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Morales-Hidalgo M, Povedano-Priego C, Martinez-Moreno MF, Ojeda JJ, Jroundi F, Merroun ML. Long-term tracking of the microbiology of uranium-amended water-saturated bentonite microcosms: A mechanistic characterization of U speciation. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135044. [PMID: 38943881 DOI: 10.1016/j.jhazmat.2024.135044] [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: 03/05/2024] [Revised: 06/14/2024] [Accepted: 06/25/2024] [Indexed: 07/01/2024]
Abstract
Deep geological repositories (DGRs) stand out as one of the optimal options for managing high-level radioactive waste (HLW) such as uranium (U) in the near future. Here, we provide novel insights into microbial behavior in the DGR bentonite barrier, addressing potential worst-case scenarios such as waste leakage (e.g., U) and groundwater infiltration of electron rich donors in the bentonite. After a three-year anaerobic incubation, Illumina sequencing results revealed a bacterial diversity dominated by anaerobic and spore-forming microorganisms mainly from the phylum Firmicutes. Highly U tolerant and viable bacterial isolates from the genera Peribacillus, Bacillus, and some SRB such as Desulfovibrio and Desulfosporosinus, were enriched from U-amended bentonite. The results obtained by XPS and XRD showed that U was present as U(VI) and as U(IV) species. Regarding U(VI), we have identified biogenic U(VI) phosphates, U(UO2)·(PO4)2, located in the inner part of the bacterial cell membranes in addition to U(VI)-adsorbed to clays such as montmorillonite. Biogenic U(IV) species as uraninite may be produced as result of bacterial enzymatic U(VI) reduction. These findings suggest that under electron donor-rich water-saturation conditions, bentonite microbial community can control U speciation, immobilizing it, and thus enhancing future DGR safety if container rupture and waste leakage occurs.
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Affiliation(s)
- Mar Morales-Hidalgo
- Faculty of Science, Department of Microbiology, University of Granada, Granada, Spain.
| | | | | | - Jesus J Ojeda
- Department of Chemical Engineering, Faculty of Science and Engineering, Swansea University, Swansea, United Kingdom
| | - Fadwa Jroundi
- Faculty of Science, Department of Microbiology, University of Granada, Granada, Spain
| | - Mohamed L Merroun
- Faculty of Science, Department of Microbiology, University of Granada, Granada, Spain
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2
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Saggese A, Barrella V, Porzio AD, Troise AD, Scaloni A, Cigliano L, Scala G, Baccigalupi L, Iossa S, Ricca E, Mazzoli A. Protective role of cells and spores of Shouchella clausii SF174 against fructose-induced gut dysfunctions in small and large intestine. J Nutr Biochem 2024; 133:109706. [PMID: 39053859 DOI: 10.1016/j.jnutbio.2024.109706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 07/09/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024]
Abstract
The oral administration of probiotics is nowadays recognized as a strategy to treat or prevent the consequences of unhealthy dietary habits. Here we analyze and compare the effects of the oral administration of vegetative cells or spores of Shouchella clausii SF174 in counteracting gut dysfunctions induced by 6 weeks of high fructose intake in a rat model. Gut microbiota composition, tight junction proteins, markers of inflammation and redox homeostasis were evaluated in ileum and colon in rats fed fructose rich diet and supplemented with cells or spores of Shouchella clausii SF174. Our results show that both spores and cells of SF174 were effective in preventing the fructose-induced metabolic damage to the gut, namely establishment of "leaky gut", inflammation and oxidative damage, thus preserving gut function. Our results also suggest that vegetative cells and germination-derived cells metabolize part of the ingested fructose at the ileum level.
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Affiliation(s)
- Anella Saggese
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Valentina Barrella
- Department of Biology, University of Naples Federico II, Naples, Italy; NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Angela Di Porzio
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Antonio Dario Troise
- National Research Council, Proteomics, Metabolomics & Mass Spectrometry Laboratory, Institute for the Animal Production System in the Mediterranean Environment, Portici Naples, Italy
| | - Andrea Scaloni
- National Research Council, Proteomics, Metabolomics & Mass Spectrometry Laboratory, Institute for the Animal Production System in the Mediterranean Environment, Portici Naples, Italy
| | - Luisa Cigliano
- Department of Biology, University of Naples Federico II, Naples, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Napoli, Italy
| | - Giovanni Scala
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Loredana Baccigalupi
- NBFC, National Biodiversity Future Center, Palermo, Italy; Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Napoli, Italy
| | - Susanna Iossa
- Department of Biology, University of Naples Federico II, Naples, Italy; NBFC, National Biodiversity Future Center, Palermo, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Napoli, Italy
| | - Ezio Ricca
- Department of Biology, University of Naples Federico II, Naples, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Napoli, Italy.
| | - Arianna Mazzoli
- Department of Biology, University of Naples Federico II, Naples, Italy
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3
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Put H, Gerstmans H, Vande Capelle H, Fauvart M, Michiels J, Masschelein J. Bacillus subtilis as a host for natural product discovery and engineering of biosynthetic gene clusters. Nat Prod Rep 2024; 41:1113-1151. [PMID: 38465694 DOI: 10.1039/d3np00065f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Covering: up to October 2023Many bioactive natural products are synthesized by microorganisms that are either difficult or impossible to cultivate under laboratory conditions, or that produce only small amounts of the desired compound. By transferring biosynthetic gene clusters (BGCs) into alternative host organisms that are more easily cultured and engineered, larger quantities can be obtained and new analogues with potentially improved biological activity or other desirable properties can be generated. Moreover, expression of cryptic BGCs in a suitable host can facilitate the identification and characterization of novel natural products. Heterologous expression therefore represents a valuable tool for natural product discovery and engineering as it allows the study and manipulation of their biosynthetic pathways in a controlled setting, enabling innovative applications. Bacillus is a genus of Gram-positive bacteria that is widely used in industrial biotechnology as a host for the production of proteins from diverse origins, including enzymes and vaccines. However, despite numerous successful examples, Bacillus species remain underexploited as heterologous hosts for the expression of natural product BGCs. Here, we review important advantages that Bacillus species offer as expression hosts, such as high secretion capacity, natural competence for DNA uptake, and the increasing availability of a wide range of genetic tools for gene expression and strain engineering. We evaluate different strain optimization strategies and other critical factors that have improved the success and efficiency of heterologous natural product biosynthesis in B. subtilis. Finally, future perspectives for using B. subtilis as a heterologous host are discussed, identifying research gaps and promising areas that require further exploration.
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Affiliation(s)
- Hanne Put
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Hans Gerstmans
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
- Biosensors Group, KU Leuven, 3001 Leuven, Belgium
| | - Hanne Vande Capelle
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- imec, 3001 Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Joleen Masschelein
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
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4
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Ucak S. Determination of Bacterial Community Structure of Table Olive via Metagenomic Approach in Şarköy. Chem Biodivers 2024; 21:e202302120. [PMID: 38613509 DOI: 10.1002/cbdv.202302120] [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: 01/02/2024] [Revised: 03/22/2024] [Accepted: 04/11/2024] [Indexed: 04/15/2024]
Abstract
One of the most popular pickled foods created worldwide is table olives. The aim was to identify the bacterial microbiota of table olive samples collected from Şarköy, Tekirdağ-Türkiye using next generation sequencing and 16S metagenomic analysis. Samples were studied as non-pre-enriched (n : 10) and after pre-enrichment (n : 10) to compare the effects of the enrichment process on the bacterial diversity. In non-pre-enriched, the most common genus found was Sphingomonas, followed by Altererythrobacter and Lysobacter. The most common phylum found was Proteobacteria, followed by Bacteroidota and Actinobacteria. In pre-enriched, Bacillus was the most commonly detected genus, followed by Pantoea and Staphylococcus. The most frequently found phylum was Firmicutes, followed by Proteobacteria and Cyanobacteria. This study is the first study for Şarköy, which is the only table olive production place in the Tekirdağ region due to its microclimate feature. Further studies are needed in more table olive samples from different geographical areas to confirm and develop current findings.
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Affiliation(s)
- Samet Ucak
- Department of Medical Biology and Genetics, Faculty of Medicine, Istanbul Aydın University, Istanbul, 34295, Türkiye
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Lodhi AF, Zhang Y, Adil M, Deng Y. Design and application of a novel culturing chip (cChip) for culturing the uncultured aquatic microorganisms. Arch Microbiol 2023; 205:285. [PMID: 37442830 DOI: 10.1007/s00203-023-03613-w] [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: 10/11/2022] [Revised: 05/18/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023]
Abstract
Culturing uncultured microorganisms is an important aspect of microbiology. Once cultured, these microorganisms can be a source of useful antibiotics, enzymes etc. In this study, we have designed a novel culturing chip (cChip) to facilitate the growth of uncultured aquatic bacterial community by concentrating the samples. cChip was optimized for microbial growth using known bacteria in the laboratory as a pre-experiment. Then microorganisms from a freshwater lake were concentrated and inoculated, before putting the inoculated cChip in a simulated lake environment and further sub-culturing on laboratory media. High-throughput sequencing and traditional culturing were also performed for comparison. These three methods were able to detect 265 genera of microorganisms in the sample, of which 78.87% were detected by high-throughput sequencing, 30.94% by cChip, while only 6.42% were obtained by traditional culture. Moreover, all microorganisms obtained by traditional culture were also cultured using the cChip. A total of 45 new strains were isolated from the cChip, and their 16S rRNA gene sequences were 91.35% to 98.7% similar to their closest relatives according to NCBI GenBank database. We conclude that the design and simple operation of cChip can improve the culture efficiency of traditional culture by almost 5 times. To the best of our knowledge, this is the first report comparing a novel culturing method with high-throughput sequencing data and traditional culturing of the same samples.
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Affiliation(s)
- Adil Farooq Lodhi
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceutical, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
- Department of Microbiology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, Pakistan
| | - Ying Zhang
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceutical, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Maria Adil
- Department of Microbiology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, Pakistan
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceutical, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
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Wang M, Deng J, Duan G, Chen L, Huang X, Wang W, Gong L, Zhang Y, Yu K, Guo L. Insights into the impacts of autotoxic allelochemicals from rhizosphere of Atractylodes lancea on soil microenvironments. FRONTIERS IN PLANT SCIENCE 2023; 14:1136833. [PMID: 36968368 PMCID: PMC10036400 DOI: 10.3389/fpls.2023.1136833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Atractylodes lancea suffers from continuous cropping obstacles that have become a major constraint in its cultivation, but there is still little information on the autotoxic allelochemicals and their interaction with soil microorganisms. In this study, we firstly identified the autotoxic allelochemicals from rhizosphere of A. lancea and determined their autotoxicity. Third-year continuous A. lancea cropping soils, i.e., rhizospheric soil and bulk soil, compared with control soil and one-year natural fallow soil were used to determine soil biochemical properties and microbial community. Eight allelochemicals from A. lancea roots were detected and exhibited significant autotoxicity effects on seed germination and seedling growth of A. lancea with the highest content of dibutyl phthalate in rhizospheric soil and lowest IC50 value of 2,4-di-tert-butylphenol inhibiting seed germination. The contents of soil nutrients and organic matter, pH value, and enzyme activity were altered between different soils, and the parameters of fallow soil were close to those of the unplanted soil. The PCoA analysis indicated that the community composition of both bacteria and fungi were differed significantly among the soil samples. Continuous cropping decreased OTUs numbers of bacterial and fungal communities, and natural fallow restored them. The relative abundance of Proteobacteria, Planctomycetes, and Actinobacteria decreased, and that of Acidobacteria and Ascomycota increased after three years cultivation. The LEfSe analysis identified 115 and 49 biomarkers for bacterial and fungal communities, respectively. The results suggested that natural fallow restored the structure of soil microbial community. Overall, our results revealed that autotoxic allelochemicals caused the variations of soil microenvironments and resulted in replantation problem of A. lancea, and natural fallow alleviated the soil deterioration by remodeling the rhizospheric microbial community and restoring soil biochemical properties. These findings provide important insights and clues for solving the continuous cropping problems and guiding the management of sustainable farmland.
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Affiliation(s)
- Meng Wang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Juan Deng
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Gonghao Duan
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Lei Chen
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Xiao Huang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
- Hubei Key Laboratory of Resources and Chemistry of Chinese Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Wenjie Wang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Ling Gong
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Yan Zhang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Kun Yu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
- Hubei Key Laboratory of Resources and Chemistry of Chinese Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Lanping Guo
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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7
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Romero-Rodríguez A, Ruiz-Villafán B, Martínez-de la Peña CF, Sánchez S. Targeting the Impossible: A Review of New Strategies against Endospores. Antibiotics (Basel) 2023; 12:antibiotics12020248. [PMID: 36830159 PMCID: PMC9951900 DOI: 10.3390/antibiotics12020248] [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: 12/05/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023] Open
Abstract
Endospore-forming bacteria are ubiquitous, and their endospores can be present in food, in domestic animals, and on contaminated surfaces. Many spore-forming bacteria have been used in biotechnological applications, while others are human pathogens responsible for a wide range of critical clinical infections. Due to their resistant properties, it is challenging to eliminate spores and avoid the reactivation of latent spores that may lead to active infections. Furthermore, endospores play an essential role in the survival, transmission, and pathogenesis of some harmful strains that put human and animal health at risk. Thus, different methods have been applied for their eradication. Nevertheless, natural products are still a significant source for discovering and developing new antibiotics. Moreover, targeting the spore for clinical pathogens such as Clostridioides difficile is essential to disease prevention and therapeutics. These strategies could directly aim at the structural components of the spore or their germination process. This work summarizes the current advances in upcoming strategies and the development of natural products against endospores. This review also intends to highlight future perspectives in research and applications.
