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Iqbal H, Onyedibe K. The utilization of an unconventional approach to introduce basic bacteriology in a medical school bridge program. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2024; 25:e0018522. [PMID: 38785387 PMCID: PMC11360412 DOI: 10.1128/jmbe.00185-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 03/24/2024] [Indexed: 05/25/2024]
Abstract
Bacteria form an intense portion of reading and learning for students enrolled in microbiology education. As a part of the foundational course outline of bacteriology, bacterial classification is a significant topic of discussion. The purpose of our study was to analyze whether bacterial classification can be taught with a phylogenetic tree approach that might be more engaging and beneficial to student learners of microbiology. This methodology is unique compared to the conventional approach applied in introductory lectures of bacteriology that relies on morphology and Gram-staining to classify bacteria. The participants of this study were students enrolled in a two-semester medical school bridge program that offers a Master's degree in Pre-clinical Sciences. We presented bacterial origin and classification in the light of evolution and used a phylogenetic tree to signify clinically relevant groups of bacteria. Students were also taught the traditional bacterial classification using Gram stains and morphology. Both methods of classification were delivered in a didactic classroom session considering equal time spent and utilizing the same format. An online survey was distributed to the students after the session to collect their feedback. The results from the survey showed that 74% of participants would prefer learning bacterial classification using a combined approach that includes both Gram-staining and morphology as well as the phylogenetic tree. When asked if the study of bacterial classification through an evolutionary tree diagram is a clear and concise way of understanding bacteria, 79% of the students either agreed or strongly agreed with this statement. Interestingly, the alternative phylogenetic tree approach was considered more engaging and regarded as a means to expand the clinical knowledge of bacteria by 78% and 71% of the students, respectively. Overall, our study strongly supports the use of tree-based classification as an additional method to improve the learning of medically important groups of bacteria at varying levels of education.
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Affiliation(s)
- Henna Iqbal
- Department of Biomedical Sciences, Mercer University School of Medicine, Macon, Georgia, USA
| | - Kenneth Onyedibe
- Department of Biomedical Sciences, Mercer University School of Medicine, Macon, Georgia, USA
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2
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Rempfert KR, Bell SL, Kasanke CP, Zhao Q, Zhao X, Lipton AS, Hofmockel KS. Biomolecular budget of persistent, microbial-derived soil organic carbon: The importance of underexplored pools. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 932:172916. [PMID: 38697544 DOI: 10.1016/j.scitotenv.2024.172916] [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: 01/04/2024] [Revised: 04/25/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
Abstract
The details of how soil microorganisms contribute to stable soil organic carbon pools are a pressing knowledge gap with direct implications for soil health and climate mitigation. It is now recognized that microbial necromass contributes substantially to the formation of stable soil carbon. However, the quantification of necromass in soils has largely been limited to model molecules such as aminosugar biomarkers. The abundance and chemical composition of other persistent microbial residues remain unresolved, particularly concerning how these pools may vary with microbial community structure, soil texture, and management practices. Here we use yearlong soil incubation experiments with an isotopic tracer to quantify the composition of persistent residues derived from microbial communities inhabiting sand or silt dominated soil with annual (corn) or perennial (switchgrass) monocultures. Persistent microbial residues were recovered in diverse soil biomolecular pools including metabolites, proteins, lipids, and mineral-associated organic matter (MAOM). The relative abundances of microbial contributions to necromass pools were consistent across cropping systems and soil textures. The greatest residue accumulation was not recovered in MAOM but in the light density fraction of soil debris that persisted after extraction by chemical fractionation using organic solvents. Necromass abundance was positively correlated with microbial biomass abundance and revealed a possible role of cell wall morphology in enhancing microbial carbon persistence; while gram-negative bacteria accounted for the greatest contribution to microbial-derived carbon by mass at one year, residues from gram-positive Actinobacteria and Firmicutes showed greater durability. Together these results offer a quantitative assessment of the relative importance of diverse molecular classes for generating durable soil carbon.
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Affiliation(s)
| | - Sheryl L Bell
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Qian Zhao
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Xiaodong Zhao
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Kirsten S Hofmockel
- Pacific Northwest National Laboratory, Richland, WA, USA; Department of Agronomy, Iowa State University, Ames, IA, USA.
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3
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Deepa N, Chauhan S, Singh A. Unraveling the functional characteristics of endophytic bacterial diversity for plant growth promotion and enhanced secondary metabolite production in Pelargonium graveolens. Microbiol Res 2024; 283:127673. [PMID: 38484575 DOI: 10.1016/j.micres.2024.127673] [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: 01/04/2024] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 04/17/2024]
Abstract
The rich diversity of microbial endophytic communities associated with plants, often referred to as the second genome, serves as a compelling illustration of efficient co-evolution. This noteworthy partnership plays a pivotal role in sustaining plant well-being and enhancing plant adaptability across diverse habitats. Therefore, examining the diversity of endophytic microbes associated with their particular host plant is valuable for gaining insights into the vast spectrum of plant-microbe interactions. The present experiments aimed at investigating the bacterial endophytic diversity in both root and shoot tissues of Pelargonium graveolens, employing culture dependent and culture independent high-throughput metagenomics approach. A total of 614 and 620 operational taxonomic units (OTUs), encompassing 291 and 229 genera, were identified in the shoot and root tissues of P. graveolens, respectively. Furthermore, the subsequent classification of OTUs revealed 15 highly abundant phyla, with Proteobacteria dominating both root and shoot tissues. Notably, an exceptionally high abundance of Firmicutes phyla was observed in the shoot compared to the root. Additionally, 30 bacterial endophytes from the root, stem, petiole, and leaves were isolated and molecularly characterized, unveiling a consistent pattern of diversity distribution between the root and shoot of P. graveolens. Upon screening all isolates for plant growth promoting traits, Pseudomonas oryzihabitans was found to be positive for major biochemical test like nitrogen fixation, phosphate solubilization etc. and on inoculation resulted in about two-fold increase in content of essential oil accompanied by a significant rise in the geraniol and citronellol content. Diving deep into the genetic constitution of P. oryzihabitans unveiled a substantial number of genes directly and indirectly contributing to the endophyte's capability in colonizing host plants effectively. In summary, data obtained from metagenomics and culture dependent approaches including glass house trials suggest potential bacterial endophytes suitable for field applications for yield enhancement and in planta secondary metabolite enhancement investigations.
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Affiliation(s)
- Nikky Deepa
- Division of Crop Production and Protection, Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shivam Chauhan
- Division of Crop Production and Protection, Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India
| | - Akanksha Singh
- Division of Crop Production and Protection, Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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Lee KK, Liu S, Crocker K, Huggins DR, Tikhonov M, Mani M, Kuehn S. Functional regimes define the response of the soil microbiome to environmental change. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.584851. [PMID: 38559185 PMCID: PMC10980070 DOI: 10.1101/2024.03.15.584851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The metabolic activity of soil microbiomes plays a central role in carbon and nitrogen cycling. Given the changing climate, it is important to understand how the metabolism of natural communities responds to environmental change. However, the ecological, spatial, and chemical complexity of soils makes understanding the mechanisms governing the response of these communities to perturbations challenging. Here, we overcome this complexity by using dynamic measurements of metabolism in microcosms and modeling to reveal regimes where a few key mechanisms govern the response of soils to environmental change. We sample soils along a natural pH gradient, construct >1500 microcosms to perturb the pH, and quantify the dynamics of respiratory nitrate utilization, a key process in the nitrogen cycle. Despite the complexity of the soil microbiome, a minimal mathematical model with two variables, the quantity of active biomass in the community and the availability of a growth-limiting nutrient, quantifies observed nitrate utilization dynamics across soils and pH perturbations. Across environmental perturbations, changes in these two variables give rise to three functional regimes each with qualitatively distinct dynamics of nitrate utilization over time: a regime where acidic perturbations induce cell death that limits metabolic activity, a nutrient-limiting regime where nitrate uptake is performed by dominant taxa that utilize nutrients released from the soil matrix, and a resurgent growth regime in basic conditions, where excess nutrients enable growth of initially rare taxa. The underlying mechanism of each regime is predicted by our interpretable model and tested via amendment experiments, nutrient measurements, and sequencing. Further, our data suggest that the long-term history of environmental variation in the wild influences the transitions between functional regimes. Therefore, quantitative measurements and a mathematical model reveal the existence of qualitative regimes that capture the mechanisms and dynamics of a community responding to environmental change.
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Affiliation(s)
- Kiseok Keith Lee
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL 60637, USA
- Center for Living Systems, The University of Chicago, Chicago, IL 60637, USA
| | - Siqi Liu
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA
| | - Kyle Crocker
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL 60637, USA
- Center for Living Systems, The University of Chicago, Chicago, IL 60637, USA
| | - David R. Huggins
- USDA-ARS, Northwest Sustainable Agroecosystems Research Unit, Pullman, WA 99164, USA
| | - Mikhail Tikhonov
- Department of Physics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Madhav Mani
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
- National Institute for Theory and Mathematics in Biology, Northwestern University and The University of Chicago, Chicago, IL
| | - Seppe Kuehn
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL 60637, USA
- National Institute for Theory and Mathematics in Biology, Northwestern University and The University of Chicago, Chicago, IL
- Center for Living Systems, The University of Chicago, Chicago, IL 60637, USA
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Lin X, Hu T, Wu Z, Li L, Wang Y, Wen D, Liu X, Li W, Liang H, Jin X, Xu X, Wang J, Yang H, Kristiansen K, Xiao L, Zou Y. Isolation of potentially novel species expands the genomic and functional diversity of Lachnospiraceae. IMETA 2024; 3:e174. [PMID: 38882499 PMCID: PMC11170972 DOI: 10.1002/imt2.174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/06/2023] [Indexed: 06/18/2024]
Abstract
The Lachnospiraceae family holds promise as a source of next-generation probiotics, yet a comprehensive delineation of its diversity is lacking, hampering the identification of suitable strains for future applications. To address this knowledge gap, we conducted an in-depth genomic and functional analysis of 1868 high-quality genomes, combining data from public databases with our new isolates. This data set represented 387 colonization-selective species-level clusters, of which eight genera represented multilineage clusters. Pan-genome analysis, single-nucleotide polymorphism (SNP) identification, and probiotic functional predictions revealed that species taxonomy, habitats, and geography together shape the functional diversity of Lachnospiraceae. Moreover, analyses of associations with atherosclerotic cardiovascular disease (ACVD) and inflammatory bowel disease (IBD) indicated that several strains of potentially novel Lachnospiraceae species possess the capacity to reduce the abundance of opportunistic pathogens, thereby imparting potential health benefits. Our findings shed light on the untapped potential of novel species enabling knowledge-based selection of strains for the development of next-generation probiotics holding promise for improving human health and disease management.
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Affiliation(s)
- Xiaoqian Lin
- BGI Research Shenzhen China
- School of Bioscience and Biotechnology South China University of Technology Guangzhou China
| | | | - Zhinan Wu
- BGI Research Shenzhen China
- College of Life Sciences University of Chinese Academy of Sciences Beijing China
| | | | | | | | - Xudong Liu
- BGI Research Shenzhen China
- College of Life Sciences University of Chinese Academy of Sciences Beijing China
| | - Wenxi Li
- BGI Research Shenzhen China
- School of Bioscience and Biotechnology South China University of Technology Guangzhou China
| | | | | | - Xun Xu
- BGI Research Shenzhen China
| | - Jian Wang
- BGI Research Shenzhen China
- James D. Watson Institute of Genome Sciences Hangzhou China
| | - Huanming Yang
- BGI Research Shenzhen China
- James D. Watson Institute of Genome Sciences Hangzhou China
| | - Karsten Kristiansen
- BGI Research Shenzhen China
- Laboratory of Genomics and Molecular Biomedicine University of Copenhagen Copenhagen Denmark
| | - Liang Xiao
- BGI Research Shenzhen China
- College of Life Sciences University of Chinese Academy of Sciences Beijing China
- Shenzhen Engineering Laboratory of Detection and Intervention of human intestinal microbiome, BGI-Shenzhen Shenzhen China
| | - Yuanqiang Zou
- BGI Research Shenzhen China
- Laboratory of Genomics and Molecular Biomedicine University of Copenhagen Copenhagen Denmark
- Shenzhen Engineering Laboratory of Detection and Intervention of human intestinal microbiome, BGI-Shenzhen Shenzhen China
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Field CJ, Bowerman KL, Hugenholtz P. Multiple independent losses of sporulation and peptidoglycan in the Mycoplasmatales and related orders of the class Bacilli. Microb Genom 2024; 10:001176. [PMID: 38189216 PMCID: PMC10868615 DOI: 10.1099/mgen.0.001176] [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: 10/24/2023] [Accepted: 12/19/2023] [Indexed: 01/09/2024] Open
Abstract
Many peptidoglycan-deficient bacteria such as the Mycoplasmatales are known host-associated lineages, lacking the environmental resistance mechanisms and metabolic capabilities necessary for a free-living lifestyle. Several peptidoglycan-deficient and non-sporulating orders of interest are thought to be descended from Gram-positive sporulating Bacilli through reductive evolution. Here we annotate 2650 genomes belonging to the class Bacilli, according to the Genome Taxonomy Database, to predict the peptidoglycan and sporulation phenotypes of three novel orders, RFN20, RF39 and ML615J-28, known only through environmental sequence surveys. These lineages are interspersed between peptidoglycan-deficient non-sporulating orders including the Mycoplasmatales and Acholeplasmatales, and more typical Gram-positive orders such as the Erysipelotrichales and Staphylococcales. We use the extant genotypes to perform ancestral state reconstructions. The novel orders are predicted to have small genomes with minimal metabolic capabilities and to comprise a mix of peptidoglycan-deficient and/or non-sporulating species. In contrast to expectations based on cultured representatives, the order Erysipelotrichales lacks many of the genes involved in peptidoglycan and endospore formation. The reconstructed evolutionary history of these traits suggests multiple independent whole-genome reductions and loss of phenotype via intermediate transition states that continue into the present. We suggest that the evolutionary history of the reduced-genome lineages within the class Bacilli is one driven by multiple independent transitions to host-associated lifestyles, with the degree of reduction in environmental resistance and metabolic capabilities correlated with degree of host association.
