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Bedree JK, Bourgeois J, Balani P, Cen L, Hendrickson EL, Kerns KA, Camilli A, McLean JS, Shi W, He X. Identifying essential genes in Schaalia odontolytica using a highly-saturated transposon library. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.604004. [PMID: 39071323 PMCID: PMC11275721 DOI: 10.1101/2024.07.17.604004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The unique epibiotic-parasitic relationship between Nanosynbacter lyticus type strain TM7x, a member of the newly identified Candidate Phyla Radiation, now referred to as Patescibacteria, and its basibiont, Schaalia odontolytica strain XH001 (formerly Actinomyces odontolyticus), require more powerful genetic tools for deeper understanding of the genetic underpinnings that mediate their obligate relationship. Previous studies have mainly characterized the genomic landscape of XH001 during or post TM7x infection through comparative genomic or transcriptomic analyses followed by phenotypic analysis. Comprehensive genetic dissection of the pair is currently cumbersome due to the lack of robust genetic tools in TM7x. However, basic genetic tools are available for XH001 and this study expands the current genetic toolset by developing high-throughput transposon insertion sequencing (Tn-seq). Tn-seq was employed to screen for essential genes in XH001 under laboratory conditions. A highly saturated Tn-seq library was generated with nearly 660,000 unique insertion mutations, averaging one insertion every 2-3 nucleotides. 203 genes, 10.5% of the XH001 genome, were identified as putatively essential.
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Affiliation(s)
- Joseph K Bedree
- Section of Oral Biology, Division of Oral Biology and Medicine, School of Dentistry, University of California-Los Angeles, Los Angeles, CA, 90095
- Department of Microbiology, The ADA Forsyth Institute; Cambridge, MA, 02142
| | - Jacob Bourgeois
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Pooja Balani
- Department of Microbiology, The ADA Forsyth Institute; Cambridge, MA, 02142
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA 02115
| | - Lujia Cen
- Department of Microbiology, The ADA Forsyth Institute; Cambridge, MA, 02142
| | - Erik L Hendrickson
- Department of Periodontics, School of Dentistry, University of Washington, Seattle, WA, 98195
| | - Kristopher A Kerns
- Department of Periodontics, School of Dentistry, University of Washington, Seattle, WA, 98195
| | - Andrew Camilli
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Jeffrey S McLean
- Department of Periodontics, School of Dentistry, University of Washington, Seattle, WA, 98195
| | - Wenyuan Shi
- Department of Microbiology, The ADA Forsyth Institute; Cambridge, MA, 02142
| | - Xuesong He
- Department of Microbiology, The ADA Forsyth Institute; Cambridge, MA, 02142
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Du D, Wang Y, Gao Y, Feng L, Zhang Z, Hu Z. Analysis of differences in the rumen microbiome and metabolic function in prepartum dairy cows with different body condition scores. Anim Microbiome 2024; 6:35. [PMID: 38915057 PMCID: PMC11194928 DOI: 10.1186/s42523-024-00324-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND The rumen is a crucial digestive organ for dairy cows. The rumen microbiota assists in the digestion of plant feed through microbe-mediated fermentation, during which the plant feed is transformed into nutrients for the cow's use. Variations in the composition and function of the rumen microbiome affect the energy utilization efficiency of dairy cows, which is one of the reasons for the varying body condition scores (BCSs). This study focused on prepartum Holstein dairy cows to analyze differences in rumen microbiota and metabolites among cows with different BCSs. Twelve prepartum dairy cows were divided into two groups, low BCS (LBCS, BCS = 2.75, n = 6) and high BCS (HBCS, BCS = 3.5, n = 6), to explore differences in microbial composition and metabolites. RESULTS In the HBCS group, the genera within the phylum Firmicutes exhibited stronger correlations and greater abundances. Phyla such as Firmicutes, Patescibacteria, Acidobacteriota, Euryarchaeota, and Desulfobacterota, in addition to most of their constituent microbial groups, were significantly more abundant in the HBCS group than in the LBCS group. At the genus level, the abundances of Anaerovibrio, Veillonellaceae_UCG_001, Ruminococcus_gauvreauii_group, Blautia, Eubacterium, Prevotellaceae_YAB2003_group, Schwartzia, and Halomonas significantly increased in the HBCS group. The citrate cycle, involved in carbohydrate metabolism, exhibited a significant enrichment trend, with a notable increase in the abundance of its key substrate, citrate, in the HBCS group. This increase was significantly positively correlated with the differential bacterial genera. CONCLUSION In this study, prepartum dairy cows with higher BCS exhibited greater abundance of Firmicutes. This study provides theoretical support for microbiological research on dairy cows with different BCSs and suggests that regulating the rumen microbiome could help maintain prepartum dairy cows within an optimal BCS range.