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Affiliation(s)
- Alba Romero-Rodríguez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
- Correspondence:
| | - Beatriz Ruiz-Villafán
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Claudia Fabiola Martínez-de la Peña
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72592, Mexico
| | - Sergio Sánchez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
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8
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Wang H, Zhao R, Wu X, Zhao D, Xue H, Zhang Y, Dai N, Song D, Zhang M, Ding H. Preparation and Properties of Bio-Based Attapulgite Copolymer (BAC) Sand-Fixing Material. Polymers (Basel) 2023; 15:polym15020265. [PMID: 36679146 PMCID: PMC9864960 DOI: 10.3390/polym15020265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
Desertification, one of the world's most pressing serious environmental problems, poses a serious threat to human survival as well as to social, economic, and political development. Nevertheless, the development of environmentally friendly sand-fixing materials is still a tremendous challenge for preventing desertification. This study developed a bio-based attapulgite copolymer (BAC) by grafting copolymerization of attapulgite, starch, sulfomethyl lignin, and biological mycelia. Water retention, anti-water erosion, and anti-wind erosion tests were conducted to assess the application performance of the BAC. Scanning electron microscopy (SEM) was then employed to determine the morphology of the attapulgite and attapulgite graft copolymer sand-fixing material (CSF). The intermolecular interactions in CSF were revealed using Fourier transform infrared spectrum (FT-IR). The role of sand-fixing materials on soil physicochemical properties and seed germination was then discussed based on the germination rate experiments, and 16S rDNA sequencing technology was used to analyze the differences in microbial communities in each sample group. The results demonstrated that the BAC not only has superior application properties and significantly increased seed germination (95%), but also promotes soil development by regulating the structure of the soil microbial community. This work provides novel insights into the design of sand-fixing material for preventing desertification while improving soil fertility.
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Affiliation(s)
- Han Wang
- School of Environment Science and Engineering, Tianjin University, Weijin Road, Tianjin 300072, China
| | - Rui Zhao
- School of Environment Science and Engineering, Tianjin University, Weijin Road, Tianjin 300072, China
| | - Xiangci Wu
- School of Environment Science and Engineering, Tianjin University, Weijin Road, Tianjin 300072, China
| | - Dan Zhao
- School of Environment Science and Engineering, Tianjin University, Weijin Road, Tianjin 300072, China
| | - Hua Xue
- School of Environment Science and Engineering, Tianjin University, Weijin Road, Tianjin 300072, China
| | - Yuxin Zhang
- College of Materials Science and Engineering, Chongqing University, Chongqing 400044, China
| | - Nan Dai
- College of Materials Science and Engineering, Chongqing University, Chongqing 400044, China
| | - Dan Song
- Chongqing Academy of Eco-Environmental Sciences, Chongqing 401147, China
| | - Mengling Zhang
- Huadian Aqua Membrane Separation Technology (Tianjin) Co., Ltd., Tianjin 301700, China
| | - Hui Ding
- School of Environment Science and Engineering, Tianjin University, Weijin Road, Tianjin 300072, China
- Correspondence:
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9
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Liu Y, Xu Y, Cui X, Zhang B, Wang X, Qin X, Wang J, Li Y, Zhang W, Liu G, Chen T, Zhang G. Temporary Survival Increasing the Diversity of Culturable Heterotrophic Bacteria in the Newly Exposed Moraine at a Glacier Snout. BIOLOGY 2022; 11:biology11111555. [PMID: 36358257 PMCID: PMC9687651 DOI: 10.3390/biology11111555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/11/2022] [Accepted: 10/20/2022] [Indexed: 11/05/2022]
Abstract
Laohugou Glacier No. 12 is located on the northern slope of the western Qilian Mountains with a temperate continental wet climate and an extremely cold winter. Bacteria in a newly exposed moraine have to cope with various pressures owing to deglaciation at the glacier snout. However, limited information is available regarding the high diversity and temporary survival of culturable heterotrophic bacteria under various environmental stresses. To examine the tolerance of extremophiles against varying environmental conditions in a newly exposed moraine, we simulated environmental stress in bacterial cultures. The results showed that the isolated strains belonged to actinobacteria, Proteobacteria, Bacteroidetes, Deinococcus-Thermus, and Firmicutes. Actinobacteria was the most abundant phylum, followed by Proteobacteria, at both high and low temperatures. Pseudarthrobacter was the most abundant genus, accounting for 14.2% of the total isolates. Although several microorganisms grew at 10 °C, the proportion of microorganisms that grew at 25 °C was substantially higher. In particular, 50% of all bacterial isolates grew only at a high temperature (HT), whereas 21.4% of the isolates grew at a low temperature (LT), and 38.6% of the isolates grew at both HT and LT. In addition, many radiation-resistant extremophiles were identified, which adapted to both cold and oxidative conditions. The nearest neighbors of approximately >90% of bacteria belonged to a nonglacial environment, such as oil-contaminated soil, rocks, and black sand, instead of glacial niches. This study provides insights into the ecological traits, stress responses, and temporary survival of culturable heterotrophic bacteria in a newly exposed moraine with variable environmental conditions and the relationship of these communities with the non-glacial environment. This study may help to understand the evolution, competition, and selective growth of bacteria in the transition regions between glaciers and retreats in the context of glacier melting and retreat owing to global warming.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Yeteng Xu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Xiaowen Cui
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- College of Geography and Environment Science, Northwest Normal University, Lanzhou 730070, China
| | - Binglin Zhang
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Xinyue Wang
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Xiang Qin
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Jinxiu Wang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yanzhao Li
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- School of Stomatology, Lanzhou University, Lanzhou 730000, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Correspondence: (T.C.); (G.Z.)
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Correspondence: (T.C.); (G.Z.)
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10
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Rodrigues CJC, de Carvalho CCCR. Cultivating marine bacteria under laboratory conditions: Overcoming the “unculturable” dogma. Front Bioeng Biotechnol 2022; 10:964589. [PMID: 36061424 PMCID: PMC9428589 DOI: 10.3389/fbioe.2022.964589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/26/2022] [Indexed: 11/22/2022] Open
Abstract
Underexplored seawater environments may contain biological resources with potential for new biotechnological applications. Metagenomic techniques revolutionized the study of bacterial communities but culture dependent methods will still be important to help the biodiscovery of new products and enzymes from marine bacteria. In this context, we promoted the growth of bacteria from a marine rock pond by culture dependent techniques and compared the results with culture independent methods. The total number of bacteria and diversity were studied in different agar plate media during 6 weeks. Agar plate counting was of the same order of magnitude of direct microscopy counts. The highest efficiency of cultivation was 45% attained in marine agar medium. Molecular analysis revealed 10 different phyla of which only four were isolated by the culture dependent method. On the other hand, four taxonomic orders were detected by cultivation but not by the molecular technique. These include bacteria from the phyla Bacillota and Actinomycetota. Our study shows that it is possible to grow more than the traditionally considered 1% of bacteria from a seawater sample using standard agar plate techniques and laboratorial conditions. The results also demonstrate the importance of culture methods to grow bacteria not detected by molecular approaches for future biotechnological applications.
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Affiliation(s)
- Carlos J. C. Rodrigues
- Department of Bioengineering, iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory I4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Carla C. C. R. de Carvalho
- Department of Bioengineering, iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory I4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- *Correspondence: Carla C. C. R. de Carvalho,
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11
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Nwachukwu BC, Ayangbenro AS, Babalola OO. Effects of soil properties and carbon substrates on bacterial diversity of two sunflower farms. AMB Express 2022; 12:47. [PMID: 35460382 PMCID: PMC9035202 DOI: 10.1186/s13568-022-01388-9] [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: 01/19/2022] [Accepted: 04/09/2022] [Indexed: 11/24/2022] Open
Abstract
The sustainable production of sunflower (Helianthus annuus) is crucial and one way to accomplish this feat is to have an understanding of the beneficial bacteria of sunflower rhizosphere. Similarly, the respiratory response of these bacteria needs to be studied to understand their roles in the ecosystem. This study was therefore conceptualized to gain insights into the effects of soil properties and carbon substrate utilization on bacterial community diversity of sunflower rhizosphere grown in Ditsobottla and Kraaipan, North West Province, South Africa. Extracted DNA from sunflower rhizosphere and bulk soils was subjected to 16S amplicon sequencing. Significant differences were observed in the alpha and beta diversities of the soil bacterial communities (p < 0.05). At the order level, among all the bacterial taxa captured in the farms, Bacillales were the most dominant. The abundance of Lactobacillales, Bacillales, Rhizobiales, Enterobacteriales, Burkholderiales, Flavobacteriales, Sphingomonadales, Myxococcales, and Nitrosomonadales obtained from Ditsobottla rhizosphere soil (R1) was positively influenced by organic matter (OM), while the abundance of Planctomycetales, Cytophagales, Gemmatimonadales, Nitrospirales and Caulobacteriales from Kraaipan rhizosphere soil (R2) was positively influenced by total N and pH. Bacterial communities of all the soil samples utilized the different carbon substrates (three amino acids, six carbohydrates, and three carboxylic acids) as an energy source. Significant differences (p < 0.05) were only observed in tryptophan and methionine amended soils. Unclassified bacteria were also captured in this study, such bacteria can further be harnessed for sustainable production of sunflower and other agricultural crops.
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12
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Ferreira WT, Hong HA, Adams JRG, Hess M, Kotowicz NK, Tan S, Ferrari E, Brisson A, Zentek J, Soloviev M, Cutting SM. Environmentally Acquired Bacillus and Their Role in C. difficile Colonization Resistance. Biomedicines 2022; 10:930. [PMID: 35625667 PMCID: PMC9138776 DOI: 10.3390/biomedicines10050930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/14/2022] [Accepted: 04/18/2022] [Indexed: 01/27/2023] Open
Abstract
Clostridioides difficile is an environmentally acquired, anaerobic, spore-forming bacterium which ordinarily causes disease following antibiotic-mediated dysbiosis of the intestinal microbiota. Although much is understood regarding the life cycle of C. difficile, the fate of C. difficile spores upon ingestion remains unclear, and the underlying factors that predispose an individual to colonization and subsequent development of C. difficile infection (CDI) are not fully understood. Here, we show that Bacillus, a ubiquitous and environmentally acquired, spore-forming bacterium is associated with colonization resistance to C. difficile. Using animal models, we first provide evidence that animals housed under conditions that mimic reduced environmental exposure have an increased susceptibility to CDI, correlating with a loss in Bacillus. Lipopeptide micelles (~10 nm) produced by some Bacilli isolated from the gastro-intestinal (GI)-tract and shown to have potent inhibitory activity to C. difficile have recently been reported. We show here that these micelles, that we refer to as heterogenous lipopeptide lytic micelles (HELMs), act synergistically with components present in the small intestine to augment inhibitory activity against C. difficile. Finally, we show that provision of HELM-producing Bacillus to microbiota-depleted animals suppresses C. difficile colonization thereby demonstrating the significant role played by Bacillus in colonization resistance. In the wider context, our study further demonstrates the importance of environmental microbes on susceptibility to pathogen colonization.
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Affiliation(s)
- William T. Ferreira
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (J.R.G.A.); (M.H.)
| | - Huynh A. Hong
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (J.R.G.A.); (M.H.)
| | - James R. G. Adams
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (J.R.G.A.); (M.H.)
| | - Mateusz Hess
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (J.R.G.A.); (M.H.)
| | - Natalia K. Kotowicz
- SporeGen Ltd., London Bioscience Innovation Centre, 2 Royal College Street, London NW1 0NH, UK;
| | - Sisareuth Tan
- Laboratoire d’Imagerie Moléculaire et Nano-Bio-Technologie, UMR-CBMN CNRS-Université de Bordeaux-IPB, 33607 Pessac, France; (S.T.); (A.B.)
| | - Enrico Ferrari
- School of Life Sciences, University of Lincoln, Lincoln LN6 7TS, UK;
| | - Alain Brisson
- Laboratoire d’Imagerie Moléculaire et Nano-Bio-Technologie, UMR-CBMN CNRS-Université de Bordeaux-IPB, 33607 Pessac, France; (S.T.); (A.B.)
| | - Jurgen Zentek
- Institute for Animal Health, Freie University of Berlin, Berlin 14195, Germany;
| | - Mikhail Soloviev
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (J.R.G.A.); (M.H.)
| | - Simon M. Cutting
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (J.R.G.A.); (M.H.)