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Affiliation(s)
- Christian J. Field
- School of Chemistry and Molecular Biosciences, The Australian Centre for Ecogenomics, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Kate L. Bowerman
- School of Chemistry and Molecular Biosciences, The Australian Centre for Ecogenomics, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Philip Hugenholtz
- School of Chemistry and Molecular Biosciences, The Australian Centre for Ecogenomics, The University of Queensland, St Lucia, QLD 4072, Australia
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Serrano M, Martins D, Henriques AO. Clostridioides difficile Sporulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:273-314. [PMID: 38175480 DOI: 10.1007/978-3-031-42108-2_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Some members of the Firmicutes phylum, including many members of the human gut microbiota, are able to differentiate a dormant and highly resistant cell type, the endospore (hereinafter spore for simplicity). Spore-formers can colonize virtually any habitat and, because of their resistance to a wide variety of physical and chemical insults, spores can remain viable in the environment for long periods of time. In the anaerobic enteric pathogen Clostridioides difficile the aetiologic agent is the oxygen-resistant spore, while the toxins produced by actively growing cells are the main cause of the disease symptoms. Here, we review the regulatory circuits that govern entry into sporulation. We also cover the role of spores in the infectious cycle of C. difficile in relation to spore structure and function and the main control points along spore morphogenesis.
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Affiliation(s)
- Mónica Serrano
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal.
| | - Diogo Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Adriano O Henriques
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
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8
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Frates ES, Spietz RL, Silverstein MR, Girguis P, Hatzenpichler R, Marlow JJ. Natural and anthropogenic carbon input affect microbial activity in salt marsh sediment. Front Microbiol 2023; 14:1235906. [PMID: 37744927 PMCID: PMC10512730 DOI: 10.3389/fmicb.2023.1235906] [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: 06/06/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Salt marshes are dynamic, highly productive ecosystems positioned at the interface between terrestrial and marine systems. They are exposed to large quantities of both natural and anthropogenic carbon input, and their diverse sediment-hosted microbial communities play key roles in carbon cycling and remineralization. To better understand the effects of natural and anthropogenic carbon on sediment microbial ecology, several sediment cores were collected from Little Sippewissett Salt Marsh (LSSM) on Cape Cod, MA, USA and incubated with either Spartina alterniflora cordgrass or diesel fuel. Resulting shifts in microbial diversity and activity were assessed via bioorthogonal non-canonical amino acid tagging (BONCAT) combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Both Spartina and diesel amendments resulted in initial decreases of microbial diversity as well as clear, community-wide shifts in metabolic activity. Multi-stage degradative frameworks shaped by fermentation were inferred based on anabolically active lineages. In particular, the metabolically versatile Marinifilaceae were prominent under both treatments, as were the sulfate-reducing Desulfovibrionaceae, which may be attributable to their ability to utilize diverse forms of carbon under nutrient limited conditions. By identifying lineages most directly involved in the early stages of carbon processing, we offer potential targets for indicator species to assess ecosystem health and highlight key players for selective promotion of bioremediation or carbon sequestration pathways.
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Affiliation(s)
- Erin S. Frates
- Department of Biology, Boston University, Boston, MA, United States
| | - Rachel L. Spietz
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
| | | | - Peter Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, United States
- Thermal Biology Institute, Montana State University, Bozeman, MT, United States
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9
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Marathe A, Zarazúa-Osorio B, Srivastava P, Fujita M. The master regulator for entry into sporulation in Bacillus subtilis becomes a mother cell-specific transcription factor for forespore engulfment. Mol Microbiol 2023; 120:439-461. [PMID: 37485800 DOI: 10.1111/mmi.15132] [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: 12/29/2022] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
The Spo0A transcription factor is activated by phosphorylation in starving Bacillus subtilis cells. The activated Spo0A (Spo0A~P) regulates genes controlling entry into sporulation and appears to control mother-cell-specific gene expression after asymmetric division, but the latter remains elusive. Here, we found that Spo0A~P directly binds to three conserved DNA sequences (0A1-3) in the promoter region of the mother cell-specific lytic transglycosylase gene spoIID, which is transcribed by σE -RNA polymerase (RNAP) and negatively controlled by the SpoIIID transcription factor and required for forespore engulfment. Systematic mutagenesis of the 0A boxes revealed that the 0A1 and 0A2 boxes located upstream of the promoter positively control the transcription of spoIID. In contrast, the 0A3 box located downstream of the promoter negatively controls the transcription of spoIID. The mutated SpoIIID binding site located between the -35 and -10 promoter elements causes increased expression of spoIID and reduced sporulation. When the mutations of 0A1, 0A2, and IIID sites are combined, sporulation is restored. Collectively, our data suggest that the mother cell-specific spoIID expression is precisely controlled by the coordination of three factors, Spo0A~P, SpoIIID, and σE -RNAP, for proper sporulation. The conservation of this mechanism across spore-forming species was discussed.
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Affiliation(s)
- Anuradha Marathe
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | | | - Priyanka Srivastava
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
- Department of Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Masaya Fujita
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
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Wang H, Lin S, Zhang H, Guo D, Dan L, Zheng X. Batch-fed composting of food waste: Microbial diversity characterization and removal of antibiotic resistance genes. BIORESOURCE TECHNOLOGY 2023:129433. [PMID: 37399965 DOI: 10.1016/j.biortech.2023.129433] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/05/2023]
Abstract
The aim of this work was to study the impact of batch-fed strategies on bacterial communities and ARGs in compost. The findings demonstrate that batch-feeding helped maintain high temperatures in the compost pile for an extended period (above 50 °C for 18 days), which in turn facilitated water dissipation. High-throughput sequencing showed that Firmicutes played a significant role in batch-fed composting (BFC). They had a high relative abundance at the beginning (98.64%) and end (45.71%) of compost. Additionally, BFC showed promising results in removing ARGs, with reductions of 3.04-1.09 log copies/g for Aminoglycoside and 2.26-2.44 log copies/g for β_Lactamase. This study provides a comprehensive survey of BFC and demonstrates its potential for eliminating resistance contamination in compost.
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Affiliation(s)
- Haichao Wang
- Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing 100089, China
| | - Shuye Lin
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Huan Zhang
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Dong Guo
- Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing 100089, China
| | - Liu Dan
- Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing 100089, China
| | - Xiaowei Zheng
- Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing 100089, China.
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11
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Toukabri H, Lereclus D, Slamti L. A Sporulation-Independent Way of Life for Bacillus thuringiensis in the Late Stages of an Infection. mBio 2023:e0037123. [PMID: 37129506 DOI: 10.1128/mbio.00371-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
The formation of endospores has been considered the unique survival and transmission mode of sporulating Firmicutes due to the exceptional resistance and persistence of this bacterial form. However, nonsporulated bacteria (Spo-) were reported at the early stages following the death of a host infected with Bacillus thuringiensis, an entomopathogenic sporulating bacterium. Here, we investigated the characteristics of the bacterial population in the late stages of an infection in the B. thuringiensis/Galleria mellonella infection model. Using fluorescent reporters and molecular markers coupled to flow cytometry, we demonstrated that the Spo- cells persist and constitute about half of the population 2 weeks post-infection (p.i.). Protein synthesis and growth recovery assays indicated that they are in a metabolically slowed-down state. These bacteria were extremely resistant to the insect cadaver environment, which did not support growth of in vitro-grown vegetative cells and spores. A transcriptomic analysis of this subpopulation at 7 days p.i. revealed a signature profile of this state, and the expression analysis of individual genes at the cell level showed that more bacteria mount an oxidative stress response as their survival time increases, in agreement with the increase of the free radical level in the host cadaver and in the number of reactive oxygen species (ROS)-producing bacteria. Altogether, these data show for the first time that nonsporulated bacteria are able to survive for a prolonged period of time in the context of an infection and indicate that they engage in a profound adaptation process that leads to their persistence in the host cadaver. IMPORTANCE Bacillus thuringiensis is an entomopathogenic bacterium widely used as a biopesticide. It belongs to the Bacillus cereus group, comprising the foodborne pathogen B. cereus sensu stricto and the anthrax agent Bacillus anthracis. Like other Firmicutes when they encounter harsh conditions, these Gram-positive bacteria can form dormant cells called spores. Due to its highly resistant nature, the spore was considered the unique mode of long-term survival, eclipsing any other form of persistence. Breaking this paradigm, we observed that B. thuringiensis was able to persist in its host cadaver in a nonsporulated form for at least 14 days. Our results show that these bacteria survived in the cadaver environment, which proved hostile for actively growing bacteria by engaging in a profound adaptation process. Studying this facet of the life cycle of a sporulating bacterium provides new fundamental knowledge and might lead to the development of strategies to combat sporulating pathogenic species.
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Affiliation(s)
- Hasna Toukabri
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Didier Lereclus
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Leyla Slamti
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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12
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Xu M, Selvaraj GK, Lu H. Environmental sporobiota: Occurrence, dissemination, and risks. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161809. [PMID: 36702282 DOI: 10.1016/j.scitotenv.2023.161809] [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: 11/22/2022] [Revised: 01/03/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Spore-forming bacteria known as sporobiota are widespread in diverse environments from terrestrial and aquatic habitats to industrial and healthcare systems. Studies on sporobiota have been mainly focused on food processing and clinical fields, while a large amount of sporobiota exist in natural environments. Due to their persistence and capabilities of transmitting virulence factors and antibiotic resistant genes, environmental sporobiota could pose significant health risks to humans. These risks could increase as global warming and environmental pollution has altered the life cycle of sporobiota. This review summarizes the current knowledge of environmental sporobiota, including their occurrence, characteristics, and functions. An interaction network among clinical-, food-related, and environment-related sporobiota is constructed. Recent and effective methods for detecting and disinfecting environmental sporobiota are also discussed. Key problems and future research needs for better understanding and reducing the risks of environmental sporobiota and sporobiome are proposed.
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Affiliation(s)
- Min Xu
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ganesh-Kumar Selvaraj
- Department of Microbiology, St. Peter's Institute of Higher Education and Research, Chennai 600054, Tamil Nadu, India.
| | - Huijie Lu
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Water Pollution Control and Environmental Safety, Zhejiang, China.
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13
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Rosa Martins PH, Rabinovitch L, de Orem JC, Silva WMC, de Araujo Mesquita F, de Magalhães MIA, de Andrade Cavalcante D, Vivoni AM, de Oliveira EJ, de Lima VCP, Brito JT, De-Souza MT. Biochemical, physiological, and molecular characterisation of a large collection of aerobic endospore-forming bacteria isolated from Brazilian soils. NEOTROPICAL BIOLOGY AND CONSERVATION 2023. [DOI: 10.3897/neotropical.18.e86548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The aerobic endospore-forming bacteria (AEFB) comprise species of Bacillus and related genera and have long been regarded as prominent constituents of the soil bacterial community. The wide diversity of AEFB renders appropriate categorisation and generalisations a challenging task. We previously isolated 312 AEFB strains from Brazilian soils that we designated SDF (Solo do Distrito Federal) strains. To better understand the SDF diversity and explore their biotechnological potential, we addressed the biochemical and physiological profiles of these 312 environmental strains by performing 30 tests in this work. Of these, the 16S rRNA gene sequences segregated 238 SDF strains into four genera in the family Bacillaceae and two in the Paenibacillaceae. Bacillus spp. were the most prevalent, followed by species of Paenibacillus. We summarised the phenotypic test relationships among selected SDF strains using a Pearson correlation-based clustering represented in heatmaps. In practice, biochemical and physiological profiles are often less discriminatory than molecular data and may be unstable because of the loss of traits. Although these test reactions are not universally positive or negative within species, they may define biotypes and be efficient strain markers, enhancing the accuracy of unknown sample identification. It can also help select the most representative phenotypes of samples. Along with the other phenotypic and genotypic data, the present results are of great importance for the robust classification of the SDF strains within the scope of the polyphasic approach.
