
Exiguobacterium mexicanum A-EM was isolated from seafloor hydrothermal vents(Caifan field, 14.0S 14.4 W) and was shown to degrade toxins and contaminants. Here, we present the complete genome sequence of A-EM, consisting of 2,412,492 bp, with a GC content of 53.16%. A-EM sequence contains genes encoding enzymes that degrade toxins and contaminants. Complete genome sequence of the strain A-EM can further provide insights into microbial adaption to the seafloor hydrothermal system and the genomic basis for the biotechnological application of strain A-EM as an efficient agent to degrade environmental contaminants.
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Affiliation(s)
- Jilin Lei
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China
| | - Minggang Zheng
- Marine Bioresources and Environment Research Center, The First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Ling Wang
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China.
| | - Guobin Yin
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China
| | - Yinghua Lou
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China
| | - Lei Shi
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China
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47
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Loofah Sponges as Bio-Carriers in a Pilot-Scale Integrated Fixed-Film Activated Sludge System for Municipal Wastewater Treatment. SUSTAINABILITY 2020. [DOI: 10.3390/su12114758] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Fixed-film biofilm reactors are considered one of the most effective wastewater treatment processes, however, the cost of their plastic bio-carriers makes them less attractive for application in developing countries. This study evaluated loofah sponges, an eco-friendly renewable agricultural product, as bio-carriers in a pilot-scale integrated fixed-film activated sludge (IFAS) system for the treatment of municipal wastewater. Tests showed that pristine loofah sponges disintegrated within two weeks resulting in a decrease in the treatment efficiencies. Accordingly, loofah sponges were modified by coating them with CaCO3 and polymer. IFAS pilot tests using the modified loofah sponges achieved 83% organic removal and 71% total nitrogen removal and met Vietnam’s wastewater effluent discharge standards. The system achieved considerably high levels of nitrification and it was not limited by the loading rate or dissolved oxygen levels. Cell concentrations in the carriers were twenty to forty times higher than those within the aeration tank. Through 16S-rRNA sequencing, the major micro-organism types identified were Kluyvera cryocrescens, Exiguobacterium indicum, Bacillus tropicus, Aeromonas hydrophila, Enterobacter cloacae, and Pseudomonas turukhanskensis. This study demonstrated that although modified loofah sponges are effective renewable bio-carriers for municipal wastewater treatment, longer-term testing is recommended.
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48
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Orizola J, Ríos-Silva M, Muñoz-Villagrán C, Vargas E, Vásquez C, Arenas F. In vitro biosynthesis of Ag, Au and Te-containing nanostructures by Exiguobacterium cell-free extracts. BMC Biotechnol 2020; 20:29. [PMID: 32471409 PMCID: PMC7260758 DOI: 10.1186/s12896-020-00625-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 05/21/2020] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The bacterial genus Exiguobacterium includes several species that inhabit environments with a wide range of temperature, salinity, and pH. This is why the microorganisms from this genus are known generically as polyextremophiles. Several environmental isolates have been explored and characterized for enzyme production as well as for bioremediation purposes. In this line, toxic metal(loid) reduction by these microorganisms represents an approach to decontaminate soluble metal ions via their transformation into less toxic, insoluble derivatives. Microbial-mediated metal(loid) reduction frequently results in the synthesis of nanoscale structures-nanostructures (NS) -. Thus, microorganisms could be used as an ecofriendly way to get NS. RESULTS We analyzed the tolerance of Exiguobacterium acetylicum MF03, E. aurantiacum MF06, and E. profundum MF08 to Silver (I), gold (III), and tellurium (IV) compounds. Specifically, we explored the ability of cell-free extracts from these bacteria to reduce these toxicants and synthesize NS in vitro, both in the presence or absence of oxygen. All isolates exhibited higher tolerance to these toxicants in anaerobiosis. While in the absence of oxygen they showed high tellurite- and silver-reducing activity at pH 9.0, whereas AuCl4- which was reduced at pH 7.0 in both conditions. Given these results, cell-free extracts were used to synthesize NS containing silver, gold or tellurium, characterizing their size, morphology and chemical composition. Silver and tellurium NS exhibited smaller size under anaerobiosis and their morphology was circular (silver NS), starred (tellurium NS) or amorphous (gold NS). CONCLUSIONS This nanostructure-synthesizing ability makes these isolates interesting candidates to get NS with biotechnological potential.
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Affiliation(s)
- Javier Orizola
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Mirtha Ríos-Silva
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.,Departamento de Ciencias Nucleares, Comisión Chilena de Energía Nuclear, Santiago, Chile
| | - Claudia Muñoz-Villagrán
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Esteban Vargas
- Center for the Development of Nanoscience and Nanotechnology, Santiago, Chile
| | - Claudio Vásquez
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Felipe Arenas
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.