- SporeGen Ltd., London Bioscience Innovation Centre, 2 Royal College Street, London NW1 0NH, UK;
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13
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Analysis of seed-associated bacteria and fungi on staple crops using the cultivation and metagenomic approaches. Folia Microbiol (Praha) 2022; 67:351-361. [PMID: 35220558 PMCID: PMC9072454 DOI: 10.1007/s12223-022-00958-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/09/2022] [Indexed: 11/04/2022]
Abstract
AbstractOne of the key factors affecting seed quality is microbial communities residing on and in the seeds. In this study, microbial populations of seeds of conventionally and organically produced wheat, barley, and maize were analyzed using two different approaches: the cultivation method and metagenomics. For cultivation, three basic media were used: DG18 (for fungi), and nutrient agar or tryptic soy agar supplemented with cycloheximide or nystatin (for bacteria). Metagenomic sequencing was performed using the Illumina MiSeq platform. A total of 452 bacterial isolates comprising 36 genera and 5 phyla and 90 fungal isolates comprising 10 genera and 3 phyla were obtained from the seed surfaces. Among bacteria, representatives from the genera Bacillus, Pantoea, Paenibacillus, and Curtobacterium predominated, and among fungi, Aspergillus predominated. A total of 142 fungal OTUs and 201 bacterial OTUs were obtained from all the samples. Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria comprised most of the bacterial OTUs, and Ascomycota comprised most of the fungal OTUs. Only 3 fungal OTUs (representatives of Curvibasidium, Venturia, and Dermateaceae) were exclusively present only within seeds and not on the seed surfaces. Barley seeds had the highest microbial load and richness, whereas corn had the lowest. Wheat and barley shared a higher number of OTUs than either of them did with corn with higher overlap between conventionally grown cereals than between organically grown cereals. Some OTUs were farming specific. This study demonstrates that the microbiome of cereal seeds is greatly dependent on the species of the host and is less affected by agricultural practices.
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López-Moreno A, Ruiz-Moreno Á, Pardo-Cacho J, Cerk K, Torres-Sánchez A, Ortiz P, Úbeda M, Aguilera M. Culturing and Molecular Approaches for Identifying Microbiota Taxa Impacting Children's Obesogenic Phenotypes Related to Xenobiotic Dietary Exposure. Nutrients 2022; 14:nu14020241. [PMID: 35057422 PMCID: PMC8778816 DOI: 10.3390/nu14020241] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/31/2021] [Accepted: 01/03/2022] [Indexed: 12/11/2022] Open
Abstract
Integrated data from molecular and improved culturomics studies might offer holistic insights on gut microbiome dysbiosis triggered by xenobiotics, such as obesity and metabolic disorders. Bisphenol A (BPA), a dietary xenobiotic obesogen, was chosen for a directed culturing approach using microbiota specimens from 46 children with obesity and normal-weight profiles. In parallel, a complementary molecular analysis was carried out to estimate the BPA metabolising capacities. Firstly, catalogues of 237 BPA directed-cultured microorganisms were isolated using five selected media and several BPA treatments and conditions. Taxa from Firmicutes, Proteobacteria, and Actinobacteria were the most abundant in normal-weight and overweight/obese children, with species belonging to the genera Enterococcus, Escherichia, Staphylococcus, Bacillus, and Clostridium. Secondly, the representative isolated taxa from normal-weight vs. overweight/obese were grouped as BPA biodegrader, tolerant, or resistant bacteria, according to the presence of genes encoding BPA enzymes in their whole genome sequences. Remarkably, the presence of sporobiota and concretely Bacillus spp. showed the higher BPA biodegradation potential in overweight/obese group compared to normal-weight, which could drive a relevant role in obesity and metabolic dysbiosis triggered by these xenobiotics.
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Affiliation(s)
- Ana López-Moreno
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, 18016 Granada, Spain
- Microbiota Laboratory, IBS: Instituto de Investigación Biosanitaria ibs, 18012 Granada, Spain
- Correspondence: (A.L.-M.); (M.A.); Tel.: +34-9-5824-5129 (M.A.)
| | - Ángel Ruiz-Moreno
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, 18016 Granada, Spain
| | - Jesús Pardo-Cacho
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
| | - Klara Cerk
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, 18016 Granada, Spain
| | - Alfonso Torres-Sánchez
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, 18016 Granada, Spain
| | - Pilar Ortiz
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, 18016 Granada, Spain
| | - Marina Úbeda
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
| | - Margarita Aguilera
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, 18016 Granada, Spain
- Microbiota Laboratory, IBS: Instituto de Investigación Biosanitaria ibs, 18012 Granada, Spain
- Correspondence: (A.L.-M.); (M.A.); Tel.: +34-9-5824-5129 (M.A.)
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15
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Rosenberg E, Zilber-Rosenberg I. Reconstitution and Transmission of Gut Microbiomes and Their Genes between Generations. Microorganisms 2021; 10:microorganisms10010070. [PMID: 35056519 PMCID: PMC8780831 DOI: 10.3390/microorganisms10010070] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/26/2021] [Accepted: 12/28/2021] [Indexed: 12/13/2022] Open
Abstract
Microbiomes are transmitted between generations by a variety of different vertical and/or horizontal modes, including vegetative reproduction (vertical), via female germ cells (vertical), coprophagy and regurgitation (vertical and horizontal), physical contact starting at birth (vertical and horizontal), breast-feeding (vertical), and via the environment (horizontal). Analyses of vertical transmission can result in false negatives (failure to detect rare microbes) and false positives (strain variants). In humans, offspring receive most of their initial gut microbiota vertically from mothers during birth, via breast-feeding and close contact. Horizontal transmission is common in marine organisms and involves selectivity in determining which environmental microbes can colonize the organism's microbiome. The following arguments are put forth concerning accurate microbial transmission: First, the transmission may be of functions, not necessarily of species; second, horizontal transmission may be as accurate as vertical transmission; third, detection techniques may fail to detect rare microbes; lastly, microbiomes develop and reach maturity with their hosts. In spite of the great variation in means of transmission discussed in this paper, microbiomes and their functions are transferred from one generation of holobionts to the next with fidelity. This provides a strong basis for each holobiont to be considered a unique biological entity and a level of selection in evolution, largely maintaining the uniqueness of the entity and conserving the species from one generation to the next.
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16
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Dai X, Wang X, Gu J, Bao J, Wang J, Guo H, Yu J, Zhao W, Lei L. Responses of bacterial communities and antibiotic resistance genes to nano-cellulose addition during pig manure composting. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 300:113734. [PMID: 34649327 DOI: 10.1016/j.jenvman.2021.113734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 08/19/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
Treatment with exogenous additives during composting can help to alleviate the accumulation of antibiotic resistance genes (ARGs) caused by the direct application of pig manure to farmland. In addition, nano-cellulose has an excellent capacity for adsorbing pollutants. Thus, the effects of adding 300, 600, and 900 mg/kg nano-cellulose to compost on the bacterial communities, mobile genetic elements (MGEs), and ARGs were determined in this study. After composting, treatment with nano-cellulose significantly reduced the relative abundance of ARGs, which was lowest in the compost product with 600 mg/kg added nano-cellulose. Nano-cellulose inhibited the rebound in ARGs from the cooling period to the maturity period, and weakened the selective pressure of heavy metals on microorganisms by passivating bio-Cu. The results also showed that MGEs explained most of the changes in the abundances of ARGs, and MGEs had direct effects on ARGs. The addition of 600 mg/kg nano-cellulose reduced the abundances of bacterial genera associated with ermQ, tetG, and other genes, and the number of links (16) between ARGs and MGEs was lowest in the treatment with 600 mg/kg added nano-cellulose. Therefore, adding 600 mg/kg nano-cellulose reduced the abundances of ARGs by affecting host bacteria and MGEs. The results obtained in this study demonstrate the positive effect of nano-cellulose on ARG pollution in poultry manure, where adding 600 mg/kg nano-cellulose was most effective at reducing the abundances of ARGs.
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Affiliation(s)
- Xiaoxia Dai
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaojuan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Jie Gu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China; Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jianfeng Bao
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jia Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Honghong Guo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jing Yu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Wenya Zhao
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Liusheng Lei
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
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17
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Metaplasmidome-encoded functions of Siberian low-centered polygonal tundra soils. THE ISME JOURNAL 2021; 15:3258-3270. [PMID: 34012103 PMCID: PMC8528913 DOI: 10.1038/s41396-021-01003-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/26/2021] [Accepted: 04/30/2021] [Indexed: 02/04/2023]
Abstract
Plasmids have the potential to transfer genetic traits within bacterial communities and thereby serve as a crucial tool for the rapid adaptation of bacteria in response to changing environmental conditions. Our knowledge of the environmental pool of plasmids (the metaplasmidome) and encoded functions is still limited due to a lack of sufficient extraction methods and tools for identifying and assembling plasmids from metagenomic datasets. Here, we present the first insights into the functional potential of the metaplasmidome of permafrost-affected active-layer soil-an environment with a relatively low biomass and seasonal freeze-thaw cycles that is strongly affected by global warming. The obtained results were compared with plasmid-derived sequences extracted from polar metagenomes. Metaplasmidomes from the Siberian active layer were enriched via cultivation, which resulted in a longer contig length as compared with plasmids that had been directly retrieved from the metagenomes of polar environments. The predicted hosts of plasmids belonged to Moraxellaceae, Pseudomonadaceae, Enterobacteriaceae, Pectobacteriaceae, Burkholderiaceae, and Firmicutes. Analysis of their genetic content revealed the presence of stress-response genes, including antibiotic and metal resistance determinants, as well as genes encoding protectants against the cold.
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18
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Mitiku AA, Vandeweyer D, Lievens B, Bossaert S, Crauwels S, Aernouts B, Kechero Y, Van Campenhout L. Microbial profile during fermentation and aerobic stability of ensiled mixtures of maize stover and banana pseudostem in South Ethiopia. J Appl Microbiol 2021; 132:126-139. [PMID: 34133817 DOI: 10.1111/jam.15183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 05/07/2021] [Accepted: 06/01/2021] [Indexed: 11/29/2022]
Abstract
AIMS This study evaluated pH reduction and microbial growth during fermentation of maize stover (MS) mixed with banana pseudostem (BPS) under South Ethiopian conditions. MATERIALS AND RESULTS The MS and BPS were chopped and mixed into six treatments (T): 80% BPS plus 20% DMS (T1), 70% BPS plus 30% DMS (T2), 40% BPS plus 60% FMS (fresh MS) (T3), 20% BPS plus 80% FMS (T4), 100% FMS (T5), and 95% BPS plus 5% molasses (T6). At 0, 7, 14, 30, 60, and 90 days, pH and dry matter were determined. Microbiological quality was assessed using plate counts and Illumina MiSeq sequencing. On day 60 and 90, aerobic stability was investigated. The results showed a significant reduction in pH in all mixtures, except in T1 and T2. Lactic acid bacteria counts reached a maximum in all treatments within 14 days. Sequencing showed marked changes in dominant bacteria, such as Buttiauxella and Acinetobacter to Lactobacillus and Bifidobacterium. CONCLUSIONS The fresh MS and BPS mixtures and fresh maize showed significant pH reduction and dominance of desirable microbial groups. SIGNIFICANCE AND IMPACT OF THE STUDY The study enables year-round livestock feed supplementation to boost milk and meat production in South Ethiopia.