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14
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Zhang W, Mao G, Zhuang J, Yang H. The co-inoculation of Pseudomonas chlororaphis H1 and Bacillus altitudinis Y1 promoted soybean [ Glycine max (L.) Merrill] growth and increased the relative abundance of beneficial microorganisms in rhizosphere and root. Front Microbiol 2023; 13:1079348. [PMID: 36699592 PMCID: PMC9868396 DOI: 10.3389/fmicb.2022.1079348] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/16/2022] [Indexed: 01/10/2023] Open
Abstract
Currently, plant growth-promoting rhizobacteria (PGPR) microbial inoculants are heavily used in agricultural production among which Pseudomonas sp. and Bacillus sp. are two excellent inoculum strains, which are widely used in plant growth promotion and disease control. However, few studies have been conducted on the combined use of the two bacteria. The aim of this study was to investigate the effects of co-inoculation of these two bacteria on soybean [Glycine max (L.) Merrill] growth and physiological indexes and further study the effect of microbial inoculants on native soil bacterial communities and plant endophyte microbiota, especially microorganisms in rhizosphere and root. A pot experiment was conducted and four treatments were designed: group without any strain inoculant (CK); group inoculated with Pseudomonas chlororaphis H1 inoculant (J); group inoculated with Bacillus altitudinis Y1 inoculant (Y) and group inoculated with equal volume of P. chlororaphis H1 inoculant and B. altitudinis Y1 inoculant (H). Compared with CK, the three inoculant groups J, Y, and H exhibited improved soybean growth and physiological indexes, and group H was the most significant (p < 0.05). In terms of rhizosphere bacterial community structure, the relative abundance of native Luteimonas (9.31%) was higher in the H group than in the J (6.07%), Y (3.40%), and CK (5.69%) groups, which has potential value of disease suppression. Besides, compared with bacterial communities of the other three groups in soybean roots, group H increased the abundance of beneficial bacterial community for the contents of Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Devosia, and Methylobacillus significantly increased (p < 0.05). In conclusion, we found that the composite inoculum of Pseudomonas chlororaphis H1 and Bacillus altitudinis Y1 could effectively promote soybean growth, increase yield and improve the beneficial bacterial community in root and rhizosphere and have certain value for soil improvement.
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Affiliation(s)
- Wentao Zhang
- Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, Nanjing Forestry University, Nanjing, China,College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Guohao Mao
- Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, Nanjing Forestry University, Nanjing, China,College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Jiayao Zhuang
- Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, Nanjing Forestry University, Nanjing, China,College of Forestry, Nanjing Forestry University, Nanjing, China,*Correspondence: Jiayao Zhuang, ✉
| | - Hao Yang
- Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, Nanjing Forestry University, Nanjing, China,College of Forestry, Nanjing Forestry University, Nanjing, China
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15
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Mrofchak R, Madden C, Evans MV, Kisseberth WC, Dhawan D, Knapp DW, Hale VL. Urine and fecal microbiota in a canine model of bladder cancer and comparison of canine and human urine microbiota. ALL LIFE 2022. [DOI: 10.1080/26895293.2022.2154858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Ryan Mrofchak
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, Columbus, OH, USA
| | - Christopher Madden
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, Columbus, OH, USA
| | - Morgan V. Evans
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, Columbus, OH, USA
- Divison of Environmental Health Sciences, Ohio State University College of Public Health, Columbus, OH, USA
| | - William C. Kisseberth
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, Columbus, OH, USA
| | - Deepika Dhawan
- Department of Veterinary Clinical Sciences, Purdue University College of Veterinary Medicine, West Lafayette, IN, USA
| | - Deborah W. Knapp
- Department of Veterinary Clinical Sciences, Purdue University College of Veterinary Medicine, West Lafayette, IN, USA
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Vanessa L. Hale
- Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, Columbus, OH, USA
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16
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Li D, Yuan J, Ding J, Wang H, Shen Y, Li G. Effects of carbon/nitrogen ratio and aeration rate on the sheep manure composting process and associated gaseous emissions. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 323:116093. [PMID: 36095985 DOI: 10.1016/j.jenvman.2022.116093] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 06/15/2023]
Abstract
There are several issues such as low maturity degree of compost product and severe pollution gas emissions during the composting process. Carbon/Nitrogen (C/N) ratio and aeration rate (AR) are the most important factors affecting the composting performance. According to the results of previous studies, the proper C/N ratio and AR were 20-30:1 and 0.1-0.4 L kg-1 DM·min-1, respectively. Therefore, a lab-scale experiment was conducted to investigate the effects of C/N ratio and AR on sheep manure composting process and associated gaseous emissions. The initial C/N ratio in this experiment were set at 23, 26 and 29 to simulate the C/N ratio at low, medium and high levels. The AR were decided at 0.12, 0.24 and 0.36 L kg-1 DM·min-1 to simulate the aeration at low, middle and high levels. The results showed that as the C/N ratio or AR increased, the methane (CH4) and hydrogen sulfide (H2S) emissions decreased. The nitrous oxide (N2O) emission peaked at the low C/N ratio or AR treatments. The total greenhouse gas (GHG) emissions decreased with the increase of C/N ratio or AR, and the maximum value occurred in the treatment with C/N ratio 23 and AR 0.24 L kg-1 DM·min-1. In the treatment with C/N ratio 26 and AR 0.36 L kg-1 DM·min-1, the GI value of compost product was the highest (about 250%), and the total greenhouse effect was the lowest (2.36 kg CO2-eq·t-1 DM). Therefore, considering reduction of pollution gas emissions and improvement of the quality of compost products comprehensively, the optimum conditions were initial C/N ratio 26 and AR 0.36 L kg-1 DM·min-1 during the co-composting of sheep manure and cornstalks. In addition, the key physicochemical factors and eight key bacterial communities were determined to regulate compost maturity and pollution gas emissions during the sheep manure composting, which could provide scientific support and theoretical reference for controlling pollution gas emissions and obtaining high quality sheep manure compost products.
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Affiliation(s)
- Danyang Li
- Institute of Energy and Environmental Protection, Academy of Agricultural Planning & Engineering, Ministry of Agriculture and Rural Affairs, Beijing, 100125, China; Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing, 100193, China
| | - Jing Yuan
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing, 100193, China
| | - Jingtao Ding
- Institute of Energy and Environmental Protection, Academy of Agricultural Planning & Engineering, Ministry of Agriculture and Rural Affairs, Beijing, 100125, China
| | - Huihui Wang
- Institute of Energy and Environmental Protection, Academy of Agricultural Planning & Engineering, Ministry of Agriculture and Rural Affairs, Beijing, 100125, China
| | - Yujun Shen
- Institute of Energy and Environmental Protection, Academy of Agricultural Planning & Engineering, Ministry of Agriculture and Rural Affairs, Beijing, 100125, China.
| | - Guoxue Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing, 100193, China.
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17
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Fatton M, Filippidou S, Junier T, Cailleau G, Berge M, Poppleton D, Blum TB, Kaminek M, Odriozola A, Blom J, Johnson SL, Abrahams JP, Chain PS, Gribaldo S, Tocheva EI, Zuber B, Viollier PH, Junier P. Cryptosporulation in Kurthia spp. forces a rethinking of asporogenesis in Firmicutes. Environ Microbiol 2022; 24:6320-6335. [PMID: 36530021 PMCID: PMC10086788 DOI: 10.1111/1462-2920.16145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 07/20/2022] [Indexed: 01/12/2023]
Abstract
Endosporulation is a complex morphophysiological process resulting in a more resistant cellular structure that is produced within the mother cell and is called endospore. Endosporulation evolved in the common ancestor of Firmicutes, but it is lost in descendant lineages classified as asporogenic. While Kurthia spp. is considered to comprise only asporogenic species, we show here that strain 11kri321, which was isolated from an oligotrophic geothermal reservoir, produces phase-bright spore-like structures. Phylogenomics of strain 11kri321 and other Kurthia strains reveals little similarity to genetic determinants of sporulation known from endosporulating Bacilli. However, morphological hallmarks of endosporulation were observed in two of the four Kurthia strains tested, resulting in spore-like structures (cryptospores). In contrast to classic endospores, these cryptospores did not protect against heat or UV damage and successive sub-culturing led to the loss of the cryptosporulating phenotype. Our findings imply that a cryptosporulation phenotype may have been prevalent and subsequently lost by laboratory culturing in other Firmicutes currently considered as asporogenic. Cryptosporulation might thus represent an ancestral but unstable and adaptive developmental state in Firmicutes that is under selection under harsh environmental conditions.
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Affiliation(s)
- Mathilda Fatton
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Sevasti Filippidou
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.,AstrobiologyOU, The Open University, Milton Keynes, UK
| | - Thomas Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.,Vital-IT group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Guillaume Cailleau
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Matthieu Berge
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Daniel Poppleton
- Unité de Biologie Moléculaire du Gène chez les Extrémophiles, Département de Microbiologie, Institut Pasteur, France
| | - Thorsten B Blum
- Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), Villigen, Switzerland
| | - Marek Kaminek
- Institute for Anatomy, University of Bern, Bern, Switzerland
| | | | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Shannon L Johnson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Jan Pieter Abrahams
- Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), Villigen, Switzerland.,Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland.,Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Patrick S Chain
- Institute for Anatomy, University of Bern, Bern, Switzerland
| | - Simonetta Gribaldo
- Unité de Biologie Moléculaire du Gène chez les Extrémophiles, Département de Microbiologie, Institut Pasteur, France
| | - Elitza I Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Benoît Zuber
- Institute for Anatomy, University of Bern, Bern, Switzerland
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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18
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Gittins DA, Desiage PA, Morrison N, Rattray JE, Bhatnagar S, Chakraborty A, Zorz J, Li C, Horanszky O, Cramm MA, Bisiach F, Bennett R, Webb J, MacDonald A, Fowler M, Campbell DC, Hubert CRJ. Geological processes mediate a microbial dispersal loop in the deep biosphere. SCIENCE ADVANCES 2022; 8:eabn3485. [PMID: 36026445 PMCID: PMC9417182 DOI: 10.1126/sciadv.abn3485] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The deep biosphere is the largest microbial habitat on Earth and features abundant bacterial endospores. Whereas dormancy and survival at theoretical energy minima are hallmarks of microbial physiology in the subsurface, ecological processes such as dispersal and selection in the deep biosphere remain poorly understood. We investigated the biogeography of dispersing bacteria in the deep sea where upward hydrocarbon seepage was confirmed by acoustic imagery and geochemistry. Thermophilic endospores in the permanently cold seabed correlated with underlying seep conduits reveal geofluid-facilitated cell migration pathways originating in deep petroleum-bearing sediments. Endospore genomes highlight adaptations to life in anoxic petroleum systems and bear close resemblance to oil reservoir microbiomes globally. Upon transport out of the subsurface, viable thermophilic endospores reenter the geosphere by sediment burial, enabling germination and environmental selection at depth where new petroleum systems establish. This microbial dispersal loop circulates living biomass in and out of the deep biosphere.