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Affiliation(s)
- Dewei Du
- Ruminant Nutrition and Physiology Laboratory, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Yanzhe Wang
- Ruminant Nutrition and Physiology Laboratory, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Yongji Gao
- Ruminant Nutrition and Physiology Laboratory, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Lei Feng
- Ruminant Nutrition and Physiology Laboratory, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Ziye Zhang
- Ruminant Nutrition and Physiology Laboratory, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Zhiyong Hu
- Ruminant Nutrition and Physiology Laboratory, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China.
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Xu S, Zhao R, Sun J, Sun Y, Xu G, Wang F. Microplastics change soil properties, plant performance, and bacterial communities in salt-affected soils. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134333. [PMID: 38643581 DOI: 10.1016/j.jhazmat.2024.134333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 04/23/2024]
Abstract
Microplastics (MPs) are emerging contaminants found globally. However, their effects on soil-plant systems in salt-affected habitats remain unknown. Here, we examined the effects of polyethylene (PE) and polylactic acid (PLA) on soil properties, maize performance, and bacterial communities in soils with different salinity levels. Overall, MPs decreased soil electrical conductivity and increased NH4+-N and NO3--N contents. Adding NaCl alone had promoting and inhibitive effects on plant growth in a concentration-dependent manner. Overall, the addition of 0.2% PLA increased shoot biomass, while 2% PLA decreased it. Salinity increased Na content and decreased K/Na ratio in plant tissues (particularly roots), which were further modified by MPs. NaCl and MPs singly and jointly regulated the expression of functional genes related to salt tolerance in leaves, including ZMSOS1, ZMHKT1, and ZMHAK1. Exposure to NaCl alone had a slight effect on soil bacterial α-diversity, but in most cases, MPs increased ACE, Chao1, and Shannon indexes. Both MPs and NaCl altered bacterial community composition, although the specific effects varied depending on the type and concentration of MPs and the salinity level. Overall, PLA had more pronounced effects on soil-plant systems compared to PE. These findings bridge knowledge gaps in the risks of MPs in salt-affected habitats.
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Affiliation(s)
- Shuang Xu
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, PR China
| | - Rong Zhao
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, PR China
| | - Jiao Sun
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, PR China; Shandong Vocational College of Science and Technology, Weifang, Shandong 261000, PR China
| | - Yuhuan Sun
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, PR China
| | - Guangjian Xu
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, PR China
| | - Fayuan Wang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, PR China.
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Peñalver M, Paradela A, Palacios-Cuéllar C, Pucciarelli MG, García-Del Portillo F. Experimental evidence of d-glutamate racemase activity in the uncultivated bacterium Candidatus Saccharimonas aalborgensis. Environ Microbiol 2024; 26:e16621. [PMID: 38558504 DOI: 10.1111/1462-2920.16621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/16/2024] [Indexed: 04/04/2024]
Abstract
The Candidate Phyla Radiation (CPR) encompasses widespread uncultivated bacteria with reduced genomes and limited metabolic capacities. Most CPR bacteria lack the minimal set of enzymes required for peptidoglycan (PG) synthesis, leaving it unclear how these bacteria produce this essential envelope component. In this study, we analysed the distribution of d-amino acid racemases that produce the universal PG components d-glutamate (d-Glu) or d-alanine (d-Ala). We also examined moonlighting enzymes that synthesize d-Glu or d-Ala. Unlike other phyla in the domain Bacteria, CPR bacteria do not exhibit these moonlighting activities and have, at most, one gene encoding either a Glu or Ala racemase. One of these 'orphan' racemases is a predicted Glu racemase (MurICPR) from the CPR bacterium Candidatus Saccharimonas aalborgenesis. The expression of MurICPR restores the growth of a Salmonella d-Glu auxotroph lacking its endogenous racemase and results in the substitution of l-Ala by serine as the first residue in a fraction of the PG stem peptides. In vitro, MurICPR exclusively racemizes Glu as a substrate. Therefore, Ca. Saccharimonas aalborgensis may couple Glu racemization to serine and d-Glu incorporation into the stem peptide. Our findings provide the first insights into the synthesis of PG by an uncultivated environmental bacterium and illustrate how to experimentally test enzymatic activities from CPR bacteria related to PG metabolism.