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Affiliation(s)
- Ashenafi A Mitiku
- Department of Microbial and Molecular Systems, Lab4Food, KU Leuven, Leuven, Belgium.,Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium.,Department of Animal Science, College of Agricultural Sciences, Arba Minch University, Arba Minch, Ethiopia
| | - Dries Vandeweyer
- Department of Microbial and Molecular Systems, Lab4Food, KU Leuven, Leuven, Belgium.,Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium
| | - Bart Lievens
- Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium.,Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Sofie Bossaert
- Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium.,Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Sam Crauwels
- Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium.,Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Ben Aernouts
- Department of Biosystems, Livestock Technology, KU Leuven, Leuven, Belgium
| | - Yisehak Kechero
- Department of Animal Science, College of Agricultural Sciences, Arba Minch University, Arba Minch, Ethiopia
| | - Leen Van Campenhout
- Department of Microbial and Molecular Systems, Lab4Food, KU Leuven, Leuven, Belgium.,Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium
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19
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Xu H, Zhao P, Ran Q, Li W, Wang P, Luo Y, Huang C, Yang X, Yin J, Zhang R. Enhanced electrokinetic remediation for Cd-contaminated clay soil by addition of nitric acid, acetic acid, and EDTA: Effects on soil micro-ecology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 772:145029. [PMID: 33770863 DOI: 10.1016/j.scitotenv.2021.145029] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/15/2020] [Accepted: 01/04/2021] [Indexed: 05/09/2023]
Abstract
Enhanced electrokinetic remediation (EKR) allows the rapid remediation of heavy metal-contaminated clay, but the impacts of this process on soil micro-ecology have rarely been evaluated. In this study, nitric acid, acetic acid, and EDTA were applied for enhancement of EKR and the effects on Cd removal, soil enzyme activity, and soil bacterial communities (SBCs) were determined. Nitric acid and acetic acid allowed 93.2% and 91.8% Cd removal, respectively, and EDTA treatment resulted in 40.4% removal due to the formation of negatively charged EDTA-Cd complexes, resulting in opposing directions of Cd electromigration and electroosmosis flow and slow electromigration rate caused by low voltage drop. Activities of soil beta-glucosidase, acid phosphatase, and urease, were all reduced by enhanced EKR treatment, especially nitric acid treatment, by 46.2%, 58.8% and 57.7%, respectively. The SBCs were analyzed by high-throughput sequencing and revealed significantly increased diversity for acetic acid treatment, no effect for EDTA treatment, and reduced diversity for nitric acid treatment. Compared with nitric acid and EDTA, acetic acid treatment enhanced EKR for higher Cd removal and improved biodiversity.
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Affiliation(s)
- Haiyin Xu
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Peiling Zhao
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Qiyang Ran
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China; Hunan Hengkai Environmental Protection Science & Technology Investment Co. Ltd, Changsha 410205, China
| | - Wenjuan Li
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Ping Wang
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China.
| | - Yuanling Luo
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China; Changsha Environmental Protection College, Changsha 410004, China.
| | - Chao Huang
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Xiong Yang
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Jingxuan Yin
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Ruiqi Zhang
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
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Wang S, Egan M, Ryan CA, Boyaval P, Dempsey EM, Ross RP, Stanton C. A good start in life is important-perinatal factors dictate early microbiota development and longer term maturation. FEMS Microbiol Rev 2021; 44:763-781. [PMID: 32821932 PMCID: PMC7685781 DOI: 10.1093/femsre/fuaa030] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 08/18/2020] [Indexed: 12/20/2022] Open
Abstract
Maternal health status is vital for the development of the offspring of humans, including physiological health and psychological functions. The complex and diverse microbial ecosystem residing within humans contributes critically to these intergenerational impacts. Perinatal factors, including maternal nutrition, antibiotic use and maternal stress, alter the maternal gut microbiota during pregnancy, which can be transmitted to the offspring. In addition, gestational age at birth and mode of delivery are indicated frequently to modulate the acquisition and development of gut microbiota in early life. The early-life gut microbiota engages in a range of host biological processes, particularly immunity, cognitive neurodevelopment and metabolism. The perturbed early-life gut microbiota increases the risk for disease in early and later life, highlighting the importance of understanding relationships of perinatal factors with early-life microbial composition and functions. In this review, we present an overview of the crucial perinatal factors and summarise updated knowledge of early-life microbiota, as well as how the perinatal factors shape gut microbiota in short and long terms. We further discuss the clinical consequences of perturbations of early-life gut microbiota and potential therapeutic interventions with probiotics/live biotherapeutics.
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Affiliation(s)
- Shaopu Wang
- APC Microbiome Ireland, Cork, Ireland, P12 YT20.,Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland, P61 C996
| | - Muireann Egan
- APC Microbiome Ireland, Cork, Ireland, P12 YT20.,Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland, P61 C996
| | - C Anthony Ryan
- APC Microbiome Ireland, Cork, Ireland, P12 YT20.,Department of Paediatrics & Child Health, University College Cork, Cork, Ireland, T12 YN60
| | - Patrick Boyaval
- DuPont Nutrition & Biosciences, Danisco France SAS - DuPont, 22, rue Brunel, F- 75017 Paris, France
| | - Eugene M Dempsey
- APC Microbiome Ireland, Cork, Ireland, P12 YT20.,Department of Paediatrics & Child Health, University College Cork, Cork, Ireland, T12 YN60
| | - R Paul Ross
- APC Microbiome Ireland, Cork, Ireland, P12 YT20
| | - Catherine Stanton
- APC Microbiome Ireland, Cork, Ireland, P12 YT20.,Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland, P61 C996
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21
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Sajjad W, Ali B, Bahadur A, Ghimire PS, Kang S. Bacterial Diversity and Communities Structural Dynamics in Soil and Meltwater Runoff at the Frontier of Baishui Glacier No.1, China. MICROBIAL ECOLOGY 2021; 81:370-384. [PMID: 32918153 DOI: 10.1007/s00248-020-01600-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 09/03/2020] [Indexed: 06/11/2023]
Abstract
Comprehensive knowledge of bacterial ecology mainly in supraglacial habitats is pivotal particularly at the frontier of accelerated glacier retreat. In this study, bacterial diversity and community composition in glacial soil and meltwater runoff at the frontier of Baishui Glacier No.1 were evaluated using high throughput sequencing. Significant variations in the physiochemical parameters formed an ecological gradient between soil and meltwater runoff. Based on the richness and evenness indexes, the bacterial diversity was relatively higher in soil compared with meltwater runoff. Hierarchical clustering and bi-plot ordination revealed that the taxonomic composition of soil samples was highly similar and significantly influenced by the ecological parameters than the meltwater runoff. The overall relative abundance trend of bacterial phyla and genera were greatly varied in soil and water samples. The relative abundance of Proteobacteria was higher in water runoff samples (40.5-87%) compared with soil samples (32-52.7%). Proteobacteria, Firmicutes, and a little part of Cyanobacteria occupied a major portion of water runoff while the soil was dominated by Acidobacteria (6-16.2%), Actinobacteria (5-16%), Bacteroidetes (0.5-8.8%), and Cyanobacteria (0.1-8.3%) besides Proteobacteria and Firmicutes. Higher numbers of biomarkers were found in soil group compared with the water group. The study area is diverse in terms of richness, while community structures are not evenly distributed. This study provides a preliminary understanding of the bacterial diversity and shifts in community structure in soil and meltwater runoff at the frontier of the glacial. The findings revealed that the environmental factors are a significantly strong determinant of bacterial community structures in such a closely linked ecosystem.
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Affiliation(s)
- Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Barkat Ali
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ali Bahadur
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
| | - Prakriti Sharma Ghimire
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Shichang Kang
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
- University of Chinese Academy of Sciences, Beijing, China.
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing, China.
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22
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Metagenomics and Culture Dependent Insights into the Distribution of Firmicutes across Two Different Sample Types Located in the Black Hills Region of South Dakota, USA. Microorganisms 2021; 9:microorganisms9010113. [PMID: 33418927 PMCID: PMC7825136 DOI: 10.3390/microorganisms9010113] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 11/17/2022] Open
Abstract
Firmicutes is almost a ubiquitous phylum. Several genera of this group, for instance, Geobacillus, are recognized for decomposing plant organic matter and for producing thermostable ligninolytic enzymes. Amplicon sequencing was used in this study to determine the prevalence and genetic diversity of the Firmicutes in two distinctly related environmental samples—South Dakota Landfill Compost (SDLC, 60 °C), and Sanford Underground Research Facility sediments (SURF, 45 °C). Although distinct microbial community compositions were observed, there was a dominance of Firmicutes in both the SDLC and SURF samples, followed by Proteobacteria. The abundant classes of bacteria in the SDLC site, within the phylum Firmicutes, were Bacilli (83.2%), and Clostridia (2.9%). In comparison, the sample from the SURF mine was dominated by the Clostridia (45.8%) and then Bacilli (20.1%). Within the class Bacilli, the SDLC sample had more diversity (a total of 11 genera with more than 1% operational taxonomic unit, OTU). On the other hand, SURF samples had just three genera, about 1% of the total population: Bacilli, Paenibacillus, and Solibacillus. With specific regard to Geobacillus, it was found to be present at a level of 0.07% and 2.5% in SURF and SDLC, respectively. Subsequently, culture isolations of endospore-forming Firmicutes members from these samples led to the isolation of a total of 117 isolates. According to colony morphologies, and identification based upon 16S rRNA and gyrB gene sequence analysis, we obtained 58 taxonomically distinct strains. Depending on the similarity indexes, a gyrB sequence comparison appeared more useful than 16S rRNA sequence analysis for inferring intra- and some intergeneric relationships between the isolates.
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23
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Egan M, Dempsey E, Ryan CA, Ross RP, Stanton C. The Sporobiota of the Human Gut. Gut Microbes 2021; 13:1-17. [PMID: 33406976 PMCID: PMC7801112 DOI: 10.1080/19490976.2020.1863134] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 02/04/2023] Open
Abstract
The human gut microbiome is a diverse and complex ecosystem that plays a critical role in health and disease. The composition of the gut microbiome has been well studied across all stages of life. In recent years, studies have investigated the production of endospores by specific members of the gut microbiome. An endospore is a tough, dormant structure formed by members of the Firmicutes phylum, which allows for greater resistance to otherwise inhospitable conditions. This innate resistance has consequences for human health and disease, as well as in biotechnology. In particular, the formation of endospores is strongly linked to antibiotic resistance and the spread of antibiotic resistance genes, also known as the resistome. The term sporobiota has been used to define the spore-forming cohort of a microbial community. In this review, we present an overview of the current knowledge of the sporobiota in the human gut. We discuss the development of the sporobiota in the infant gut and the perinatal factors that may have an effect on vertical transmission from mother to infant. Finally, we examine the sporobiota of critically important food sources for the developing infant, breast milk and powdered infant formula.
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Affiliation(s)
- Muireann Egan
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Eugene Dempsey
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Neonatology, Cork University Maternity Hospital, Cork, Ireland
| | - C. Anthony Ryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Neonatology, Cork University Maternity Hospital, Cork, Ireland
| | - R. Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Catherine Stanton
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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24
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Steuer P, Tejeda C, Martinez O, Ramirez-Reveco A, González N, Grant IR, Foddai ACG, Collins MT, Salgado M. Effectiveness of copper ions against Mycobacterium avium subsp. paratuberculosis and bacterial communities in naturally contaminated raw cow's milk. J Appl Microbiol 2020; 131:146-154. [PMID: 33151641 DOI: 10.1111/jam.14923] [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: 09/28/2020] [Accepted: 11/02/2020] [Indexed: 01/14/2023]
Abstract
AIM The focus of the present study was to evaluate the copper ions treatment on the viability of Mycobacterium avium subsp. paratuberculosis (MAP) and other bacterial communities in cow's milk. METHODS AND RESULTS A copper ions treatment was evaluated in naturally contaminated cow's milk to assay MAP load and/or viability, and relative abundance of other bacterial communities. In addition, physical-chemical analyses of the milk were also performed. All analyses were carried out before and after a copper ions treatment. After copper ions treatment, pH and copper concentration markedly increased in milk; the numbers of viable MAP significantly decreased. The relative abundance of the four target phyla decreased, with the phyla Bacteroidetes and Firmicutes surviving treatment in higher proportions (4 and 2·1% of original populations, respectively). A progressively higher percentage of dead bacterial cells after 5 and 20 min copper ions treatments was found (12 and 35%, respectively). CONCLUSION With the exception of some MAP-tolerant strains, we have once again demonstrated that copper ions have a significant inactivating effect on MAP as well as certain other bacterial communities found in naturally contaminated cow's milk. SIGNIFICANCE AND IMPACT OF THE STUDY This study showed a significant inactivation of both MAP and other bacteria by copper ions in raw cow's milk, information that could be useful as a tool for MAP control.
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Affiliation(s)
- P Steuer
- Instituto de Medicina Preventiva Veterinaria, Valdivia, Chile.,Facultad de Ciencias Veterinarias, Escuela de Graduados, Valdivia, Chile
| | - C Tejeda
- Instituto de Medicina Preventiva Veterinaria, Valdivia, Chile
| | - O Martinez
- Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile
| | | | - N González
- Instituto de Medicina Preventiva Veterinaria, Valdivia, Chile
| | - I R Grant
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - A C G Foddai
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - M T Collins
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - M Salgado
- Instituto de Medicina Preventiva Veterinaria, Valdivia, Chile
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25
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Heuer VB, Inagaki F, Morono Y, Kubo Y, Spivack AJ, Viehweger B, Treude T, Beulig F, Schubotz F, Tonai S, Bowden SA, Cramm M, Henkel S, Hirose T, Homola K, Hoshino T, Ijiri A, Imachi H, Kamiya N, Kaneko M, Lagostina L, Manners H, McClelland HL, Metcalfe K, Okutsu N, Pan D, Raudsepp MJ, Sauvage J, Tsang MY, Wang DT, Whitaker E, Yamamoto Y, Yang K, Maeda L, Adhikari RR, Glombitza C, Hamada Y, Kallmeyer J, Wendt J, Wörmer L, Yamada Y, Kinoshita M, Hinrichs KU. Temperature limits to deep subseafloor life in the Nankai Trough subduction zone. Science 2020; 370:1230-1234. [PMID: 33273103 DOI: 10.1126/science.abd7934] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 10/13/2020] [Indexed: 02/06/2023]
Abstract
Microorganisms in marine subsurface sediments substantially contribute to global biomass. Sediments warmer than 40°C account for roughly half the marine sediment volume, but the processes mediated by microbial populations in these hard-to-access environments are poorly understood. We investigated microbial life in up to 1.2-kilometer-deep and up to 120°C hot sediments in the Nankai Trough subduction zone. Above 45°C, concentrations of vegetative cells drop two orders of magnitude and endospores become more than 6000 times more abundant than vegetative cells. Methane is biologically produced and oxidized until sediments reach 80° to 85°C. In 100° to 120°C sediments, isotopic evidence and increased cell concentrations demonstrate the activity of acetate-degrading hyperthermophiles. Above 45°C, populated zones alternate with zones up to 192 meters thick where microbes were undetectable.