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Affiliation(s)
- Daniel A. Gittins
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
- Corresponding author.
| | | | - Natasha Morrison
- Department of Natural Resources and Renewables, Government of Nova Scotia, Halifax, Canada
| | - Jayne E. Rattray
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Srijak Bhatnagar
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | | | - Jackie Zorz
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Carmen Li
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Oliver Horanszky
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Margaret A. Cramm
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Francesco Bisiach
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Robbie Bennett
- Natural Resources Canada, Geological Survey of Canada-Atlantic, Dartmouth, Canada
| | - Jamie Webb
- Applied Petroleum Technology, Calgary, Canada
| | - Adam MacDonald
- Department of Natural Resources and Renewables, Government of Nova Scotia, Halifax, Canada
| | | | - D. Calvin Campbell
- Natural Resources Canada, Geological Survey of Canada-Atlantic, Dartmouth, Canada
| | - Casey R. J. Hubert
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
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19
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Qi J, Ji M, Wang W, Zhang Z, Liu K, Huang Z, Liu Y. Effect of Indian monsoon on the glacial airborne bacteria over the Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 831:154980. [PMID: 35378188 DOI: 10.1016/j.scitotenv.2022.154980] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/26/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
The glacier of the Tibetan Plateau (TP) is influenced by the Indian monsoon and continental westerlies. Wind flow can carry a variety of bacteria and disperse across the TP. Once these bacteria are colonized to the glacier surface, they could affect the biogeochemical cycle of the glacial ecosystems. However, very few studies have focused on the relationships between these airborne bacteria and atmospheric circulation over glaciers of the TP. Here we studied the diversity, taxonomic composition, and community structure of airborne bacteria on six TP glaciers using 16S rRNA gene sequencing. The results revealed an increase in the airborne bacterial diversity over the glaciers under the effect of the Indian monsoon. Airborne bacteria were dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, while relative abundances of Bacteroidetes and Firmicutes were significantly higher under the influence of the Indian monsoon in the southern and central of the TP, respectively. Moreover, significantly different airborne bacterial community structures were observed over glaciers under the influence of the Indian monsoon, which could be explained by the increased community stochasticity. In addition, the Indian monsoon increases the diversity and relative abundance of potential pathogens, which includes the most notorious bacteria such as Pseudomonas fluorescens, Staphylococcus aureus, and Clostridium butyricum. Our results revealed for the first time that atmospheric circulation influences the composition of airborne bacteria over the glaciers on the TP, this may provide critical insights into the distinct microbial community structure and function in glaciers across the TP.
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Affiliation(s)
- Jing Qi
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China; School of Life Sciences, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Mukan Ji
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Wenqiang Wang
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China; School of Life Sciences, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhihao Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhongwei Huang
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yongqin Liu
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.
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20
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Conservation and Evolution of the Sporulation Gene Set in Diverse Members of the Firmicutes. J Bacteriol 2022; 204:e0007922. [PMID: 35638784 DOI: 10.1128/jb.00079-22] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The current classification of the phylum Firmicutes (new name, Bacillota) features eight distinct classes, six of which include known spore-forming bacteria. In Bacillus subtilis, sporulation involves up to 500 genes, many of which do not have orthologs in other bacilli and/or clostridia. Previous studies identified about 60 sporulation genes of B. subtilis that were shared by all spore-forming members of the Firmicutes. These genes are referred to as the sporulation core or signature, although many of these are also found in genomes of nonsporeformers. Using an expanded set of 180 firmicute genomes from 160 genera, including 76 spore-forming species, we investigated the conservation of the sporulation genes, in particular seeking to identify lineages that lack some of the genes from the conserved sporulation core. The results of this analysis confirmed that many small acid-soluble spore proteins (SASPs), spore coat proteins, and germination proteins, which were previously characterized in bacilli, are missing in spore-forming members of Clostridia and other classes of Firmicutes. A particularly dramatic loss of sporulation genes was observed in the spore-forming members of the families Planococcaceae and Erysipelotrichaceae. Fifteen species from diverse lineages were found to carry skin (sigK-interrupting) elements of different sizes that all encoded SpoIVCA-like recombinases but did not share any other genes. Phylogenetic trees built from concatenated alignments of sporulation proteins and ribosomal proteins showed similar topology, indicating an early origin and subsequent vertical inheritance of the sporulation genes. IMPORTANCE Many members of the phylum Firmicutes (Bacillota) are capable of producing endospores, which enhance the survival of important Gram-positive pathogens that cause such diseases as anthrax, botulism, colitis, gas gangrene, and tetanus. We show that the core set of sporulation genes, defined previously through genome comparisons of several bacilli and clostridia, is conserved in a wide variety of sporeformers from several distinct lineages of Firmicutes. We also detected widespread loss of sporulation genes in many organisms, particularly within the families Planococcaceae and Erysipelotrichaceae. Members of these families, such as Lysinibacillus sphaericus and Clostridium innocuum, could be excellent model organisms for studying sporulation mechanisms, such as engulfment, formation of the spore coat, and spore germination.
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21
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Comparative Analysis of the Endophytic Bacterial Diversity of Populus euphratica Oliv. in Environments of Different Salinity Intensities. Microbiol Spectr 2022; 10:e0050022. [PMID: 35587636 PMCID: PMC9241684 DOI: 10.1128/spectrum.00500-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Populus euphratica Oliv. has a high tolerance for drought, salinity, and alkalinity. The main purpose of this study is to explore the effects of environments of different salinity intensities on endophytic community structure and the possible roles of endophytes in the tolerance of host plants. The characterization of endogenous bacteria in diversity has been investigated by using the Illumina high-throughput sequencing technique. The research showed that endophytic bacteria of P. euphratica in an extremely saline environment had low species diversity, especially in sap tissue. The dominant phyla in all groups were Proteobacteria, Actinobacteria, and Bacteroidetes. Notably, Firmicutes (relative abundance >5%) was a different dominant phylum in the samples from the high-saline environment compared with the relatively low-saline-environment group. The linear discriminant analysis effect size (LEfSe) analysis found that there were significant differences in different saline environments of Cytophagaceae (family), Rhodobacteraceae (family), and Rhodobacterales (order). These results indicated that the composition of the endogenous bacterial community was related to the growth environment of host plants. The predictive analysis of KEGG pathways and enzymes showed that the abundance of some enzymes and metabolic pathways of endophytes of P. euphratica increased with the increase of soil salinity, and most of the enzymes were related to energy metabolism and carbohydrate metabolism. These findings suggested that the endogenous bacteria of the host plant had different expression mechanisms under different degrees of stress, and this mechanism was very obvious in the distribution of endophytes, while the function of the endogenous bacteria needs to be further explored. IMPORTANCE Euphrates poplar (Populus euphratica Oliv.), as the only tree species that grows in the desert, has tenacious vitality with the characteristics of cold tolerance, drought tolerance, salt-alkali tolerance, and wind-sand resistance. P. euphratica has a long growth cycle and a high growth rate, which can break wind, fix sand, green the environment, and protect farmland, making it an important afforestation tree species in arid and semiarid areas. The area of P. euphratica in Xinjiang accounts for 91.1% of its area in China. Studying the endophytic bacteria of P. euphratica can give people a systematic understanding of it and the adaptability of the endogenous flora to the host and special environments. In this study, by analyzing the endophytic bacteria of P. euphratica in different saline-alkali regions of Xinjiang, it was found that the bacteria in different tissues of P. euphratica changed with the change of soil salinity. Especially in the sap tissue of P. euphratica under extremely high salinity, the diversity of endogenous bacteria was significantly lower than that in other tissues. These differential bacteria under different salinities were mostly related to the stress resistance of themselves and the host. Not only that, we also selected a strain of Bacillus with high stress resistance from the tissues of P. euphratica, which can survive under the extreme conditions of 10% NaCl and pH 11. We obtained a genome completion map of this strain, named it Bacillus haynesii P19 (GenBank accession no. PRJNA648288), and tried to use it for fermentation but in a different work, so as to develop it into a promising industrial fermentation chassis bacterium. Therefore, this study was of great significance for the understanding of endophytic bacteria in P. euphratica and the acquisition of extremophilic microbial resources.
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22
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Liu H, Cheng J, Jin H, Xu Z, Yang X, Min D, Xu X, Shao X, Lu D, Qin B. Characterization of Rhizosphere and Endophytic Microbial Communities Associated with Stipa purpurea and Their Correlation with Soil Environmental Factors. PLANTS 2022; 11:plants11030363. [PMID: 35161345 PMCID: PMC8839079 DOI: 10.3390/plants11030363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/19/2022] [Accepted: 01/25/2022] [Indexed: 11/16/2022]
Abstract
This study was to explore the diversity of rhizosphere and endophytic microbial communities and the correlation with soil environmental factors of Stipa purpurea on the Qinghai-Tibetan Plateau. The bacterial phylum of Proteobacteria, Firmicutes and Bacteroidota, and the fungal phylum of Ascomycota, Basidiomycota and Zygomycota were dominant in microbial communities of S. purpurea in all three sampling sites. Multiple comparison analysis showed that there were significant differences in the composition of microbial communities in the roots, leaves and rhizosphere soil. Whether it is fungi or bacteria, the OTU abundance of rhizosphere soils was higher than that of leaves and roots at the same location, while the difference among locations was not obvious. Moreover, RDA analysis showed that Zygomycota, Cercozoa, Glomeromycota, Chytridiomycota and Rozellomycota possessed strongly positive associations with altitude, dehydrogenase, alkaline phosphatase, neutral phosphatase, available kalium and available phosphate, while Ascomycota was strongly negatively associated. Changes in ammonium nitrate, alkaline phosphatase, polyphenol oxidase, total phosphorus, and altitude had a significant impact on the bacterial communities in different habitats and altitudes. Taken together, we provide evidence that S. purpurea has abundant microbial communities in the alpine grassland of the Qinghai-Tibetan Plateau, whose composition and diversity are affected by various soil environmental factors.
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Affiliation(s)
- Haoyue Liu
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources/Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; (H.L.); (X.Y.); (D.M.); (X.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinan Cheng
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China;
| | - Hui Jin
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources/Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; (H.L.); (X.Y.); (D.M.); (X.X.)
- Yantai Zhongke Research Institute of Advanced Materials and Green Chemical Engineering, Yantai 264006, China
- Correspondence: (H.J.); (B.Q.)
| | - Zhongxiang Xu
- Animal, Plant & Food Inspection Center of Nanjing Customs, Nanjing 210000, China;
| | - Xiaoyan Yang
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources/Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; (H.L.); (X.Y.); (D.M.); (X.X.)
| | - Deng Min
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources/Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; (H.L.); (X.Y.); (D.M.); (X.X.)
| | - Xinxin Xu
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources/Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; (H.L.); (X.Y.); (D.M.); (X.X.)
| | - Xiangfeng Shao
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China;
| | - Dengxue Lu
- Institute of Biology, Gansu Academy of Sciences, Lanzhou 730000, China;
| | - Bo Qin
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources/Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; (H.L.); (X.Y.); (D.M.); (X.X.)
- Correspondence: (H.J.); (B.Q.)
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23
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Kobziar LN, Vuono D, Moore R, Christner BC, Dean T, Betancourt D, Watts AC, Aurell J, Gullett B. Wildland fire smoke alters the composition, diversity, and potential atmospheric function of microbial life in the aerobiome. ISME COMMUNICATIONS 2022; 2:8. [PMID: 37938277 PMCID: PMC9723787 DOI: 10.1038/s43705-022-00089-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 01/03/2022] [Accepted: 01/13/2022] [Indexed: 04/29/2023]
Abstract
The atmosphere contains a diverse reservoir of microbes but the sources and factors contributing to microbial aerosol variability are not well constrained. To advance understanding of microbial emissions in wildfire smoke, we used unmanned aircraft systems to analyze the aerosols above high-intensity forest fires in the western United States. Our results show that samples of the smoke contained ~four-fold higher concentrations of cells (1.02 ± 0.26 × 105 m-3) compared to background air, with 78% of microbes in smoke inferred to be viable. Fivefold higher taxon richness and ~threefold enrichment of ice nucleating particle concentrations in smoke implies that wildfires are an important source of diverse bacteria and fungi as well as meteorologically relevant aerosols. We estimate that such fires emit 3.71 × 1014 microbial cells ha-1 under typical wildfire conditions in western US forests and demonstrate that wildland biomass combustion has a large-scale influence on the local atmospheric microbial assemblages. Given the long-range transport of wildfire smoke emissions, these results expand the concept of a wildfire's perimeter of biological impact and have implications to biogeography, gene flow, the dispersal of plant, animal, and human pathogens, and meteorology.