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49
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Abdi DE, Owen JS, Brindley JC, Birnbaum AC, Wilson PC, Hinz FO, Reguera G, Lee JY, Cregg BM, Kort DR, Fernandez RT. Nutrient and pesticide remediation using a two-stage bioreactor-adsorptive system under two hydraulic retention times. WATER RESEARCH 2020; 170:115311. [PMID: 31783190 DOI: 10.1016/j.watres.2019.115311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 11/12/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
Nutrients and pesticides in agricultural runoff contribute to the degradation of water resources. Nitrates and phosphates can be remediated through the use of treatment systems such as woodchip bioreactors and adsorbent aggregate filters; however, concerns remain over potential effects of pesticides on nutrient removal efficiency in these systems. To test this, we designed laboratory-scale woodchip bioreactors equipped with secondary adsorbent aggregate filters and investigated the capacity of these systems to remediate nutrients when operated under two hydraulic retention times (HRT) and in the presence of commonly used pesticides. The woodchip bioreactors effectively removed over 99% of nitrate per day when operated under a 72 h hydraulic retention time, with the secondary expanded shale aggregate filters consistently reducing phosphate concentrations by 80-87%. Treatment efficacy of both systems was maintained in the presence of the insecticide chlorpyrifos. Reducing HRT in the bioreactors to 21 min decreased nitrate removal efficiency; however, the insecticides bifenthrin, chlorpyrifos, and the herbicide oxyfluorfen were reduced by 76%, 63%, and 31%, respectively. Cultivation approaches led to the isolation of 45 different species from the woodchip bioreactors operated under a 21 min HRT, with Bacillus species being the most prevalent throughout the treatment. By contrast, pesticide application decreased the number and diversity of Bacillus isolates and enriched for Pseudomonas and Exiguobacterium species. Woodchip bioreactors and adsorbent aggregate filters provide effective treatment platforms to remediate agrochemicals, where they maintain treatment efficacy in the presence of pesticides and can be modulated through HRT management to achieve environmental and operational water quality goals.
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Affiliation(s)
- Damon E Abdi
- Department of Horticulture, Michigan State University, 1066 Bogue St. Room A288, East Lansing, MI, 48824, USA
| | - James S Owen
- Department of Plant and Environmental Sciences, Virginia Tech Agricultural Experiment Station, 1444 Diamond Springs Road, Virginia Beach, VA, 23455, USA
| | - Julie C Brindley
- Department of Plant and Environmental Sciences, Virginia Tech Agricultural Experiment Station, 1444 Diamond Springs Road, Virginia Beach, VA, 23455, USA
| | - Anna C Birnbaum
- Department of Plant and Environmental Sciences, Virginia Tech Agricultural Experiment Station, 1444 Diamond Springs Road, Virginia Beach, VA, 23455, USA
| | - P Chris Wilson
- Department of Soil and Water Sciences, University of Florida, 2181 McCarty Hall, Gainesville, FL, 32611, USA
| | - Francisca O Hinz
- Department of Soil and Water Sciences, University of Florida, 2181 McCarty Hall, Gainesville, FL, 32611, USA
| | - Gemma Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University, 6190 Biomedical Physical Sciences, East Lansing, MI, 48824, USA
| | - Joo-Young Lee
- Department of Microbiology and Molecular Genetics, Michigan State University, 6190 Biomedical Physical Sciences, East Lansing, MI, 48824, USA
| | - Bert M Cregg
- Department of Horticulture, Michigan State University, 1066 Bogue St. Room A288, East Lansing, MI, 48824, USA
| | - Daniel R Kort
- Department of Horticulture, Michigan State University, 1066 Bogue St. Room A288, East Lansing, MI, 48824, USA
| | - R Thomas Fernandez
- Department of Horticulture, Michigan State University, 1066 Bogue St. Room A288, East Lansing, MI, 48824, USA.
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50
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Ramos-Silva P, Serrano M, Henriques AO. From Root to Tips: Sporulation Evolution and Specialization in Bacillus subtilis and the Intestinal Pathogen Clostridioides difficile. Mol Biol Evol 2020; 36:2714-2736. [PMID: 31350897 PMCID: PMC6878958 DOI: 10.1093/molbev/msz175] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Bacteria of the Firmicutes phylum are able to enter a developmental pathway that culminates with the formation of highly resistant, dormant endospores. Endospores allow environmental persistence, dissemination and for pathogens, are also infection vehicles. In both the model Bacillus subtilis, an aerobic organism, and in the intestinal pathogen Clostridioides difficile, an obligate anaerobe, sporulation mobilizes hundreds of genes. Their expression is coordinated between the forespore and the mother cell, the two cells that participate in the process, and is kept in close register with the course of morphogenesis. The evolutionary mechanisms by which sporulation emerged and evolved in these two species, and more broadly across Firmicutes, remain largely unknown. Here, we trace the origin and evolution of sporulation using the genes known to be involved in the process in B. subtilis and C. difficile, and estimating their gain-loss dynamics in a comprehensive bacterial macroevolutionary framework. We show that sporulation evolution was driven by two major gene gain events, the first at the base of the Firmicutes and the second at the base of the B. subtilis group and within the Peptostreptococcaceae family, which includes C. difficile. We also show that early and late sporulation regulons have been coevolving and that sporulation genes entail greater innovation in B. subtilis with many Bacilli lineage-restricted genes. In contrast, C. difficile more often recruits new sporulation genes by horizontal gene transfer, which reflects both its highly mobile genome, the complexity of the gut microbiota, and an adjustment of sporulation to the gut ecosystem.
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Affiliation(s)
- Paula Ramos-Silva
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Marine Biodiversity Group, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Mónica Serrano
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Adriano O Henriques
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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