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Affiliation(s)
- Verena B Heuer
- Center for Marine Environmental Sciences (MARUM), University of Bremen, Bremen, Germany
| | - Fumio Inagaki
- Research and Development Center for Ocean Drilling Science, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama, Japan.,Kochi Institute for Core Sample Research, JAMSTEC, Kochi, Japan
| | - Yuki Morono
- Kochi Institute for Core Sample Research, JAMSTEC, Kochi, Japan
| | - Yusuke Kubo
- Center for Deep Earth Exploration (CDEX), JAMSTEC, Yokohama, Japan
| | - Arthur J Spivack
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - Bernhard Viehweger
- Center for Marine Environmental Sciences (MARUM), University of Bremen, Bremen, Germany
| | - Tina Treude
- Department of Earth, Planetary, and Space Sciences, Department of Atmospheric and Oceanic Sciences, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Felix Beulig
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Florence Schubotz
- Center for Marine Environmental Sciences (MARUM), University of Bremen, Bremen, Germany
| | - Satoshi Tonai
- Faculty of Science and Technology, Kochi University, Kochi, Japan
| | - Stephen A Bowden
- Department of Geology and Petroleum Geology, School of Geosciences, University of Aberdeen, Aberdeen, UK
| | - Margaret Cramm
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Susann Henkel
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Takehiro Hirose
- Kochi Institute for Core Sample Research, JAMSTEC, Kochi, Japan
| | - Kira Homola
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | | | - Akira Ijiri
- Kochi Institute for Core Sample Research, JAMSTEC, Kochi, Japan
| | - Hiroyuki Imachi
- Institute for Extra-cutting-edge Science and Technology Avantgarde Research, JAMSTEC, Yokosuka, Japan
| | - Nana Kamiya
- Graduate School of Integrated Basic Sciences, Nihon University, Tokyo, Japan
| | - Masanori Kaneko
- Geomicrobiology Research Group, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Lorenzo Lagostina
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Hayley Manners
- School of Geography, Earth and Environmental Sciences, Faculty of Science and Engineering, Plymouth University, Plymouth, UK
| | - Harry-Luke McClelland
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, USA
| | - Kyle Metcalfe
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Natsumi Okutsu
- Atmosphere and Ocean Research Institute, University of Tokyo, Tokyo, Japan
| | - Donald Pan
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka, Japan
| | - Maija J Raudsepp
- School of Earth Sciences, University of Queensland, St. Lucia, QLD, Australia
| | - Justine Sauvage
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - Man-Yin Tsang
- Department of Earth Sciences, University of Toronto, Toronto, ON, Canada
| | - David T Wang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emily Whitaker
- Department of Oceanography, Texas A&M University, College Station, TX, USA
| | - Yuzuru Yamamoto
- Department of Mathematical Science and Advanced Technology, JAMSTEC, Yokosuka, Japan
| | - Kiho Yang
- Department of Earth System Sciences, Yonsei University, Seoul, Republic of Korea
| | - Lena Maeda
- Center for Deep Earth Exploration (CDEX), JAMSTEC, Yokohama, Japan
| | - Rishi R Adhikari
- Center for Marine Environmental Sciences (MARUM), University of Bremen, Bremen, Germany
| | - Clemens Glombitza
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland
| | - Yohei Hamada
- Kochi Institute for Core Sample Research, JAMSTEC, Kochi, Japan
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Potsdam, Germany
| | - Jenny Wendt
- Center for Marine Environmental Sciences (MARUM), University of Bremen, Bremen, Germany
| | - Lars Wörmer
- Center for Marine Environmental Sciences (MARUM), University of Bremen, Bremen, Germany
| | - Yasuhiro Yamada
- Research and Development Center for Ocean Drilling Science, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama, Japan
| | | | - Kai-Uwe Hinrichs
- Center for Marine Environmental Sciences (MARUM), University of Bremen, Bremen, Germany.
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26
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Kazemian N, Ramezankhani M, Sehgal A, Khalid FM, Kalkhoran AHZ, Narayan A, Wong GKS, Kao D, Pakpour S. The trans-kingdom battle between donor and recipient gut microbiome influences fecal microbiota transplantation outcome. Sci Rep 2020; 10:18349. [PMID: 33110112 PMCID: PMC7591866 DOI: 10.1038/s41598-020-75162-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/12/2020] [Indexed: 01/29/2023] Open
Abstract
Fundamental restoration ecology and community ecology theories can help us better understand the underlying mechanisms of fecal microbiota transplantation (FMT) and to better design future microbial therapeutics for recurrent Clostridioides difficile infections (rCDI) and other dysbiosis-related conditions. In this study, stool samples were collected from donors and rCDI patients one week prior to FMT (pre-FMT), as well as from patients one week following FMT (post-FMT). Using metagenomic sequencing and machine learning, our results suggested that FMT outcome is not only dependent on the ecological structure of the recipients, but also the interactions between the donor and recipient microbiomes at the taxonomical and functional levels. We observed that the presence of specific bacteria in donors (Clostridioides spp., Desulfovibrio spp., Odoribacter spp. and Oscillibacter spp.) and the absence of fungi (Yarrowia spp.) and bacteria (Wigglesworthia spp.) in recipients prior to FMT could predict FMT success. Our results also suggested a series of interlocked mechanisms for FMT success, including the repair of the disturbed gut ecosystem by transient colonization of nexus species followed by secondary succession of bile acid metabolizers, sporulators, and short chain fatty acid producers.
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Affiliation(s)
- Negin Kazemian
- School of Engineering, University of British Columbia, Kelowna, BC, Canada
| | - Milad Ramezankhani
- School of Engineering, University of British Columbia, Kelowna, BC, Canada
| | - Aarushi Sehgal
- Department of Computer Science and Engineering, National Institute of Technology, Hamirpur, Himachal Pradesh, India
| | | | | | - Apurva Narayan
- Department of Computer Science, University of British Columbia, Kelowna, BC, Canada
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.,Department of Medicine, University of Alberta, Edmonton, AB, Canada.,BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | - Dina Kao
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, AB, Canada.
| | - Sepideh Pakpour
- School of Engineering, University of British Columbia, Kelowna, BC, Canada.
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27
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Gionfriddo CM, Wymore AM, Jones DS, Wilpiszeski RL, Lynes MM, Christensen GA, Soren A, Gilmour CC, Podar M, Elias DA. An Improved hgcAB Primer Set and Direct High-Throughput Sequencing Expand Hg-Methylator Diversity in Nature. Front Microbiol 2020; 11:541554. [PMID: 33123100 PMCID: PMC7573106 DOI: 10.3389/fmicb.2020.541554] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 08/25/2020] [Indexed: 01/27/2023] Open
Abstract
The gene pair hgcAB is essential for microbial mercury methylation. Our understanding of its abundance and diversity in nature is rapidly evolving. In this study we developed a new broad-range primer set for hgcAB, plus an expanded hgcAB reference library, and used these to characterize Hg-methylating communities from diverse environments. We applied this new Hg-methylator database to assign taxonomy to hgcA sequences from clone, amplicon, and metagenomic datasets. We evaluated potential biases introduced in primer design, sequence length, and classification, and suggest best practices for studying Hg-methylator diversity. Our study confirms the emerging picture of an expanded diversity of HgcAB-encoding microbes in many types of ecosystems, with abundant putative mercury methylators Nitrospirae and Chloroflexi in several new environments including salt marsh and peat soils. Other common microbes encoding HgcAB included Phycisphaerae, Aminicenantes, Spirochaetes, and Elusimicrobia. Combined with high-throughput amplicon specific sequencing, the new primer set also indentified novel hgcAB sequences similar to Lentisphaerae, Bacteroidetes, Atribacteria, and candidate phyla WOR-3 and KSB1 bacteria. Gene abundance data also corroborate the important role of two "classic" groups of methylators (Deltaproteobacteria and Methanomicrobia) in many environments, but generally show a scarcity of hgcAB+ Firmicutes. The new primer set was developed to specifically target hgcAB sequences found in nature, reducing degeneracy and providing increased sensitivity while maintaining broad diversity capture. We evaluated mock communities to confirm primer improvements, including culture spikes to environmental samples with variable DNA extraction and PCR amplification efficiencies. For select sites, this new workflow was combined with direct high-throughput hgcAB sequencing. The hgcAB diversity generated by direct amplicon sequencing confirmed the potential for novel Hg-methylators previously identified using metagenomic screens. A new phylogenetic analysis using sequences from freshwater, saline, and terrestrial environments showed Deltaproteobacteria HgcA sequences generally clustered among themselves, while metagenome-resolved HgcA sequences in other phyla tended to cluster by environment, suggesting horizontal gene transfer into many clades. HgcA from marine metagenomes often formed distinct subtrees from those sequenced from freshwater ecosystems. Overall the majority of HgcA sequences branch from a cluster of HgcAB fused proteins related to Thermococci, Atribacteria (candidate division OP9), Aminicenantes (OP8), and Chloroflexi. The improved primer set and library, combined with direct amplicon sequencing, provide a significantly improved assessment of the abundance and diversity of hgcAB+ microbes in nature.
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Affiliation(s)
- Caitlin M Gionfriddo
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Ann M Wymore
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Daniel S Jones
- BioTechnology Institute, University of Minnesota, St. Paul, MN, United States.,Department of Earth Sciences, Minneapolis, MN, United States
| | - Regina L Wilpiszeski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Mackenzie M Lynes
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Geoff A Christensen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Ally Soren
- Smithsonian Environmental Research Center, Edgewater, MD, United States
| | | | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Dwayne A Elias
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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28
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Mitiku AA, Andeta AF, Borremans A, Lievens B, Bossaert S, Crauwels S, Aernouts B, Kechero Y, Van Campenhout L. Silage making of maize stover and banana pseudostem under South Ethiopian conditions: evolution of pH, dry matter and microbiological profile. Microb Biotechnol 2020; 13:1477-1488. [PMID: 32705812 PMCID: PMC7415364 DOI: 10.1111/1751-7915.13626] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 05/24/2020] [Accepted: 06/24/2020] [Indexed: 11/29/2022] Open
Abstract
The study was conducted to evaluate the microbial dynamics during silage of maize stover and banana pseudostem in the environmental conditions of southern Ethiopia. To meet this objective, microsilos containing either maize stover or banana pseudostem, both with and without molasses, were prepared. Subsequently, samples were analysed on day 0, 7, 14, 30, 60 and 90 of the fermentation process. As a result, on day 7, all treatments except banana pseudostem without molasses showed a significant reduction in pH. It was also this silage type that supported the growth of Enterobacteriaceae longer than three other silage types, i.e. until 30 days. The yeasts and moulds and the Clostridum endospore counts also showed a reducing trend in early fermentation and afterwards remained constant until day 90. Illumina MiSeq sequencing revealed that Leuconostoc, Buttiauxella species and Enterobacteriaceae were the most abundant bacteria in the initial phases of the fermentation. Later on, Buttiauxella, Lactobacillus, Weissella and Bifidobacterium species were found to be dominant. In conclusion, silage of the two crop by-products is possible under South Ethiopian conditions. For banana pseudostem, the addition of molasses is crucial for a fast fermentation, in contrast to maize. Upscaling needs to be investigated for the two by-products.