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Affiliation(s)
- Leda N Kobziar
- Department of Natural Resources and Society, University of Idaho, Coeur d'Alene, ID, 83814, USA.
| | - David Vuono
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, 80401, USA
| | - Rachel Moore
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
- Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Brent C Christner
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Timothy Dean
- U. S. Environmental Protection Agency, Office of Research and Development, Research Triangle Park, NC, 27711, USA
| | - Doris Betancourt
- U. S. Environmental Protection Agency, Office of Research and Development, Research Triangle Park, NC, 27711, USA
| | - Adam C Watts
- Pacific Wildland Fire Sciences Laboratory, USDA Forest Service, Seattle, WA, 98103, USA
| | - Johanna Aurell
- University of Dayton Research Institute, 300 College Park, Dayton, OH, 45469, USA
| | - Brian Gullett
- U. S. Environmental Protection Agency, Office of Research and Development, Research Triangle Park, NC, 27711, USA
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24
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Darnaud M, De Vadder F, Bogeat P, Boucinha L, Bulteau AL, Bunescu A, Couturier C, Delgado A, Dugua H, Elie C, Mathieu A, Novotná T, Ouattara DA, Planel S, Saliou A, Šrůtková D, Yansouni J, Stecher B, Schwarzer M, Leulier F, Tamellini A. A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes. Nat Commun 2021; 12:6686. [PMID: 34795236 PMCID: PMC8602333 DOI: 10.1038/s41467-021-26963-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 10/28/2021] [Indexed: 01/14/2023] Open
Abstract
Mus musculus is the classic mammalian model for biomedical research. Despite global efforts to standardize breeding and experimental procedures, the undefined composition and interindividual diversity of the microbiota of laboratory mice remains a limitation. In an attempt to standardize the gut microbiome in preclinical mouse studies, here we report the development of a simplified mouse microbiota composed of 15 strains from 7 of the 20 most prevalent bacterial families representative of the fecal microbiota of C57BL/6J Specific (and Opportunistic) Pathogen-Free (SPF/SOPF) animals and the derivation of a standardized gnotobiotic mouse model called GM15. GM15 recapitulates extensively the functionalities found in the C57BL/6J SOPF microbiota metagenome, and GM15 animals are phenotypically similar to SOPF or SPF animals in two different facilities. They are also less sensitive to the deleterious effects of post-weaning malnutrition. In this work, we show that the GM15 model provides increased reproducibility and robustness of preclinical studies by limiting the confounding effect of fluctuation in microbiota composition, and offers opportunities for research focused on how the microbiota shapes host physiology in health and disease.
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Affiliation(s)
- Marion Darnaud
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France.
| | - Filipe De Vadder
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, Unité Mixte de Recherche 5242, 46 Allée d'Italie, 69364, Lyon, Cedex, 07, France
| | - Pascaline Bogeat
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Lilia Boucinha
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Anne-Laure Bulteau
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, Unité Mixte de Recherche 5242, 46 Allée d'Italie, 69364, Lyon, Cedex, 07, France
| | - Andrei Bunescu
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Céline Couturier
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Ana Delgado
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Hélène Dugua
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Céline Elie
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Alban Mathieu
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Tereza Novotná
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, 54922, Nový Hrádek, Czech Republic
| | | | - Séverine Planel
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Adrien Saliou
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Dagmar Šrůtková
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, 54922, Nový Hrádek, Czech Republic
| | - Jennifer Yansouni
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Bärbel Stecher
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich, 80336, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Martin Schwarzer
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, 54922, Nový Hrádek, Czech Republic
| | - François Leulier
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, Unité Mixte de Recherche 5242, 46 Allée d'Italie, 69364, Lyon, Cedex, 07, France
| | - Andrea Tamellini
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
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Comparative genomic analysis of hyper-ammonia producing Acetoanaerobium sticklandii DSM 519 with purinolytic Gottschalkia acidurici 9a and pathogenic Peptoclostridium difficile 630. Genomics 2021; 113:4196-4205. [PMID: 34780936 DOI: 10.1016/j.ygeno.2021.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/18/2021] [Accepted: 11/10/2021] [Indexed: 10/19/2022]
Abstract
Acetoanaerobium sticklandii DSM519 (CST) is a hype-ammonia producing non-pathogenic anaerobe that can use amino acids as important carbon and energy sources through the Stickland reactions. Biochemical aspects of this organism have been extensively studied, but systematic studies addressing its metabolic discrepancy remain scant. In this perspective, we have intensively analyzed its genomic and metabolic characteristics to comprehend the evolutionary conservation of amino acid catabolism by a comparative genomic approach. The whole-genome data indicated that CST has shown a phylogenomic similarity with hyper-ammonia producing, purinolytic, and proteolytic pathogenic Clostridia. CST has shown to common genomic context sharing across the purinolytic Gottschalkia acidurici 9a and pathogenic Peptoclostridium difficile 630. Genome syntenic analysis described that syntenic orthologs might be originated from the recent ancestor at a slow evolution rate and syntenic-out paralogs evolved from either CDF or CAC via α-event and β-event. Collinearity of either gene orders or gene families was adjusted with syntenic out-paralogs across these genomes. The genome-wide metabolic analysis predicted 11 unique putative metabolic subsystems from the CST genome for amino acid catabolism and hydrogen production. The in silico analysis of our study revealed that a characteristic system for amino acid catabolism-directed biofuel synthesis might have slowly evolved and established as a core genomic content of CST.
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Doelman A, Tigchelaar S, McConeghy B, Sinha S, Keung MS, Manouchehri N, Webster M, Fisk S, Morrison C, Streijger F, Nislow C, Kwon BK. Characterization of the gut microbiome in a porcine model of thoracic spinal cord injury. BMC Genomics 2021; 22:775. [PMID: 34717545 PMCID: PMC8557039 DOI: 10.1186/s12864-021-07979-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 09/01/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The gut microbiome is a diverse network of bacteria which inhabit our digestive tract and is crucial for efficient cellular metabolism, nutrient absorption, and immune system development. Spinal cord injury (SCI) disrupts autonomic function below the level of injury and can alter the composition of the gut microbiome. Studies in rodent models have shown that SCI-induced bacterial imbalances in the gut can exacerbate the spinal cord damage and impair recovery. In this study we, for the first time, characterized the composition of the gut microbiome in a Yucatan minipig SCI model. We compared the relative abundance of the most dominant bacterial phyla in control samples to those collected from animals who underwent a contusion-compression SCI at the 2nd or 10th Thoracic level. RESULTS We identify specific bacterial fluctuations that are unique to SCI animals, which were not found in uninjured animals given the same dietary regimen or antibiotic administration. Further, we identified a specific time-frame, "SCI-acute stage", during which many of these bacterial fluctuations occur before returning to "baseline" levels. CONCLUSION This work presents a dynamic view of the microbiome changes that accompany SCI, establishes a resource for future studies and to understand the changes that occur to gut microbiota after spinal cord injury and may point to a potential therapeutic target for future treatment.
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Affiliation(s)
- Adam Doelman
- International Collaboration on Repair Discoveries, University of British Columbia, Vancouver, BC Canada
| | - Seth Tigchelaar
- International Collaboration on Repair Discoveries, University of British Columbia, Vancouver, BC Canada
| | - Brian McConeghy
- Sequencing and Bioinformatics Consortium, University of British Columbia, Vancouver, BC Canada
| | - Sunita Sinha
- Sequencing and Bioinformatics Consortium, University of British Columbia, Vancouver, BC Canada
| | - Martin S. Keung
- International Collaboration on Repair Discoveries, University of British Columbia, Vancouver, BC Canada
| | - Neda Manouchehri
- International Collaboration on Repair Discoveries, University of British Columbia, Vancouver, BC Canada
| | - Megan Webster
- International Collaboration on Repair Discoveries, University of British Columbia, Vancouver, BC Canada
| | - Shera Fisk
- International Collaboration on Repair Discoveries, University of British Columbia, Vancouver, BC Canada
| | - Charlotte Morrison
- International Collaboration on Repair Discoveries, University of British Columbia, Vancouver, BC Canada
| | - Femke Streijger
- International Collaboration on Repair Discoveries, University of British Columbia, Vancouver, BC Canada
| | - Corey Nislow
- Sequencing and Bioinformatics Consortium, University of British Columbia, Vancouver, BC Canada
| | - Brian K. Kwon
- International Collaboration on Repair Discoveries, University of British Columbia, Vancouver, BC Canada
- Department of Orthopedics, Vancouver Spine Surgery Institute, University of British Columbia, Vancouver, BC Canada
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27
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Vignale FA, Kurth D, Lencina AI, Poiré DG, Chihuailaf E, Muñoz-Herrera NC, Novoa F, Contreras M, Turjanski AG, Farías ME. Geobiology of Andean Microbial Ecosystems Discovered in Salar de Atacama, Chile. Front Microbiol 2021; 12:762076. [PMID: 34777316 PMCID: PMC8581658 DOI: 10.3389/fmicb.2021.762076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/28/2021] [Indexed: 11/23/2022] Open
Abstract
The Salar de Atacama in the Chilean Central Andes harbors unique microbial ecosystems due to extreme environmental conditions, such as high altitude, low oxygen pressure, high solar radiation, and high salinity. Combining X-ray diffraction analyses, scanning electron microscopy and molecular diversity studies, we have characterized twenty previously unexplored Andean microbial ecosystems in eight different lakes and wetlands from the middle-east and south-east regions of this salt flat. The mats and microbialites studied are mainly formed by calcium carbonate (aragonite and calcite) and halite, whereas the endoevaporites are composed predominantly of gypsum and halite. The carbonate-rich mats and microbialites are dominated by Bacteroidetes and Proteobacteria phyla. Within the phylum Proteobacteria, the most abundant classes are Alphaproteobacteria, Gammaproteobacteria and Deltaproteobacteria. While in the phylum Bacteroidetes, the most abundant classes are Bacteroidia and Rhodothermia. Cyanobacteria, Chloroflexi, Planctomycetes, and Verrucomicrobia phyla are also well-represented in the majority of these systems. Gypsum endoevaporites, on the contrary, are dominated by Proteobacteria, Bacteroidetes, and Euryarchaeota phyla. The Cyanobacteria phylum is also abundant in these systems, but it is less represented in comparison to mats and microbialites. Regarding the eukaryotic taxa, diatoms are key structural components in most of the microbial ecosystems studied. The genera of diatoms identified were Achnanthes, Fallacia, Halamphora, Mastogloia, Navicula, Nitzschia, and Surirella. Normally, in the mats and microbialites, diatoms form nano-globular carbonate aggregates with filamentous cyanobacteria and other prokaryotic cells, suggesting their participation in the mineral precipitation process. This work expands our knowledge of the microbial ecosystems inhabiting the extreme environments from the Central Andes region, which is important to ensure their protection and conservation.
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Affiliation(s)
- Federico A. Vignale
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Argentina
- Laboratorio de Bioinformática Estructural, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN)-CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Daniel Kurth
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Argentina
| | - Agustina I. Lencina
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Argentina
| | - Daniel G. Poiré
- Centro de Investigaciones Geológicas (CIG), Universidad Nacional de La Plata (UNLP)-CONICET, La Plata, Argentina
| | | | | | | | | | - Adrián G. Turjanski
- Laboratorio de Bioinformática Estructural, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN)-CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María E. Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Argentina
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28
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Gaballa A, Cheng RA, Trmcic A, Kovac J, Kent DJ, Martin NH, Wiedmann M. Development of a database and standardized approach for rpoB sequence-based subtyping and identification of aerobic spore-forming Bacillales. J Microbiol Methods 2021; 191:106350. [PMID: 34710512 DOI: 10.1016/j.mimet.2021.106350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 10/20/2022]
Abstract
Aerobic spore-forming Bacillales are a highly diverse and ubiquitous group that includes organisms that cause foodborne illnesses and food spoilage. Classical microbiological and biochemical identification of members of the order Bacillales represents a challenge due to the diversity of organisms in this group as well as the fact that the phenotypic-based taxonomic assignment of some named species in this group is not consistent with their phylogenomic characteristics. DNA-sequencing-based tools, on the other hand, can be fast and cost-effective, and can provide for a more reliable identification and characterization of Bacillales isolates. In comparison to 16S rDNA, rpoB was shown to better discriminate between Bacillales isolates and to allow for improved taxonomic assignment to the species level. However, the lack of a publicly accessible rpoB database, as well as the lack of standardized protocols for rpoB-based typing and strain identification, is a major challenge. Here, we report (i) the curation of a DNA sequence database for rpoB-based subtype classification of Bacillales isolates; (ii) the development of standardized protocols for generating rpoB sequence data, and a scheme for rpoB-based initial taxonomic identification of Bacillales isolates at the species level; and (iii) the integration of the database in a publicly accessible online platform that allows for the analysis of rpoB sequence data from uncharacterized Bacillales isolates. Specifically, we curated a database of DNA sequences for a 632-nt internal variable region within the rpoB gene from representative Bacillales reference type strains and a large number of isolates that we have previously isolated and characterized through multiple projects. As of May 21, 2021, the rpoB database contained more than 8350 rpoB sequences representing 1902 distinct rpoB allelic types that can be classified into 160 different genera. The database also includes 1129 rpoB sequences for representative Bacillales reference type strains as available on May 21, 2021 in the NCBI database. The rpoB database is integrated into the online Food Microbe Tracker platform (www.foodmicrobetracker.com) and can be queried using the integrated BLAST tool to initially subtype and taxonomically identify aerobic and facultative anaerobic spore-formers. While whole-genome sequencing is increasingly used in bacterial taxonomy, the rpoB sequence-based identification scheme described here provides a valuable tool as it allows for rapid and cost-effective initial isolate characterization, which can help to identify and characterize foodborne pathogens and food spoilage bacteria. In addition, the database and primers described here can also be adopted for metagenomics approaches that include rpoB as a target, improving discriminatory power and identification over what can be achieved using 16S rDNA as a target.