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Affiliation(s)
- Marcos Peñalver
- Laboratory of Intracellular Bacterial Pathogens, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
- Department of Molecular Biology, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Biologia Molecular Severo Ochoa (CBM), CSIC-UAM, Madrid, Spain
| | - Alberto Paradela
- Proteomics Facility, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
| | - César Palacios-Cuéllar
- Laboratory of Intracellular Bacterial Pathogens, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
| | - M Graciela Pucciarelli
- Laboratory of Intracellular Bacterial Pathogens, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
- Department of Molecular Biology, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Biologia Molecular Severo Ochoa (CBM), CSIC-UAM, Madrid, Spain
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Reva ON, La Cono V, Crisafi F, Smedile F, Mudaliyar M, Ghosal D, Giuliano L, Krupovic M, Yakimov MM. Interplay of intracellular and trans-cellular DNA methylation in natural archaeal consortia. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13258. [PMID: 38589217 PMCID: PMC11001535 DOI: 10.1111/1758-2229.13258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/15/2024] [Indexed: 04/10/2024]
Abstract
DNA methylation serves a variety of functions across all life domains. In this study, we investigated archaeal methylomics within a tripartite xylanolytic halophilic consortium. This consortium includes Haloferax lucertense SVX82, Halorhabdus sp. SVX81, and an ectosymbiotic Candidatus Nanohalococcus occultus SVXNc, a nano-sized archaeon from the DPANN superphylum. We utilized PacBio SMRT and Illumina cDNA sequencing to analyse samples from consortia of different compositions for methylomics and transcriptomics. Endogenous cTAG methylation, typical of Haloferax, was accompanied in this strain by methylation at four other motifs, including GDGcHC methylation, which is specific to the ectosymbiont. Our analysis of the distribution of methylated and unmethylated motifs suggests that autochthonous cTAG methylation may influence gene regulation. The frequency of GRAGAaG methylation increased in highly expressed genes, while CcTTG and GTCGaGG methylation could be linked to restriction-modification (RM) activity. Generally, the RM activity might have been reduced during the evolution of this archaeon to balance the protection of cells from intruders, the reduction of DNA damage due to self-restriction in stressful environments, and the benefits of DNA exchange under extreme conditions. Our methylomics, transcriptomics and complementary electron cryotomography (cryo-ET) data suggest that the nanohaloarchaeon exports its methyltransferase to methylate the Haloferax genome, unveiling a new aspect of the interaction between the symbiont and its host.
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Affiliation(s)
- Oleg N. Reva
- Department of Biochemistry, Genetics and Microbiology, Centre for Bioinformatics and Computational BiologyUniversity of PretoriaPretoriaSouth Africa
| | - Violetta La Cono
- Extreme Microbiology, Biotechnology and Astrobiology GroupInstitute of Polar Sciences, ISP‐CNRMessinaItaly
| | - Francesca Crisafi
- Extreme Microbiology, Biotechnology and Astrobiology GroupInstitute of Polar Sciences, ISP‐CNRMessinaItaly
| | - Francesco Smedile
- Extreme Microbiology, Biotechnology and Astrobiology GroupInstitute of Polar Sciences, ISP‐CNRMessinaItaly
| | - Manasi Mudaliyar
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneMelbourneVictoriaAustralia
- ARC Centre for Cryo‐electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVictoriaAustralia
| | - Debnath Ghosal
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneMelbourneVictoriaAustralia
- ARC Centre for Cryo‐electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVictoriaAustralia
| | | | - Mart Krupovic
- Istitut Pasteur, Archaeal Virology UnitUniversité Paris CitéParisFrance
| | - Michail M. Yakimov
- Extreme Microbiology, Biotechnology and Astrobiology GroupInstitute of Polar Sciences, ISP‐CNRMessinaItaly
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Rumora A, Hopkins L, Yim K, Baykus MF, Martinez L, Jimenez L. Detection and Characterization of Electrogenic Bacteria from Soils. BIOTECH 2023; 12:65. [PMID: 38131677 PMCID: PMC10871078 DOI: 10.3390/biotech12040065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/21/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023] Open
Abstract
Soil microbial fuel cells (SMFCs) are bioelectrical devices powered by the oxidation of organic and inorganic compounds due to microbial activity. Seven soils were randomly selected from Bergen Community College or areas nearby, located in the state of New Jersey, USA, were used to screen for the presence of electrogenic bacteria. SMFCs were incubated at 35-37 °C. Electricity generation and electrogenic bacteria were determined using an application developed for cellular phones. Of the seven samples, five generated electricity and enriched electrogenic bacteria. Average electrical output for the seven SMFCs was 155 microwatts with the start-up time ranging from 1 to 11 days. The highest output and electrogenic bacterial numbers were found with SMFC-B1 with 143 microwatts and 2.99 × 109 electrogenic bacteria after 15 days. Optimal electrical output and electrogenic bacterial numbers ranged from 1 to 21 days. Microbial DNA was extracted from the top and bottom of the anode of SMFC-B1 using the ZR Soil Microbe DNA MiniPrep Protocol followed by PCR amplification of 16S rRNA V3-V4 region. Next-generation sequencing of 16S rRNA genes generated an average of 58 k sequences. BLAST analysis of the anode bacterial community in SMFC-B1 demonstrated that the predominant bacterial phylum was Bacillota of the class Clostridia (50%). However, bacteria belonging to the phylum Pseudomonadota (15%) such as Magnetospirillum sp. and Methylocaldum gracile were also part of the predominant electrogenic bacterial community in the anode. Unidentified uncultured bacteria accounted for 35% of the predominant bacterial community. Bioelectrical devices such as MFCs provide sustainable and clean alternatives to future applications for electricity generation, waste treatment, and biosensors.
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Affiliation(s)
| | | | | | | | | | - Luis Jimenez
- Biology and Horticulture Department, Bergen Community College, 400 Paramus Road, Paramus, NJ 07652, USA; (A.R.); (K.Y.); (L.M.)
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