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Affiliation(s)
- Ashenafi Azage Mitiku
- Department of Microbial and Molecular SystemsLab4FoodKU LeuvenGeel CampusGeelBelgium
- Leuven Food Science and Nutrition Research Centre (LFoRCe)KU LeuvenLeuvenBelgium
- Department of Animal SciencesCollege of Agricultural SciencesArba Minch UniversityArba MinchEthiopia
| | - Addisu Fekadu Andeta
- Department of BiologyCollege of Natural SciencesArba Minch UniversityArba MinchEthiopia
| | - An Borremans
- Department of Microbial and Molecular SystemsLab4FoodKU LeuvenGeel CampusGeelBelgium
- Leuven Food Science and Nutrition Research Centre (LFoRCe)KU LeuvenLeuvenBelgium
| | - Bart Lievens
- Leuven Food Science and Nutrition Research Centre (LFoRCe)KU LeuvenLeuvenBelgium
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME and BIM)Department of Microbial and Molecular SystemsKU LeuvenDe Nayer CampusSint‐Katelijne WaverBelgium
| | - Sofie Bossaert
- Leuven Food Science and Nutrition Research Centre (LFoRCe)KU LeuvenLeuvenBelgium
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME and BIM)Department of Microbial and Molecular SystemsKU LeuvenDe Nayer CampusSint‐Katelijne WaverBelgium
| | - Sam Crauwels
- Leuven Food Science and Nutrition Research Centre (LFoRCe)KU LeuvenLeuvenBelgium
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME and BIM)Department of Microbial and Molecular SystemsKU LeuvenDe Nayer CampusSint‐Katelijne WaverBelgium
| | - Ben Aernouts
- Department of BiosystemsLivestock TechnologyKU LeuvenGeel CampusGeelBelgium
| | - Yisehak Kechero
- Department of Animal SciencesCollege of Agricultural SciencesArba Minch UniversityArba MinchEthiopia
| | - Leen Van Campenhout
- Department of Microbial and Molecular SystemsLab4FoodKU LeuvenGeel CampusGeelBelgium
- Leuven Food Science and Nutrition Research Centre (LFoRCe)KU LeuvenLeuvenBelgium
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29
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Neukamm J, Pfrengle S, Molak M, Seitz A, Francken M, Eppenberger P, Avanzi C, Reiter E, Urban C, Welte B, Stockhammer PW, Teßmann B, Herbig A, Harvati K, Nieselt K, Krause J, Schuenemann VJ. 2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals. BMC Biol 2020; 18:108. [PMID: 32859198 PMCID: PMC7456089 DOI: 10.1186/s12915-020-00839-8] [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] [Received: 06/05/2020] [Accepted: 07/29/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Recent advances in sequencing have facilitated large-scale analyses of the metagenomic composition of different samples, including the environmental microbiome of air, water, and soil, as well as the microbiome of living humans and other animals. Analyses of the microbiome of ancient human samples may provide insights into human health and disease, as well as pathogen evolution, but the field is still in its very early stages and considered highly challenging. RESULTS The metagenomic and pathogen content of Egyptian mummified individuals from different time periods was investigated via genetic analysis of the microbial composition of various tissues. The analysis of the dental calculus' microbiome identified Red Complex bacteria, which are correlated with periodontal diseases. From bone and soft tissue, genomes of two ancient pathogens, a 2200-year-old Mycobacterium leprae strain and a 2000-year-old human hepatitis B virus, were successfully reconstructed. CONCLUSIONS The results show the reliability of metagenomic studies on Egyptian mummified individuals and the potential to use them as a source for the extraction of ancient pathogen DNA.
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Affiliation(s)
- Judith Neukamm
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Saskia Pfrengle
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Martyna Molak
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warsaw, Poland.,Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097, Warsaw, Poland
| | - Alexander Seitz
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Michael Francken
- Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.,Paleoanthropology, Dept. of Geosciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Partick Eppenberger
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Charlotte Avanzi
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, USA
| | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Christian Urban
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Beatrix Welte
- Institute of Pre- and Protohistory and Medieval Archaeology, Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Philipp W Stockhammer
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University Munich, 80799, Munich, Germany.,Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | - Barbara Teßmann
- Berlin Society of Anthropology, Ethnology and Prehistory, 10117, Berlin, Germany.,Museum of Prehistory and Early History, SMPK Berlin, 10117, Berlin, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | - Katerina Harvati
- Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.,Paleoanthropology, Dept. of Geosciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.,DFG Centre for Advanced Studies Words, Bones, Genes, Tools: Tracking Linguistic, Cultural and Biological Trajectories of the Human Past, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Kay Nieselt
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. .,Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. .,Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany.
| | - Verena J Schuenemann
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. .,Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. .,Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.
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30
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Ben Maamar S, Hu J, Hartmann EM. Implications of indoor microbial ecology and evolution on antibiotic resistance. JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY 2020; 30:1-15. [PMID: 31591493 PMCID: PMC8075925 DOI: 10.1038/s41370-019-0171-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 07/17/2019] [Accepted: 08/18/2019] [Indexed: 05/19/2023]
Abstract
The indoor environment is an important source of microbial exposures for its human occupants. While we naturally want to favor positive health outcomes, built environment design and operation may counter-intuitively favor negative health outcomes, particularly with regard to antibiotic resistance. Indoor environments contain microbes from both human and non-human origins, providing a unique venue for microbial interactions, including horizontal gene transfer. Furthermore, stressors present in the built environment could favor the exchange of genetic material in general and the retention of antibiotic resistance genes in particular. Intrinsic and acquired antibiotic resistance both pose a potential threat to human health; these phenomena need to be considered and controlled separately. The presence of both environmental and human-associated microbes, along with their associated antibiotic resistance genes, in the face of stressors, including antimicrobial chemicals, creates a unique opportunity for the undesirable spread of antibiotic resistance. In this review, we summarize studies and findings related to various interactions between human-associated bacteria, environmental bacteria, and built environment conditions, and particularly their relation to antibiotic resistance, aiming to guide "healthy" building design.
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Affiliation(s)
- Sarah Ben Maamar
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Jinglin Hu
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Erica M Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA.
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31
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Nutrient germination improves DNA recovery from industrial Bacillus subtilis endospores during qPCR enumeration assays. Heliyon 2019; 5:e02917. [PMID: 31872115 PMCID: PMC6911885 DOI: 10.1016/j.heliyon.2019.e02917] [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: 10/08/2019] [Revised: 11/05/2019] [Accepted: 11/22/2019] [Indexed: 11/24/2022] Open
Abstract
Growth-independent microbial enumeration methods such as quantitative PCR require the efficient extraction of genomic DNA from targeted cells. Bacillus endospores are popular inclusions in commercial products due to their hardiness and metabolic dormancy; however, this hardiness is known to render Bacillus endospores resistant to traditional DNA isolation techniques. Metagenomic studies have sought to address this resistance through nutrient-based germination of bacterial endospores in environmental samples. In the present study, we sought to apply this technique to the enumeration of microbial products using an industrial strain of Bacillus subtilis as a model organism. Germination was induced through incubation of axenic spore suspensions in an AGFK-based rich medium. Total spore count, dipicolinic acid release and OD600 absorbance were monitored over time to track the progression of spore populations through the stages of germination and outgrowth. Aerobic plate counts and flow cytometry were used to monitor cell populations for proliferation during the incubation period. Finally, quantitative PCR with taxon-specific primers was used to examine DNA recovery as a function of time. Results show that customized germination protocols, once appropriately validated for the species and product matrix under consideration, can result in more efficient DNA extraction and thus lower limits of detection for qPCR assays targeting industrial Bacillus endospores in microbial products.
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32
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Shifts in microbial community composition in tannery-contaminated soil in response to increased gamma radiation. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01541-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Abstract
Purpose
Contaminated sites from man-made activities such as old-fashioned tanneries are inhabited by virulent microorganisms that exhibit more resistance against extreme and toxic environmental conditions. We investigated the effect of different Gamma radiation doses on microbial community composition in the sediment of an old-fashioned tannery.
Methods
Seven samples collected from the contaminated sites received different gamma radiation doses (I = 0.0, II = 5, III = 10, VI = 15, V = 20, VI = 25, and VII = 30 kGy) as an acute exposure. The shift in microbial community structure was assessed using the high throughput 454 pyrosequencing. Variations in diversity, richness, and the shift in operational taxonomic units (OTUs) were investigated using statistical analysis.
Result
Our results showed that the control sample (I) had the highest diversity, richness, and OTUs when compared with the irradiated samples. Species of Halocella, Parasporobacterium, and Anaerosporobacter had the highest relative abundance at the highest radiation dose of 30 kGy. Members of the Firmicutes also increased by 20% at the highest radiation dose when compared with the control sample (0.0 kGy). Representatives of Synergistetes decreased by 25% while Bacteroidetes retained a steady distribution across the range of gamma radiation intensities.
Conclusion
This study provides information about potential “radioresistant” and/or “radiotolerant” microbial species that are adapted to elevated level of chemical toxicity such as Cr and Sr in tannery. These species can be of a high biotechnological and environmental importance.
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33
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Tremblay J, Yergeau E. Systematic processing of ribosomal RNA gene amplicon sequencing data. Gigascience 2019; 8:giz146. [PMID: 31816087 PMCID: PMC6901069 DOI: 10.1093/gigascience/giz146] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/07/2019] [Accepted: 11/14/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND With the advent of high-throughput sequencing, microbiology is becoming increasingly data-intensive. Because of its low cost, robust databases, and established bioinformatic workflows, sequencing of 16S/18S/ITS ribosomal RNA (rRNA) gene amplicons, which provides a marker of choice for phylogenetic studies, has become ubiquitous. Many established end-to-end bioinformatic pipelines are available to perform short amplicon sequence data analysis. These pipelines suit a general audience, but few options exist for more specialized users who are experienced in code scripting, Linux-based systems, and high-performance computing (HPC) environments. For such an audience, existing pipelines can be limiting to fully leverage modern HPC capabilities and perform tweaking and optimization operations. Moreover, a wealth of stand-alone software packages that perform specific targeted bioinformatic tasks are increasingly accessible, and finding a way to easily integrate these applications in a pipeline is critical to the evolution of bioinformatic methodologies. RESULTS Here we describe AmpliconTagger, a short rRNA marker gene amplicon pipeline coded in a Python framework that enables fine tuning and integration of virtually any potential rRNA gene amplicon bioinformatic procedure. It is designed to work within an HPC environment, supporting a complex network of job dependencies with a smart-restart mechanism in case of job failure or parameter modifications. As proof of concept, we present end results obtained with AmpliconTagger using 16S, 18S, ITS rRNA short gene amplicons and Pacific Biosciences long-read amplicon data types as input. CONCLUSIONS Using a selection of published algorithms for generating operational taxonomic units and amplicon sequence variants and for computing downstream taxonomic summaries and diversity metrics, we demonstrate the performance and versatility of our pipeline for systematic analyses of amplicon sequence data.
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Affiliation(s)
- Julien Tremblay
- Energy Mining and Environment, National Research Council Canada, Montreal, QC H4P-2R2, Canada
| | - Etienne Yergeau
- Centre INRS-Institut Armand-Frappier, Institut national de la recherche scientifique, 531ad Boul. des Prairies, Laval, QC H7V-1B7, Canada
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34
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Seasonal Health Risks Due to Zoonotic Pathogens from Hand-dug Well Water in Ohangwena and Omusati Regions of Namibia. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.3.31] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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35
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Gołębiewski M, Tretyn A. Generating amplicon reads for microbial community assessment with next‐generation sequencing. J Appl Microbiol 2019; 128:330-354. [DOI: 10.1111/jam.14380] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 07/03/2019] [Accepted: 07/05/2019] [Indexed: 12/12/2022]
Affiliation(s)
- M. Gołębiewski
- Plant Physiology and Biotechnology Nicolaus Copernicus University Toruń Poland
- Centre for Modern Interdisciplinary Technologies Nicolaus Copernicus University Toruń Poland
| | - A. Tretyn
- Plant Physiology and Biotechnology Nicolaus Copernicus University Toruń Poland
- Centre for Modern Interdisciplinary Technologies Nicolaus Copernicus University Toruń Poland
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36
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Metagenomics Reveals Seasonality of Human Pathogenic Bacteria from Hand-Dug Well Water in the Cuvelai Etosha Basin of Namibia. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.2.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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37
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Vasconcelos EAF, Santaella ST, Viana MB, Dos Santos AB, Pinheiro GC, Leitão RC. Composition and ecology of bacterial and archaeal communities in anaerobic reactor fed with residual glycerol. Anaerobe 2019; 59:145-153. [PMID: 31254652 DOI: 10.1016/j.anaerobe.2019.06.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 05/31/2019] [Accepted: 06/26/2019] [Indexed: 11/28/2022]
Abstract
Glycerol, the main residue of biodiesel production, can be used to produce organic acids and energy through anaerobic digestion. This study aimed to assess microbial structure, diversity, productivity, and stability and the influence of these parameters on the performance of an anaerobic reactor. The experimental setup consisted of an upflow anaerobic sludge blanket (UASB) reactor fed residual glycerol and nutrients. The organic loading rate (OLR) was gradually increased through five stages, and sludge samples were collected at each, followed by DNA extraction and PCR denaturing gradient gel electrophoresis (PCR-DGGE). The resulting bands were excised, amplified, and purified. The results showed increased bacterial diversity and richness from the inoculum (Rr 38.72 and H 2.32) and along stages I and II, reaching the highest populational parameters (Rr 194.06 and H 3.32). The following stages promote decreases in richness and diversity, achieving the lowest populational parameters on this study (Rr 11.53 and H 2.04). Biogas production increased along with functional organization due to the specialization of the bacterial community and a decrease in the methanogenic population, both promoted by the increase in OLR.