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Affiliation(s)
- Ahmed Gaballa
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA.
| | - Rachel A Cheng
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Aljosa Trmcic
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Jasna Kovac
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA; Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - David J Kent
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Nicole H Martin
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
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Liu H, Ye X, Chen S, Sun A, Duan X, Zhang Y, Zou H, Zhang Y. Chitosan as additive affects the bacterial community, accelerates the removals of antibiotics and related resistance genes during chicken manure composting. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 792:148381. [PMID: 34146805 DOI: 10.1016/j.scitotenv.2021.148381] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/07/2021] [Accepted: 06/07/2021] [Indexed: 06/12/2023]
Abstract
Manures, storages for antibiotic resistance genes (ARGs), pollute soil and water as well as endanger human health. Recently, we have been searching a better solution to remove antibiotics and ARGs during aerobic composting. Here, the dynamics of chitosan addition on the profiles of 71 ARGs, bacterial communities, chlortetracycline (CTC), ofloxacin (OFX) were investigated in chicken manure composting and compared with zeolite addition. Chitosan addition effectively reduces antibiotics contents (CTC under detection limit, OFX 90.96%), amounts (18) and abundance (56.7%, 11.1% higher than zeolite addition) of ARGs and mobile genetic elements (MGEs) after 42 days composting. Network analysis indicated that a total of 27 genera strains assigned into 4 phyla (Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes) were the potential hosts of ARGs. Redundancy analysis (RDA) demonstrated that bacterial community succession is the main contributor in the variation of ARGs. Overall, chitosan addition may effect bacterial composition by influencing physic-chemical properties and the concentration of antibiotics, Cu2+, Zn2+ to reduce the risk of ARG transmission. This study gives a new strategy about antibiotics and ARGs removal from composting on the basis of previous studies.
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Affiliation(s)
- Hongdou Liu
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China
| | - Xuhong Ye
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China
| | - Songling Chen
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China
| | - Aobo Sun
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China
| | - Xinying Duan
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China
| | - Yanqing Zhang
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China; Institute of Agricultural Environment and Sustainable Development, Chinese Academy of Agricultural Sciences, China
| | - Hongtao Zou
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China.
| | - Yulong Zhang
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China
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30
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Czatzkowska M, Harnisz M, Korzeniewska E, Rusanowska P, Bajkacz S, Felis E, Jastrzębski JP, Paukszto Ł, Koniuszewska I. The impact of antimicrobials on the efficiency of methane fermentation of sewage sludge, changes in microbial biodiversity and the spread of antibiotic resistance. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125773. [PMID: 33831706 DOI: 10.1016/j.jhazmat.2021.125773] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 03/11/2021] [Accepted: 03/25/2021] [Indexed: 05/23/2023]
Abstract
The study was designed to simultaneously evaluate the influence of high doses (512-1024 µg/g) the most commonly prescribed antimicrobials on the efficiency of anaerobic digestion of sewage sludge, qualitative and quantitative changes in microbial consortia responsible for the fermentation process, the presence of methanogenic microorganisms, and the fate of antibiotic resistance genes (ARGs). The efficiency of antibiotic degradation during anaerobic treatment was also determined. Metronidazole, amoxicillin and ciprofloxacin exerted the greatest effect on methane fermentation by decreasing its efficiency. Metronidazole, amoxicillin, cefuroxime and sulfamethoxazole were degraded in 100%, whereas ciprofloxacin and nalidixic acid were least susceptible to degradation. The most extensive changes in the structure of digestate microbiota were observed in sewage sludge exposed to metronidazole, where a decrease in the percentage of bacteria of the phylum Bacteroidetes led to an increase in the proportions of bacteria of the phyla Firmicutes and Proteobacteria. The results of the analysis examining changes in the concentration of the functional methanogen gene (mcrA) did not reflect the actual efficiency of methane fermentation. In sewage sludge exposed to antimicrobials, a significant increase was noted in the concentrations of β-lactam, tetracycline and fluoroquinolone ARGs and integrase genes, but selective pressure was not specific to the corresponding ARGs.
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Affiliation(s)
- Małgorzata Czatzkowska
- Department of Water Protection Engineering and Environmental Microbiology, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720 Olsztyn, Poland
| | - Monika Harnisz
- Department of Water Protection Engineering and Environmental Microbiology, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720 Olsztyn, Poland.
| | - Ewa Korzeniewska
- Department of Water Protection Engineering and Environmental Microbiology, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720 Olsztyn, Poland
| | - Paulina Rusanowska
- Department of Environmental Engineering, University of Warmia and Mazury in Olsztyn, Warszawska 117a, 10-720 Olsztyn, Poland
| | - Sylwia Bajkacz
- Department of Inorganic, Analytical Chemistry and Electrochemistry, Silesian University of Technology, Krzywoustego 6, 44-100 Gliwice, Poland; Centre for Biotechnology, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland
| | - Ewa Felis
- Department of Environmental Biotechnology, Silesian University of Technology, Akademicka 2, 44-100 Gliwice, Poland; Centre for Biotechnology, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland
| | - Jan P Jastrzębski
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - Łukasz Paukszto
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - Izabela Koniuszewska
- Department of Water Protection Engineering and Environmental Microbiology, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720 Olsztyn, Poland
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Browne HP, Almeida A, Kumar N, Vervier K, Adoum AT, Viciani E, Dawson NJR, Forster SC, Cormie C, Goulding D, Lawley TD. Host adaptation in gut Firmicutes is associated with sporulation loss and altered transmission cycle. Genome Biol 2021; 22:204. [PMID: 34348764 PMCID: PMC8340488 DOI: 10.1186/s13059-021-02428-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 07/01/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Human-to-human transmission of symbiotic, anaerobic bacteria is a fundamental evolutionary adaptation essential for membership of the human gut microbiota. However, despite its importance, the genomic and biological adaptations underpinning symbiont transmission remain poorly understood. The Firmicutes are a dominant phylum within the intestinal microbiota that are capable of producing resistant endospores that maintain viability within the environment and germinate within the intestine to facilitate transmission. However, the impact of host transmission on the evolutionary and adaptive processes within the intestinal microbiota remains unknown. RESULTS We analyze 1358 genomes of Firmicutes bacteria derived from host and environment-associated habitats. Characterization of genomes as spore-forming based on the presence of sporulation-predictive genes reveals multiple losses of sporulation in many distinct lineages. Loss of sporulation in gut Firmicutes is associated with features of host-adaptation such as genome reduction and specialized metabolic capabilities. Consistent with these data, analysis of 9966 gut metagenomes from adults around the world demonstrates that bacteria now incapable of sporulation are more abundant within individuals but less prevalent in the human population compared to spore-forming bacteria. CONCLUSIONS Our results suggest host adaptation in gut Firmicutes is an evolutionary trade-off between transmission range and colonization abundance. We reveal host transmission as an underappreciated process that shapes the evolution, assembly, and functions of gut Firmicutes.
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Affiliation(s)
- Hilary P Browne
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.
| | - Alexandre Almeida
- Wellcome Sanger Institute, Hinxton, UK
- European Bioinformatics Institute, Hinxton, UK
| | - Nitin Kumar
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Kevin Vervier
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | | | - Elisa Viciani
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Nicholas J R Dawson
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Samuel C Forster
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, 3168, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria, 3800, Australia
| | | | | | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.
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Abdelhamid MK, Rychlik I, Hess C, Hatfaludi T, Crhanova M, Karasova D, Lagler J, Liebhart D, Hess M, Paudel S. Typhlitis induced by Histomonas meleagridis affects relative but not the absolute Escherichia coli counts and invasion in the gut in turkeys. Vet Res 2021; 52:92. [PMID: 34158121 PMCID: PMC8220719 DOI: 10.1186/s13567-021-00962-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 05/28/2021] [Indexed: 12/22/2022] Open
Abstract
Unlike in chickens, dynamics of the gut microbiome in turkeys is limitedly understood and no data were yet published in context of pathological changes following experimental infection. Thus, the impact of Histomonas meleagridis-associated inflammatory changes in the caecal microbiome, especially the Escherichia coli population and their caecal wall invasion in turkeys was investigated. Birds experimentally inoculated with attenuated and/or virulent H. meleagridis and non-inoculated negative controls were divided based on the severity of macroscopic caecal lesions. The high throughput amplicon sequencing of 16SrRNA showed that the species richness and diversity of microbial community significantly decreased in severely affected caeca. The relative abundances of operational taxonomic units belonging to Anaerotignum lactatifermentans, E. coli, and Faecalibacterium prausnitzii were higher and paralleled with a decreased abundances of those belonging to Alistipes putredinis, Streptococcusalactolyticus, Lactobacillus salivarius and Lactobacillus reuteri in birds with the highest lesion scores. Although the relative abundance of E. coli was higher, the absolute count was not affected by the severity of pathological lesions. Immunohistochemistry showed that E. coli was only present in the luminal content of caecum and did not penetrate even severely inflamed and necrotized caecal wall. Overall, it was demonstrated that the fundamental shift in caecal microbiota of turkeys infected with H. meleagridis was attributed to the pathology induced by the parasite, which only led to relative but not absolute changes in E. coli population. Furthermore, E. coli cells did not show tendency to penetrate the caecal tissue even when the intestinal mucosal barriers were severely compromised.
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Affiliation(s)
- Mohamed Kamal Abdelhamid
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Department of Pathology, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Ivan Rychlik
- Department of Immunology, Veterinary Research Institute, 62100, Brno, Czech Republic
| | - Claudia Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Tamas Hatfaludi
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Christian Doppler Laboratory for Innovative Poultry Vaccines (IPOV), University of Veterinary Medicine, Vienna, Austria
| | - Magdalena Crhanova
- Department of Immunology, Veterinary Research Institute, 62100, Brno, Czech Republic
| | - Daniela Karasova
- Department of Immunology, Veterinary Research Institute, 62100, Brno, Czech Republic
| | - Julia Lagler
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Section of Immunology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Dieter Liebhart
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Michael Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Christian Doppler Laboratory for Innovative Poultry Vaccines (IPOV), University of Veterinary Medicine, Vienna, Austria
| | - Surya Paudel
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.
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Kubasova T, Seidlerova Z, Rychlik I. Ecological Adaptations of Gut Microbiota Members and Their Consequences for Use as a New Generation of Probiotics. Int J Mol Sci 2021; 22:5471. [PMID: 34067354 PMCID: PMC8196900 DOI: 10.3390/ijms22115471] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/19/2021] [Accepted: 05/19/2021] [Indexed: 12/16/2022] Open
Abstract
In this review, we link ecological adaptations of different gut microbiota members with their potential for use as a new generation of probiotics. Gut microbiota members differ in their adaptations to survival in aerobic environments. Interestingly, there is an inverse relationship between aerobic survival and abundance or potential for prolonged colonization of the intestinal tract. Facultative anaerobes, aerotolerant Lactobacilli and endospore-forming Firmicutes exhibit high fluctuation, and if such bacteria are to be used as probiotics, they must be continuously administered to mimic their permanent supply from the environment. On the other hand, species not expressing any form of aerobic resistance, such as those from phylum Bacteroidetes, commonly represent host-adapted microbiota members characterized by vertical transmission from mothers to offspring, capable of long-term colonization following a single dose administration. To achieve maximal probiotic efficacy, the mode of their administration should thus reflect their natural ecology.
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Affiliation(s)
| | | | - Ivan Rychlik
- Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (T.K.); (Z.S.)
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34
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Diallo M, Kengen SWM, López-Contreras AM. Sporulation in solventogenic and acetogenic clostridia. Appl Microbiol Biotechnol 2021; 105:3533-3557. [PMID: 33900426 PMCID: PMC8102284 DOI: 10.1007/s00253-021-11289-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/03/2021] [Accepted: 04/07/2021] [Indexed: 02/07/2023]
Abstract
The Clostridium genus harbors compelling organisms for biotechnological production processes; while acetogenic clostridia can fix C1-compounds to produce acetate and ethanol, solventogenic clostridia can utilize a wide range of carbon sources to produce commercially valuable carboxylic acids, alcohols, and ketones by fermentation. Despite their potential, the conversion by these bacteria of carbohydrates or C1 compounds to alcohols is not cost-effective enough to result in economically viable processes. Engineering solventogenic clostridia by impairing sporulation is one of the investigated approaches to improve solvent productivity. Sporulation is a cell differentiation process triggered in bacteria in response to exposure to environmental stressors. The generated spores are metabolically inactive but resistant to harsh conditions (UV, chemicals, heat, oxygen). In Firmicutes, sporulation has been mainly studied in bacilli and pathogenic clostridia, and our knowledge of sporulation in solvent-producing or acetogenic clostridia is limited. Still, sporulation is an integral part of the cellular physiology of clostridia; thus, understanding the regulation of sporulation and its connection to solvent production may give clues to improve the performance of solventogenic clostridia. This review aims to provide an overview of the triggers, characteristics, and regulatory mechanism of sporulation in solventogenic clostridia. Those are further compared to the current knowledge on sporulation in the industrially relevant acetogenic clostridia. Finally, the potential applications of spores for process improvement are discussed.Key Points• The regulatory network governing sporulation initiation varies in solventogenic clostridia.• Media composition and cell density are the main triggers of sporulation.• Spores can be used to improve the fermentation process.
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Affiliation(s)
- Mamou Diallo
- Wageningen Food and Biobased Research, Wageningen, The Netherlands.
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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Soto-Avila L, Merce RC, Santos W, Castañeda N, Gutierrez-Ríos RM. Distribution and preservation of the components of the engulfment. What is beyond representative genomes? PLoS One 2021; 16:e0246651. [PMID: 33651833 PMCID: PMC7924749 DOI: 10.1371/journal.pone.0246651] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/24/2021] [Indexed: 12/16/2022] Open
Abstract
Engulfment requires the coordinated, targeted synthesis and degradation of peptidoglycan at the leading edge of the engulfing membrane to allow the mother cell to completely engulf the forespore. Proteins such as the DMP and Q:AH complexes in Bacillus subtilis are essential for engulfment, as are a set of accessory proteins including GerM and SpoIIB, among others. Experimental and bioinformatic studies of these proteins in bacteria distinct from Bacillus subtilis indicate that fundamental differences exist regarding the organization and mechanisms used to successfully perform engulfment. As a consequence, the distribution and prevalence of the proteins involved in engulfment and other proteins that participate in different sporulation stages have been studied using bioinformatic approaches. These works are based on the prediction of orthologs in the genomes of representative Firmicutes and have been helpful in tracing hypotheses about the origin and evolution of sporulation genes, some of which have been postulated as sporulation signatures. To date, an extensive study of these signatures outside of the representative Firmicutes is not available. Here, we asked whether phyletic profiles of proteins involved in engulfment can be used as signatures able to describe the sporulation phenotype. We tested this hypothesis in a set of 954 Firmicutes, finding preserved phyletic profiles defining signatures at the genus level. Finally, a phylogenetic reconstruction based on non-redundant phyletic profiles at the family level shows the non-monophyletic origin of these proteins due to gain/loss events along the phylum Firmicutes.
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Affiliation(s)
- Lizeth Soto-Avila
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico
- Centro de Investigacion en Dinamica Celular, Instituto de Investigacion en Ciencias Basicas y Aplicadas, Universidad Autonoma del Estado de Morelos (UAEM), Cuernavaca, Morelos, Mexico
| | - Ricardo Ciria Merce
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico
| | - Walter Santos
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico
| | - Nori Castañeda
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico
| | - Rosa-María Gutierrez-Ríos
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico
- * E-mail:
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36
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Puentes Jácome LA, Lomheim L, Gaspard S, Edwards EA. Biodegradation of Lindane (γ-Hexachlorocyclohexane) To Nontoxic End Products by Sequential Treatment with Three Mixed Anaerobic Microbial Cultures. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:2968-2979. [PMID: 33557520 DOI: 10.1021/acs.est.0c07221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The γ isomer of hexachlorocyclohexane (HCH), also known as lindane, is a carcinogenic persistent organic pollutant. Lindane was used worldwide as an agricultural insecticide. Legacy soil and groundwater contamination with lindane and other HCH isomers is still a big concern. The biotic reductive dechlorination of HCH to nondesirable and toxic lower chlorinated compounds such as monochlorobenzene (MCB) and benzene, among others, has been broadly documented. Here, we demonstrate that complete biodegradation of lindane to nontoxic end products is attainable using a sequential treatment approach with three mixed anaerobic microbial cultures referred to as culture I, II, and III. Biaugmentation with culture I achieved dechlorination of lindane to MCB and benzene. Culture II was able to dechlorinate MCB to benzene, and finally, culture III carried out methanogenic benzene degradation. Distinct Dehalobacter populations, corresponding to different 16S rRNA amplicon sequence variants in culture I and culture II, were responsible for lindane and MCB dechlorination, respectively. This study continues to highlight key roles of Dehalobacter as chlorobenzene- and HCH -respiring bacteria and demonstrates that sequential treatment with specialized anaerobic cultures may be explored at field sites in order to address legacy soil and groundwater contamination with HCH.
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Affiliation(s)
- Luz A Puentes Jácome
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Line Lomheim
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Sarra Gaspard
- Laboratory COVACHIMM2E, Université des Antilles, Pointe à Pitre, Guadeloupe, French West-Indies 97157, France
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3E5, Canada
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Abstract
Endospore formation is used by members of the phylum Firmicutes to withstand extreme environmental conditions. Several recent studies have proposed endospore formation in species outside of Firmicutes, particularly in Rhodobacter johrii and Serratia marcescens, members of the phylum Proteobacteria. Here, we aimed to investigate endospore formation in these two species by using advanced imaging and analytical approaches. Examination of the phase-bright structures observed in R. johrii and S. marcescens using cryo-electron tomography failed to identify endospores or stages of endospore formation. We determined that the phase-bright objects in R. johrii cells were triacylglycerol storage granules and those in S. marcescens were aggregates of cellular debris. In addition, R. johrii and S. marcescens containing phase-bright objects do not possess phenotypic and genetic features of endospores, including enhanced resistance to heat, presence of dipicolinic acid, or the presence of many of the genes associated with endospore formation. Our results support the hypothesis that endospore formation is restricted to the phylum Firmicutes.Importance: Bacterial endospore formation is an important process that allows the formation of dormant life forms called spores. As such, organisms able to sporulate can survive harsh environmental conditions for hundreds of years. Here, we follow up on previous claims that two members of Proteobacteria, Serratia marcescens and Rhodobacter johrii, are able to form spores. We conclude that those claims were incorrect and show that the putative spores in R. johrii and S. marcescens are storage granules and cellular debris, respectively. This study concludes that endospore formation is still unique to the phylum Firmicutes.
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Ting ASY, Zoqratt MZHM, Tan HS, Hermawan AA, Talei A, Khu ST. Bacterial and eukaryotic microbial communities in urban water systems profiled via Illumina MiSeq platform. 3 Biotech 2021; 11:40. [PMID: 33479595 PMCID: PMC7794265 DOI: 10.1007/s13205-020-02617-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/26/2020] [Indexed: 01/04/2023] Open
Abstract
Microbial communities from a lake and river flowing through a highly dense urbanized township in Malaysia were profiled by sequencing amplicons of the 16S V3-V4 and 18S V9 hypervariable rRNA gene regions via Illumina MiSeq. Results revealed that Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes were the dominant prokaryotic phyla; whereas, eukaryotic communities were predominantly of the SAR clade and Opisthokonta. The abundance of Pseudomonas and Flavobacterium in all sites suggested the possible presence of pathogens in the urban water systems, supported by the most probable number (MPN) values of more than 1600 per 100 mL. Urbanization could have impacted the microbial communities as transient communities (clinical, water-borne and opportunistic pathogens) coexisted with common indigenous aquatic communities (Cyanobacteria). It was concluded that in urban water systems, microbial communities vary in their abundance of microbial phyla detected along the water systems. The influences of urban land use and anthropogenic activities influenced the physicochemical properties and the microbial dynamics in the water systems. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-020-02617-3.
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Affiliation(s)
- Adeline Su Yien Ting
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 46150 Bandar Sunway, Selangor Darul Ehsan Malaysia
| | - Muhammad Zarul Hanifah Md Zoqratt
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Petaling Jaya, Selangor Malaysia
| | - Hock Siew Tan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
| | - Andreas Aditya Hermawan
- School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
| | - Amin Talei
- School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
| | - Soon Thiam Khu
- School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
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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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Izadi P, Fontmorin JM, Lim SS, Head IM, Yu EH. Enhanced bio-production from CO 2 by microbial electrosynthesis (MES) with continuous operational mode. Faraday Discuss 2021; 230:344-359. [PMID: 34259692 DOI: 10.1039/d0fd00132e] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Technologies able to convert CO2 to various feedstocks for fuels and chemicals are emerging due to the urge of reducing greenhouse gas emissions and de-fossilizing chemical production. Microbial electrosynthesis (MES) has been shown a promising technique to synthesize organic products particularly acetate using microorganisms and electrons. However, the efficiency of the system is low. In this study, we demonstrated the simple yet efficient strategy in enhancing the efficiency of MES by applying continuous feeding regime. Compared to the fed-batch system, continuous operational mode provided better control of pH and constant medium refreshment, resulting in higher acetate production rate and more diverse bio-products, when the cathodic potential of -1.0 V Ag/AgCl and dissolved CO2 were provided. It was observed that hydraulic retention time (HRT) had a direct effect on the pattern of production, acetate production rate and coulombic efficiency. At HRT of 3 days, pH was around 5.2 and acetate was the dominant product with the highest production rate of 651.8 ± 214.2 ppm per day and a significant coulombic efficiency of 90%. However at the HRT of 7 days, pH was lower at around 4.5, and lower but stable acetate production rate of 280 ppm per day and a maximum coulombic efficiency of 80% was obtained. In addition, more diverse and longer chain products, such as butyrate, isovalerate and caproate, were detected with low concentrations only at the HRT of 7 days. Although microbial community analysis showed the change in the planktonic cells communities after switching the fed-batch mode to continuous feeding regime, Acetobacterium still remained as the responsible bacteria for CO2 reduction to acetate, dominating the cathodic biofilm.
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Affiliation(s)
- Paniz Izadi
- School of Engineering, Newcastle University, Newcastle upon Tyne, UK.
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B Henry A, Maung CEH, Kim KY. Metagenomic analysis reveals enhanced biodiversity and composting efficiency of lignocellulosic waste by thermoacidophilic effective microorganism (tEM). JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 276:111252. [PMID: 32927192 DOI: 10.1016/j.jenvman.2020.111252] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 08/13/2020] [Accepted: 08/16/2020] [Indexed: 06/11/2023]
Abstract
Composting is a microbiological process that converts organic waste into organic soil amendment. We reveal enhanced biodiversity and microbial population with subsequent enhancement of composting efficiency of lignocellulosic waste using thermoacidophilic effective microorganisms (tEM). Composting with tEM + shading (tEMA) or tEM without shading (tEMB) increased the average microbial population by 12.0% or 6.7%, respectively compared to non-tEM composting without shading/control (C). The biodiversity in tEMA or tEMB treated groups was increased by 34.7% or 43.7%, respectively, compared to C. The highest increase in population (31.7% and 9.4%) and diversity (91.2% and 91.6%) were observed in tEMA and tEMB at 30 d, respectively. Regarding microbial structure, the most dominant phylum shifted from Proteobacteria to Bacteroidetes during composting. From 60 to 120 d, tEM notably improved the average abundance of Firmicutes (mainly Bacillus) by 166.7% and 75.8% in tEMA and tEMB groups, respectively. The overall gradation rate of large compost granules (<2 mm) increased by 36.4% and 24.7%, following tEMA and tEMB treatment, respectively. The average rate of increase in bulk density was 42.6% or 33.3% by tEMA or tEMB, respectively, compared to C. We reveal the major differences in microbial structure, including a higher abundance of beneficial microbes like Bacillus in tEM treated composts. The study revealed that tEM could improve biodiversity and population of microbes, especially during thermophilic phase (above 45 °C), with a subsequent increase in composting rate, mineralization, and product quality. The results of this study are particularly invaluable in the areas of environmental conservation and organic agriculture.
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Affiliation(s)
- Ajuna B Henry
- Department of Agriculture Chemistry, College of Agriculture and Life Science, Chonnam National University, 77 Yongbong-ro, Buk-Ku Gwangju, 61186, Republic of Korea.
| | - Chaw Ei Htwe Maung
- Department of Agriculture Chemistry, College of Agriculture and Life Science, Chonnam National University, 77 Yongbong-ro, Buk-Ku Gwangju, 61186, Republic of Korea.
| | - Kil Yong Kim
- Department of Agriculture Chemistry, College of Agriculture and Life Science, Chonnam National University, 77 Yongbong-ro, Buk-Ku Gwangju, 61186, Republic of Korea.
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Abstract
Within the last decade, our understanding of the role of the intestinal microbiota in health and disease has rapidly increased due to significant advances in next-generation sequencing technologies. Scientists have discovered more and more gut microbes with supposedly "beneficial" roles for human health and are starting to identify the underlying mechanisms. In this review, we summarize the latest knowledge about the human intestinal microbiota, including the intestinal bacteriome, virome and mycobiome. We discuss the function that recent studies attribute to the intestinal microbiota in preventing or controlling selected diseases and present recent research on biotherapeutic approaches to control these diseases.