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Affiliation(s)
- E A F Vasconcelos
- Ecology and Natural Resources, Department of Biology, Federal University of Ceará, Campus Pici, Block 902, 60455-970, Fortaleza, CE, Brazil
| | - S T Santaella
- Institute of Marine Science, Federal University of Ceará, Av Abolição, 3207, 60165-081, Fortaleza, CE, Brazil
| | - M B Viana
- Institute of Marine Science, Federal University of Ceará, Av Abolição, 3207, 60165-081, Fortaleza, CE, Brazil
| | - A B Dos Santos
- Department of Hydraulics and Environmental Engineering, Federal University of Ceará, Campus Pici, Block 713, 60.451-970, Fortaleza, CE, Brazil
| | - G C Pinheiro
- Department of Technology and Environmental Management, Federal Institute of Education, Science and Technology of Ceará, Campus Maracanaú, Avenida Parque Central, Distrito Industrial I, Maracanaú, 61939-140, Brazil
| | - R C Leitão
- Embrapa Agroindústria Tropical, Rua Dra, Sara Mesquita, 2270, 60511-110, Fortaleza, CE, Brazil.
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38
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Andeta A, Vandeweyer D, Teffera E, Woldesenbet F, Verreth C, Crauwels S, Lievens B, Vancampenhout K, Van Campenhout L. Traditional starter cultures for enset fermentation: Unravelling their production and microbial composition. FOOD BIOSCI 2019. [DOI: 10.1016/j.fbio.2019.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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39
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Cupit C, Lomstein BA, Kjeldsen KU. Contrasting community composition of endospores and vegetative Firmicutes in a marine sediment suggests both endogenous and exogenous sources of endospore accumulation. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:352-360. [PMID: 30043505 DOI: 10.1111/1758-2229.12679] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 07/09/2018] [Accepted: 07/12/2018] [Indexed: 06/08/2023]
Abstract
Bacterial endospores are highly abundant in marine sediments, but their taxonomic identity and ecology is largely unknown. We selectively extracted DNA from endospores and vegetative cells and sequenced 16S rRNA genes to characterize the composition of the endospore and vegetative Firmicutes communities in the sediment and water column of Aarhus Bay (Denmark). The endospore community in the sediment was dominated by the families Bacillaceae, Lachnospiraceae, Clostridiaceae and Ruminoccocaceae. These families were also represented in the vegetative community in the sediment and the endospore community in the water column. OTUs of high relative abundance in the endospore community were also represented in the vegetative Firmicutes community. Other OTUs were exclusively found in the endospore communities. This suggests that endospores accumulate in marine sediments due to passive deposition from the water column and sporulation of vegetative cells in the sediment. Some OTUs were detected in the endospore community of the water column and the vegetative community the sediment indicating that endospores deposited from the water column may germinate upon burial/deposition in the sediment. We provide novel insight into the composition of endospore communities in marine sediments and highlight their role in microbial dispersal and as a seed bank in subsurface sediments.
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Affiliation(s)
- Carina Cupit
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Bente Aagaard Lomstein
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kasper Urup Kjeldsen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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40
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Phylogenetic diversity of aerobic spore-forming Bacillalles isolated from Brazilian soils. Int Microbiol 2019; 22:511-520. [PMID: 31049768 DOI: 10.1007/s10123-019-00080-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 03/20/2019] [Accepted: 04/15/2019] [Indexed: 10/26/2022]
Abstract
The phylum Firmicutes comprises seven classes where most species are either aerobic or anaerobic endospore former. Inside Firmicutes, species allocated in the genus Bacillus and related genera are collectively named aerobic endospore-forming bacteria (AEFB), and the soil is their major reservoir. AEFB have great importance in health, agriculture, and biotechnology although the more studied species are Bacillus subtilis and the human pathogens Bacillus cereus and Bacillus anthracis. AEFB have great importance in health, agriculture, and biotechnology; although the knowledge about these organisms is based on few species, notably, Bacillus subtilis, Bacillus cereus, and Bacillus anthracis. In this work, we generated partial 16S rRNA gene sequences of both strands of 192 AEFB strains isolated from soils of Distrito Federal, Brazil (SDF strains). The resulting consensus sequences were used to obtain taxonomic assignment and establish the phylogenetic relationships among these strains. Through this approach, we could observe that classified SDF strains were distributed among genera Bacillus (169 strains; 88.02%), Paenibacillus (11; 5.73%), Lysinibacillus (6; 3.13%), Brevibacillus (4; 2.08%), Terribacillus (1; 0.52%), and Rummeliibacillus (1; 0.52%). Phylogenetic trees revealed these 192 SDF strains can be segregated into eight groups spanning families Bacillaceae and Paenibacillaceae belonging to the order Bacillales. To expand the knowledge about the diversity of these SDF strains, further studies regarding characterization with different methodologies are underway.
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Wynants E, Frooninckx L, Crauwels S, Verreth C, De Smet J, Sandrock C, Wohlfahrt J, Van Schelt J, Depraetere S, Lievens B, Van Miert S, Claes J, Van Campenhout L. Assessing the Microbiota of Black Soldier Fly Larvae (Hermetia illucens) Reared on Organic Waste Streams on Four Different Locations at Laboratory and Large Scale. MICROBIAL ECOLOGY 2019; 77:913-930. [PMID: 30430196 DOI: 10.1007/s00248-018-1286-x] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/02/2018] [Indexed: 06/09/2023]
Abstract
This study aimed to gain insight into the microbial quality, safety and bacterial community composition of black soldier fly larvae (Hermetia illucens) reared at different facilities on a variety of organic waste streams. For seven rearing cycles, both on laboratory-scale and in large-scale facilities at several locations, the microbiota of the larvae was studied. Also samples of the substrate used and the residue (= leftover substrate after rearing, existing of non-consumed substrate, exuviae and faeces) were investigated. Depending on the sample, it was subjected to plate counting, Illumina Miseq sequencing and/or detection of specific food pathogens. The results revealed that the substrates applied at the various locations differed substantially in microbial numbers as well as in the bacterial community composition. Furthermore, little similarity was observed between the microbiota of the substrate and that of the larvae reared on that substrate. Despite substantial differences between the microbiota of larvae reared at several locations, 48 species-level operational taxonomic units (OTUs) were shared by all larvae, among which most belonged to the phyla Firmicutes and Proteobacteria. Although the substrate is assumed to be an important source of bacteria, our results suggest that a variety of supposedly interacting factors-both abiotic and biotic-are likely to affect the microbiota in the larvae. In some larvae and/or residue samples, potential foodborne pathogens such as Salmonella and Bacillus cereus were detected, emphasising that decontamination technologies are required when the larvae are used in feed, just as for other feed ingredients, or eventually in food.
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Affiliation(s)
- E Wynants
- Department of Microbial and Molecular Systems (M2S), Lab4Food, KU Leuven, Campus Geel, Kleinhoefstraat 4, 2440, Geel, Belgium.
| | - L Frooninckx
- Thomas More University of Applied Sciences, RADIUS, Campus Geel, 2440, Geel, Belgium
| | - S Crauwels
- Department of Microbial and Molecular Systems (M2S), Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), KU Leuven, Campus De Nayer, 2860, Sint-Katelijne-Waver, Belgium
| | - C Verreth
- Department of Microbial and Molecular Systems (M2S), Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), KU Leuven, Campus De Nayer, 2860, Sint-Katelijne-Waver, Belgium
| | - J De Smet
- Department of Microbial and Molecular Systems (M2S), Lab4Food, KU Leuven, Campus Geel, Kleinhoefstraat 4, 2440, Geel, Belgium
| | - C Sandrock
- Research Institute of Organic Agriculture (FiBL), 5070, Frick, Switzerland
| | - J Wohlfahrt
- Research Institute of Organic Agriculture (FiBL), 5070, Frick, Switzerland
| | - J Van Schelt
- Koppert Biological Systems, Berkel en Rodenrijs, 2650, AD, The Netherlands
| | | | - B Lievens
- Department of Microbial and Molecular Systems (M2S), Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), KU Leuven, Campus De Nayer, 2860, Sint-Katelijne-Waver, Belgium
| | - S Van Miert
- Thomas More University of Applied Sciences, RADIUS, Campus Geel, 2440, Geel, Belgium
| | - J Claes
- Department of Microbial and Molecular Systems (M2S), Lab4Food, KU Leuven, Campus Geel, Kleinhoefstraat 4, 2440, Geel, Belgium
| | - L Van Campenhout
- Department of Microbial and Molecular Systems (M2S), Lab4Food, KU Leuven, Campus Geel, Kleinhoefstraat 4, 2440, Geel, Belgium
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Luláková P, Perez-Mon C, Šantrůčková H, Ruethi J, Frey B. High-Alpine Permafrost and Active-Layer Soil Microbiomes Differ in Their Response to Elevated Temperatures. Front Microbiol 2019; 10:668. [PMID: 31001236 PMCID: PMC6456652 DOI: 10.3389/fmicb.2019.00668] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 03/18/2019] [Indexed: 02/01/2023] Open
Abstract
The response of microbial communities to the predicted rising temperatures in alpine regions might be an important part of the ability of these ecosystems to deal with climate change. Soil microbial communities might be significantly affected by elevated temperatures, which influence the functioning of soils within high-alpine ecosystems. To evaluate the potential of the permafrost microbiome to adapt to short-term moderate and extreme warming, we set up an incubation experiment with permafrost and active soil layers from northern and southern slopes of a high-alpine mountain ridge on Muot da Barba Peider in the Swiss Alps. Soils were acclimated to increasing temperatures (4–40°C) for 26 days before being exposed to a heat shock treatment of 40°C for 4 days. Alpha-diversity in all soils increased slightly under gradual warming, from 4 to 25°C, but then dropped considerably at 40°C. Similarly, heat shock induced strong changes in microbial community structures and functioning in the active layer of soils from both northern and southern slope aspects. In contrast, permafrost soils showed only minor changes in their microbial community structures and no changes in their functioning, except regarding specific respiration activity. Shifts in microbial community structures with increasing temperature were significantly more pronounced for bacteria than for fungi, regardless of the soil origin, suggesting higher resistance of high-alpine fungi to short-term warming. Firmicutes, mainly represented by Tumebacillus and Alicyclobacillaceae OTUs, increased strongly at 40°C in active layer soils, reaching almost 50% of the total abundance. In contrast, Saccharibacteria decreased significantly with increasing temperature across all soil samples. Overall, our study highlights the divergent responses of fungal and bacterial communities to increased temperature. Fungi were highly resistant to increased temperatures compared to bacteria, and permafrost communities showed surprisingly low response to rising temperature. The unique responses were related to both site aspect and soil origin indicating that distinct differences within high-alpine soils may be driven by substrate limitation and legacy effects of soil temperatures at the field site.
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Affiliation(s)
- Petra Luláková
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland.,Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Carla Perez-Mon
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Hana Šantrůčková
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Joel Ruethi
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
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Wörmer L, Hoshino T, Bowles MW, Viehweger B, Adhikari RR, Xiao N, Uramoto GI, Könneke M, Lazar CS, Morono Y, Inagaki F, Hinrichs KU. Microbial dormancy in the marine subsurface: Global endospore abundance and response to burial. SCIENCE ADVANCES 2019; 5:eaav1024. [PMID: 30801015 PMCID: PMC6382399 DOI: 10.1126/sciadv.aav1024] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 01/11/2019] [Indexed: 05/19/2023]
Abstract
Marine sediments host an unexpectedly large microbial biosphere, suggesting unique microbial mechanisms for surviving burial and slow metabolic turnover. Although dormancy is generally considered an important survival strategy, its specific role in subsurface sediments remains unclear. We quantified dormant bacterial endospores in 331 marine sediment samples from diverse depositional types and geographical origins. The abundance of endospores relative to vegetative cells increased with burial depth and endospores became dominant below 25 m, with an estimated population of 2.5 × 1028 to 1.9 × 1029 endospores in the uppermost kilometer of sediment and a corresponding biomass carbon of 4.6 to 35 Pg surpassing that of vegetative cells. Our data further identify distinct endospore subgroups with divergent resistance to burial and aging. Endospores may shape the deep biosphere by providing a core population for colonization of new habitats and/or through low-frequency germination to sustain slow growth in this environment.
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Affiliation(s)
- Lars Wörmer
- MARUM—Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, 28359 Bremen, Germany
- Corresponding author.
| | - Tatsuhiko Hoshino
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
| | | | - Bernhard Viehweger
- MARUM—Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, 28359 Bremen, Germany
| | - Rishi R. Adhikari
- MARUM—Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, 28359 Bremen, Germany
| | - Nan Xiao
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
| | - Go-ichiro Uramoto
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
- Center for Advanced Marine Core Research, Kochi University, Kochi 783-8502, Japan
| | - Martin Könneke
- MARUM—Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, 28359 Bremen, Germany
| | - Cassandre S. Lazar
- MARUM—Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, 28359 Bremen, Germany
- Department of Biological Sciences, Université du Québec à Montréal (UQAM), Montreal, Quebec H3C 3P8, Canada
| | - Yuki Morono
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
| | - Fumio Inagaki
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
- Research and Development Center for Ocean Drilling Science, JAMSTEC, Yokohama 236-0001, Japan
| | - Kai-Uwe Hinrichs
- MARUM—Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, 28359 Bremen, Germany
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Andeta AF, Vandeweyer D, Teffera EF, Woldesenbet F, Verreth C, Crauwels S, Lievens B, Vancampenhout K, Van Campenhout L. Effect of fermentation system on the physicochemical and microbial community dynamics during enset (Ensete ventricosum) fermentation. J Appl Microbiol 2019; 126:842-853. [PMID: 30520189 DOI: 10.1111/jam.14173] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/26/2018] [Accepted: 12/02/2018] [Indexed: 01/06/2023]
Abstract
AIMS The present study was conducted to assess the effect of three different fermentation systems on fermentation of enset into kocho. METHODS AND RESULTS Nine enset plants were processed, mixed and fermented in either a pit, a bamboo basket or a sauerkraut jar. Samples were taken on days 1, 7, 15, 31, 60 and 90. Moisture content and pH generally decreased and titratable acidity increased during fermentation. Total viable aerobic counts were generally high for all samples and Enterobacteriaceae counts were reduced to below the detectable level after day 1 for the pits and jars and after day 7 for the baskets. Illumina MiSeq sequencing of 16S ribosomal RNA genes revealed that Leuconostoc and Lactococcus spp. were the most abundant lactic acid bacteria in the initial phases of the fermentation. Later on, Lactobacillus, Weissella and Bifidobacterium dominated. CONCLUSIONS The type of fermentation system used had an effect on the microbial dynamics and the effect increased towards the end of fermentation. SIGNIFICANCE AND IMPACT OF THE STUDY Millions of people in Ethiopia daily consume kocho prepared in either a pit or a basket. These systems show practical problems, but this study shows that fermentation is also possible in a sauerkraut jar.
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Affiliation(s)
- A F Andeta
- Lab4Food, Department of Microbial and Molecular Systems, Technology Cluster Bioengineering Technology, KU Leuven, Geel, Belgium.,Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium.,Department of Biology, College of Natural Sciences, Arba Minch University, Arba Minch, Ethiopia
| | - D Vandeweyer
- Lab4Food, Department of Microbial and Molecular Systems, Technology Cluster Bioengineering Technology, KU Leuven, Geel, Belgium.,Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium
| | - E F Teffera
- Department of Biology, College of Natural Sciences, Arba Minch University, Arba Minch, Ethiopia
| | - F Woldesenbet
- Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia
| | - C Verreth
- Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium.,Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems, Technology Cluster Bioengineering Technology, KU Leuven, Sint-Katelijne Waver, Belgium
| | - S Crauwels
- Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium.,Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems, Technology Cluster Bioengineering Technology, KU Leuven, Sint-Katelijne Waver, Belgium
| | - B Lievens
- Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium.,Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems, Technology Cluster Bioengineering Technology, KU Leuven, Sint-Katelijne Waver, Belgium
| | - K Vancampenhout
- Lab4Food, Department of Microbial and Molecular Systems, Technology Cluster Bioengineering Technology, KU Leuven, Geel, Belgium
| | - L Van Campenhout
- Lab4Food, Department of Microbial and Molecular Systems, Technology Cluster Bioengineering Technology, KU Leuven, Geel, Belgium.,Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium
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Kovalski Mitter E, de Freitas R, Germida JJ. Microbial communities associated with barley growing in an oil sands reclamation area in Alberta, Canada. Can J Microbiol 2018; 64:1004-1019. [DOI: 10.1139/cjm-2018-0324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Microbial communities that colonize the plant rhizosphere and the root interior can ameliorate plant stress and promote growth. These plant–microbe associations are being investigated to assist in reclamation soils in northern Alberta. This study assessed the diversity of bacterial species associated with barley plants growing at different cover managements and slope positions in an oil sands reclamation area. Phospholipid fatty acid analysis of the microbial communities indicated that both cover type and slope, in addition to soil total and organic carbon, NH4+, and organic matter, were significant determinants of microbial community composition. However, analysis of denaturing gel gradient electrophoresis (DGGE) banding patterns revealed that while most bulk and rhizosphere soils differentiated by cover management, no clustering was observed in endophytes. In addition, techniques to assess culture-dependent endophytic bacteria revealed a dominance of the class Gammaproteobacteria, in which Enterobacteriaceae (44%), Xanthomonaceae (30%), and Pseudomonaceae (26%) were the most abundant families in this class. Several endophytic isolates also matched those from DGGE profiles. The results of this study suggest that plants growing on oil sands reclamation covers host a wide range of bacterial endophytes, which should be assessed as to their potential to assist plant establishment and growth at such sites.
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Affiliation(s)
- Eduardo Kovalski Mitter
- Department of Food and Bioproduct Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Renato de Freitas
- Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - James J. Germida
- Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
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Paul C, Filippidou S, Jamil I, Kooli W, House GL, Estoppey A, Hayoz M, Junier T, Palmieri F, Wunderlin T, Lehmann A, Bindschedler S, Vennemann T, Chain PSG, Junier P. Bacterial spores, from ecology to biotechnology. ADVANCES IN APPLIED MICROBIOLOGY 2018; 106:79-111. [PMID: 30798805 DOI: 10.1016/bs.aambs.2018.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The production of a highly specialized cell structure called a spore is a remarkable example of a survival strategy displayed by bacteria in response to challenging environmental conditions. The detailed analysis and description of the process of sporulation in selected model organisms have generated a solid background to understand the cellular processes leading to the formation of this specialized cell. However, much less is known regarding the ecology of spore-formers. This research gap needs to be filled as the feature of resistance has important implications not only on the survival of spore-formers and their ecology, but also on the use of spores for environmental prospection and biotechnological applications.
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Affiliation(s)
- Christophe Paul
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Sevasti Filippidou
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Isha Jamil
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Wafa Kooli
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Geoffrey L House
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Aislinn Estoppey
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Mathilda Hayoz
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Thomas Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland; Vital-IT group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Tina Wunderlin
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Anael Lehmann
- Laboratory of stable isotope geochemistry, Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Torsten Vennemann
- Laboratory of stable isotope geochemistry, Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
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47
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Leis ML, Costa MO. Initial description of the core ocular surface microbiome in dogs: Bacterial community diversity and composition in a defined canine population. Vet Ophthalmol 2018; 22:337-344. [PMID: 30095241 DOI: 10.1111/vop.12599] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
OBJECTIVE To characterize the bacterial community residing on the conjunctiva of clinically healthy dogs. METHODS Bacterial DNA from conjunctival swabs of 10 dogs with normal ocular examinations (both OD and OS, n = 20) was extracted, and 16S rRNA amplicons were sequenced using Illumina MiSeq 600. Resulting data were subjected to quality control steps, and analyzed for bacterial community richness and diversity, within- and between-group dissimilarity, and relative taxonomic composition. RESULTS High-quality reads (2.22 million bp) resulted in a mean of 159 068 sequences per sample. Bacterial community evenness and diversity was high when compared to other species, and did not significantly differ when samples were grouped by dogs or eyes. As expected, within-dog samples were more similar than between-dog samples. Taxonomic classification revealed that >95% of the community consisted of Firmicutes (34.9 ± 8.8%), Actinobacteria (26.3 ± 7.1%), Proteobacteria (26.2 ± 6.6%), and Bacteroidetes (9.4 ± 2.4%). Key members of the dog ocular surface microbiome, found in all dogs and corresponding to >25% of all identified OTUs (operational taxonomic units), were part of the Bifidobacteriaceae, Lachnospiraceae, Moraxellaceae, Corynebacteriaceae families. Genera previously thought to account for the majority of the core ocular surface microbiome in the dog (Staphylococcus sp., Streptococcus sp., and Bacillus sp.) were associated with only 2.63% of overall reads. CONCLUSIONS This study shows the feasibility of conjunctival swabs and high-throughput sequencing to profile the bacterial community structure of the canine ocular surface. A core ocular surface microbiome was identified for this canine population.
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Affiliation(s)
- Marina L Leis
- Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Matheus O Costa
- Faculty of Veterinary Medicine, Department of Farm Animal Health, Utrecht University, Utrecht, Netherlands.,Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
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48
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Fermentation of enset ( Ensete ventricosum ) in the Gamo highlands of Ethiopia: Physicochemical and microbial community dynamics. Food Microbiol 2018. [DOI: 10.1016/j.fm.2018.02.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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49
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Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota. ISME JOURNAL 2018; 12:2403-2416. [PMID: 29899513 DOI: 10.1038/s41396-018-0192-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/20/2018] [Accepted: 03/27/2018] [Indexed: 12/21/2022]
Abstract
Endospore-formers in the human microbiota are well adapted for host-to-host transmission, and an emerging consensus points to their role in determining health and disease states in the gut. The human gut, more than any other environment, encourages the maintenance of endospore formation, with recent culture-based work suggesting that over 50% of genera in the microbiome carry genes attributed to this trait. However, there has been limited work on the ecological role of endospores and other stress-resistant cellular states in the human gut. In fact, there is no data to indicate whether organisms with the genetic potential to form endospores actually form endospores in situ and how sporulation varies across individuals and over time. Here we applied a culture-independent protocol to enrich for endospores and other stress-resistant cells in human feces to identify variation in these states across people and within an individual over time. We see that cells with resistant states are more likely than those without to be shared among multiple individuals, which suggests that these resistant states are particularly adapted for cross-host dissemination. Furthermore, we use untargeted fecal metabolomics in 24 individuals and within a person over time to show that these organisms respond to shared environmental signals, and in particular, dietary fatty acids, that likely mediate colonization of recently disturbed human guts.
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50
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Morales‐Cruz A, Allenbeck G, Figueroa‐Balderas R, Ashworth VE, Lawrence DP, Travadon R, Smith RJ, Baumgartner K, Rolshausen PE, Cantu D. Closed-reference metatranscriptomics enables in planta profiling of putative virulence activities in the grapevine trunk disease complex. MOLECULAR PLANT PATHOLOGY 2018; 19:490-503. [PMID: 28218463 PMCID: PMC6638111 DOI: 10.1111/mpp.12544] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/13/2017] [Indexed: 05/20/2023]
Abstract
Grapevines, like other perennial crops, are affected by so-called 'trunk diseases', which damage the trunk and other woody tissues. Mature grapevines typically contract more than one trunk disease and often multiple grapevine trunk pathogens (GTPs) are recovered from infected tissues. The co-existence of different GTP species in complex and dynamic microbial communities complicates the study of the molecular mechanisms underlying disease development, especially under vineyard conditions. The objective of this study was to develop and optimize a community-level transcriptomics (i.e. metatranscriptomics) approach that could monitor simultaneously the virulence activities of multiple GTPs in planta. The availability of annotated genomes for the most relevant co-infecting GTPs in diseased grapevine wood provided the unprecedented opportunity to generate a multi-species reference for the mapping and quantification of DNA and RNA sequencing reads. We first evaluated popular sequence read mappers using permutations of multiple simulated datasets. Alignment parameters of the selected mapper were optimized to increase the specificity and sensitivity for its application to metagenomics and metatranscriptomics analyses. Initial testing on grapevine wood experimentally inoculated with individual GTPs confirmed the validity of the method. Using naturally infected field samples expressing a variety of trunk disease symptoms, we show that our approach provides quantitative assessments of species composition, as well as genome-wide transcriptional profiling of potential virulence factors, namely cell wall degradation, secondary metabolism and nutrient uptake for all co-infecting GTPs.
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Affiliation(s)
- Abraham Morales‐Cruz
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
| | - Gabrielle Allenbeck
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
| | | | - Vanessa E. Ashworth
- Department of Botany and Plant SciencesUniversity of California RiversideRiversideCA92521USA
| | - Daniel P. Lawrence
- Department of Plant PathologyUniversity of California DavisDavisCA95616USA
| | - Renaud Travadon
- Department of Plant PathologyUniversity of California DavisDavisCA95616USA
| | - Rhonda J. Smith
- University of California Cooperative Extension, Sonoma CountySanta RosaCA95403USA
| | - Kendra Baumgartner
- United States Department of Agriculture ‐ Agricultural Research ServiceCrops Pathology and Genetics Research UnitDavisCA95616USA
| | - Philippe E. Rolshausen
- Department of Botany and Plant SciencesUniversity of California RiversideRiversideCA92521USA
| | - Dario Cantu
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
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