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Affiliation(s)
- Pipat Piewngam
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, U.S. National Institutes of Health, 50 South Drive, Bethesda, Maryland 20814, USA
| | - François De Mets
- Department of Biology, Georgetown University, Washington, DC, 20057, USA
| | - Michael Otto
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, U.S. National Institutes of Health, 50 South Drive, Bethesda, Maryland 20814, USA
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Sun X, Zhao J, Wang Q, Ren X, Li R, Kumar Awasthi M, Zhang Z. Behaviors and related mechanisms of Zn resistance and antibiotic resistance genes during co-composting of erythromycin manufacturing wastes and pig manure. BIORESOURCE TECHNOLOGY 2020; 318:124048. [PMID: 32871319 DOI: 10.1016/j.biortech.2020.124048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/15/2020] [Accepted: 08/19/2020] [Indexed: 06/11/2023]
Abstract
This study explored the fate of Zn- resistance genes (ZRGs), antibiotic- resistance genes (ARGs) and related mechanisms associated with bacterial communities during co-composting of erythromycin manufacturing wastes (EMW) and pig manure (PM) at the ratio of 0% (control), 5% (L) and 20% (H) (PM basis). The relative abundance (RAs) of erm genes in most treatments were decreased by 77.75-99.97% after composting. But total RA of czc genes were increased by 8.34, 15.86 and 12.03 times in control, L and H treatment respectively. The higher EMW in H showed a negative impact on removing of erm genes and aggravated the enrichment of ZRGs compared with control and L. Redundancy analysis showed that Firmicutes accounted for the highest explanation of ARGs and ZRGs variations, and Zn in EMW had significant impact on the succession of bacterial community.
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Affiliation(s)
- Xining Sun
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, PR China
| | - Junchao Zhao
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, PR China
| | - Quan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, PR China
| | - Xiuna Ren
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, PR China
| | - Ronghua Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, PR China
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, PR China
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, PR China.
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Riley EP, Schwarz C, Derman AI, Lopez-Garrido J. Milestones in Bacillus subtilis sporulation research. MICROBIAL CELL (GRAZ, AUSTRIA) 2020; 8:1-16. [PMID: 33490228 PMCID: PMC7780723 DOI: 10.15698/mic2021.01.739] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/21/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022]
Abstract
Endospore formation has been a rich field of research for more than a century, and has benefited from the powerful genetic tools available in Bacillus subtilis. In this review, we highlight foundational discoveries that shaped the sporulation field, from its origins to the present day, tracing a chronology that spans more than one hundred eighty years. We detail how cell-specific gene expression has been harnessed to investigate the existence and function of intercellular proteinaceous channels in sporulating cells, and we illustrate the rapid progress in our understanding of the cell biology of sporulation in recent years using the process of chromosome translocation as a storyline. Finally, we sketch general aspects of sporulation that remain largely unexplored, and that we envision will be fruitful areas of future research.
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Affiliation(s)
- Eammon P. Riley
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Corinna Schwarz
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Alan I. Derman
- Max Planck Institute for Evolutionary Biology, Plön, Germany
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45
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The Diversity, Composition, and Putative Functions of Gill-Associated Bacteria of Bathymodiolin Mussel and Vesicomyid Clam from Haima Cold Seep, South China Sea. Microorganisms 2020; 8:microorganisms8111699. [PMID: 33143295 PMCID: PMC7694083 DOI: 10.3390/microorganisms8111699] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 01/11/2023] Open
Abstract
The Haima cold seep, which is one of the two active cold seeps in the South China Sea, is known for its great ecological importance. The seep bivalves are assumed to depend mainly on their bacterial symbiosis for survival and growth. However, information on the bacterial diversity, composition, and putative function of gill-associated of dominant dwelling animals in Haima cold seep remain elusive. Herein, we adopted a high-throughput sequencing of 16S rRNA gene amplicons, and function prediction methods (Functional Annotation of Prokaryotic Taxa (FAPROTAX) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICURUSTs)) to purposely illustrate the taxonomic and phylogenetic diversity, composition, and putative functions of the symbionts in bathymodiolin mussel Gigantidas haimaensis (Bivalvia: Mytilidae: Gigantidas) and vesicomyid clam Archivesica marissinica (Bivalvia: Glossoidea: Vesicomyidae). The predominant microbes of both species were Proteobacteria and Gammaproteobacteria on the phylum and class level, respectively. The taxonomic and phylogenetic diversity of gill microbial communities in G. haimaensis were significantly different from those in A. marissinica (p < 0.05). Nine functional groups, including seven carbon-related biogeochemical groups, were identified through the FAPROTAX analysis. However, the most dominant groups for G. haimaensis and A. marissinica were both chemoheterotrophic. G. haimaensis and A. marissinica shared many pathways, however, 16 obtained Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologous groups (42.11%) significantly differed between the two species (p < 0.05). These findings would provide insight into the functions of microbes in the element cycling and energy flow as well as the host-symbiont relationship of bivalves in the Haima cold seep environment.
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Secaira-Morocho H, Castillo JA, Driks A. Diversity and evolutionary dynamics of spore-coat proteins in spore-forming species of Bacillales. Microb Genom 2020; 6. [PMID: 33052805 PMCID: PMC7725329 DOI: 10.1099/mgen.0.000451] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Among members of the Bacillales order, there are several species capable of forming a structure called an endospore. Endospores enable bacteria to survive under unfavourable growth conditions and germinate when environmental conditions are favourable again. Spore-coat proteins are found in a multilayered proteinaceous structure encasing the spore core and the cortex. They are involved in coat assembly, cortex synthesis and germination. Here, we aimed to determine the diversity and evolutionary processes that have influenced spore-coat genes in various spore-forming species of Bacillales using an in silico approach. For this, we used sequence similarity searching algorithms to determine the diversity of coat genes across 161 genomes of Bacillales. The results suggest that among Bacillales, there is a well-conserved core genome, composed mainly by morphogenetic coat proteins and spore-coat proteins involved in germination. However, some spore-coat proteins are taxa-specific. The best-conserved genes among different species may promote adaptation to changeable environmental conditions. Because most of the Bacillus species harbour complete or almost complete sets of spore-coat genes, we focused on this genus in greater depth. Phylogenetic reconstruction revealed eight monophyletic groups in the Bacillus genus, of which three are newly discovered. We estimated the selection pressures acting over spore-coat genes in these monophyletic groups using classical and modern approaches and detected horizontal gene transfer (HGT) events, which have been further confirmed by scanning the genomes to find traces of insertion sequences. Although most of the genes are under purifying selection, there are several cases with individual sites evolving under positive selection. Finally, the HGT results confirm that sporulation is an ancestral feature in Bacillus.
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Affiliation(s)
- Henry Secaira-Morocho
- School of Biological Sciences and Engineering, Yachay Tech University, San Miguel de Urcuquí, Imbabura, Ecuador
| | - José A Castillo
- School of Biological Sciences and Engineering, Yachay Tech University, San Miguel de Urcuquí, Imbabura, Ecuador
| | - Adam Driks
- Department of Microbiology and Immunology, Loyola University Chicago, Chicago, IL, USA
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47
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Alpha-amylase conjugated biogenic silver nanoparticles as innovative strategy against biofilm-forming multidrug resistant bacteria. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101784] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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48
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Tanaka M, Onizuka S, Mishima R, Nakayama J. Cultural isolation of spore-forming bacteria in human feces using bile acids. Sci Rep 2020; 10:15041. [PMID: 32929101 PMCID: PMC7490687 DOI: 10.1038/s41598-020-71883-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/31/2020] [Indexed: 01/01/2023] Open
Abstract
Structurally-diversified bile acids (BAs) are involved in shaping of intestinal microbiota as well as absorption of dietary lipids. Taurocholic acid, a conjugated form of BA, has been reported to be a factor triggering germination of a wide range of spore-forming bacteria in intestine. To test a hypothesis that other BAs also promote germination of intestinal bacteria, we attempted culture of bacteria from ethanol-treated feces by using a series of BAs. It was found that conjugated-BAs, notably three glycine-conjugated BAs, glycodeoxycholic acid and glycochenodeoxycholic acid, significantly increased the number and the species variety of colonies formed on the agar plate. These colonized bacteria mostly belonged to class Clostridia, mainly consisting of families Lachnospiraceae, Clostridiaceae, and Peptostreptococcaceae. There were several types of bacteria associated with different sensitivity to each BA. Eventually, we isolated 72 bacterial species of which 61 are known and 11 novel. These results demonstrate that the culturable range of bacteria in intestine can be widened using the germination-inducing activity of BAs. This approach would advance the research on spore-forming Clostridia that contains important but difficult-to-cultured bacteria associate with host health and diseases.
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Affiliation(s)
- Masaru Tanaka
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
| | - Sakura Onizuka
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
| | - Riko Mishima
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
| | - Jiro Nakayama
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan.
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Khanna K, Lopez-Garrido J, Pogliano K. Shaping an Endospore: Architectural Transformations During Bacillus subtilis Sporulation. Annu Rev Microbiol 2020; 74:361-386. [PMID: 32660383 PMCID: PMC7610358 DOI: 10.1146/annurev-micro-022520-074650] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Endospore formation in Bacillus subtilis provides an ideal model system for studying development in bacteria. Sporulation studies have contributed a wealth of information about the mechanisms of cell-specific gene expression, chromosome dynamics, protein localization, and membrane remodeling, while helping to dispel the early view that bacteria lack internal organization and interesting cell biological phenomena. In this review, we focus on the architectural transformations that lead to a profound reorganization of the cellular landscape during sporulation, from two cells that lie side by side to the endospore, the unique cell within a cell structure that is a hallmark of sporulation in B. subtilis and other spore-forming Firmicutes. We discuss new insights into the mechanisms that drive morphogenesis, with special emphasis on polar septation, chromosome translocation, and the phagocytosis-like process of engulfment, and also the key experimental advances that have proven valuable in revealing the inner workings of bacterial cells.
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Affiliation(s)
- Kanika Khanna
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, USA; ,
| | | | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, USA; ,
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50
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Appert O, Garcia AR, Frei R, Roduit C, Constancias F, Neuzil-Bunesova V, Ferstl R, Zhang J, Akdis C, Lauener R, Lacroix C, Schwab C. Initial butyrate producers during infant gut microbiota development are endospore formers. Environ Microbiol 2020; 22:3909-3921. [PMID: 32686173 DOI: 10.1111/1462-2920.15167] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/09/2020] [Accepted: 07/15/2020] [Indexed: 12/12/2022]
Abstract
The acquisition of the infant gut microbiota is key to establishing a host-microbiota symbiosis. Microbially produced metabolites tightly interact with the immune system, and the fermentation-derived short-chain fatty acid butyrate is considered an important mediator linked to chronic diseases later in life. The intestinal butyrate-forming bacterial population is taxonomically and functionally diverse and includes endospore formers with high transmission potential. Succession, and contribution of butyrate-producing taxa during infant gut microbiota development have been little investigated. We determined the abundance of major butyrate-forming groups and fermentation metabolites in faeces, isolated, cultivated and characterized the heat-resistant cell population, which included endospores, and compared butyrate formation efficiency of representative taxa in batch cultures. The endospore community contributed about 0.001% to total cells, and was mainly composed of the pioneer butyrate-producing Clostridium sensu stricto. We observed an increase in abundance of Faecalibacterium prausnitzii, butyrate-producing Lachnospiraceae and faecal butyrate levels with age that is likely explained by higher butyrate production capacity of contributing taxa compared with Clostridium sensu stricto. Our data suggest that a successional arrangement and an overall increase in abundance of butyrate forming populations occur during the first year of life, which is associated with an increase of intestinal butyrate formation capacity.
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Affiliation(s)
- Olivia Appert
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Alejandro Ramirez Garcia
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Remo Frei
- Christine Kühne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland.,Division of Respiratory Medicine, Department of Paediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Caroline Roduit
- Christine Kühne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland.,University Children's Hospital Zürich, Zürich, Switzerland.,Children's Hospital St. Gallen, St. Gallen, Switzerland
| | - Florentin Constancias
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Vera Neuzil-Bunesova
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Prague, Czech Republic
| | - Ruth Ferstl
- Christine Kühne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland.,Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
| | - Jianbo Zhang
- Laboratory of Toxicology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Cezmi Akdis
- Christine Kühne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland.,Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
| | - Roger Lauener
- Christine Kühne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland.,Children's Hospital St. Gallen, St. Gallen, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Clarissa Schwab
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland.,Division of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
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