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Silva I, Alves M, Malheiro C, Silva ARR, Loureiro S, Henriques I, González-Alcaraz MN. Short-Term Responses of Soil Microbial Communities to Changes in Air Temperature, Soil Moisture and UV Radiation. Genes (Basel) 2022; 13:genes13050850. [PMID: 35627235 PMCID: PMC9142034 DOI: 10.3390/genes13050850] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/04/2022] [Accepted: 05/07/2022] [Indexed: 01/31/2023] Open
Abstract
We analyzed the effects on a soil microbial community of short-term alterations in air temperature, soil moisture and ultraviolet radiation and assessed the role of invertebrates (species Enchytraeus crypticus) in modulating the community’s response to these factors. The reference soil, Lufa 2.2, was incubated for 48 h, with and without invertebrates, under the following conditions: standard (20 °C + 50% water holding capacity (WHC)); increased air temperature (15–25 °C or 20–30 °C + 50% WHC); flood (20 °C + 75% WHC); drought (20 °C + 25% WHC); and ultraviolet radiation (UV) (20 °C + 50% WHC + UV). BIOLOG EcoPlates and 16S rDNA sequencing (Illumina) were used to assess the microbial community’s physiological profile and the bacterial community’s structure, respectively. The bacterial abundance (estimated by 16S rDNA qPCR) did not change. Most of the conditions led to an increase in microbial activity and a decrease in diversity. The structure of the bacterial community was particularly affected by higher air temperatures (20–30 °C, without E. crypticus) and floods (with E. crypticus). Effects were observed at the class, genera and OTU levels. The presence of invertebrates mostly resulted in the attenuation of the observed effects, highlighting the importance of considering microbiome–invertebrate interactions. Considering future climate changes, the effects described here raise concern. This study provides fundamental knowledge to develop effective strategies to mitigate these negative outcomes. However, long-term studies integrating biotic and abiotic factors are needed.
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Affiliation(s)
- Isabel Silva
- CEF (Center for Functional Ecology), Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, 3000-456 Coimbra, Portugal;
- CESAM (Centre for Marine and Environmental Studies), Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (C.M.); (A.R.R.S.); (S.L.)
| | - Marta Alves
- CBQF—Center for Biotechnology and Fine Chemistry, School of Biotechnology, Portuguese Catholic University, 4169-005 Porto, Portugal;
| | - Catarina Malheiro
- CESAM (Centre for Marine and Environmental Studies), Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (C.M.); (A.R.R.S.); (S.L.)
| | - Ana Rita R. Silva
- CESAM (Centre for Marine and Environmental Studies), Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (C.M.); (A.R.R.S.); (S.L.)
| | - Susana Loureiro
- CESAM (Centre for Marine and Environmental Studies), Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (C.M.); (A.R.R.S.); (S.L.)
| | - Isabel Henriques
- CEF (Center for Functional Ecology), Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, 3000-456 Coimbra, Portugal;
- Correspondence: (I.H.); (M.N.G.-A.)
| | - M. Nazaret González-Alcaraz
- Department of Agricultural Engineering of the E.T.S.I.A. & Soil Ecology and Biotechnology Unit of the Institute of Plant Biotechnology, Technical University of Cartagena, 30203 Cartagena, Spain
- Correspondence: (I.H.); (M.N.G.-A.)
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Yang Y, Li L, Sun H, Li Z, Qi Z, Liu X. Improving CoQ 10 productivity by strengthening glucose transmembrane of Rhodobacter sphaeroides. Microb Cell Fact 2021; 20:207. [PMID: 34717624 PMCID: PMC8557541 DOI: 10.1186/s12934-021-01695-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 10/18/2021] [Indexed: 02/01/2023] Open
Abstract
Background Several Rhodobacter sphaeroides have been widely applied in commercial CoQ10 production, but they have poor glucose use. Strategies for enhancing glucose use have been widely exploited in R. sphaeroides. Nevertheless, little research has focused on the role of glucose transmembrane in the improvement of production. Results There are two potential glucose transmembrane pathways in R. sphaeroides ATCC 17023: the fructose specific-phosphotransferase system (PTSFru, fruAB) and non-PTS that relied on glucokinase (glk). fruAB mutation revealed two effects on bacterial growth: inhibition at the early cultivation phase (12–24 h) and promotion since 36 h. Glucose metabolism showed a corresponding change in characteristic vs. the growth. For ΔfruAΔfruB, maximum biomass (Biomax) was increased by 44.39% and the CoQ10 content was 27.08% more than that of the WT. glk mutation caused a significant decrease in growth and glucose metabolism. Over-expressing a galactose:H+ symporter (galP) in the ΔfruAΔfruB relieved the inhibition and enhanced the growth further. Finally, a mutant with rapid growth and high CoQ10 titer was constructed (ΔfruAΔfruB/tac::galPOP) using several glucose metabolism modifications and was verified by fermentation in 1 L fermenters. Conclusions The PTSFru mutation revealed two effects on bacterial growth: inhibition at the early cultivation phase and promotion later. Additionally, biomass yield to glucose (Yb/glc) and CoQ10 synthesis can be promoted using fruAB mutation, and glk plays a key role in glucose metabolism. Strengthening glucose transmembrane via non-PTS improves the productivity of CoQ10 fermentation. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01695-z.
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Affiliation(s)
- Yuying Yang
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China.,State Key Laboratory of Bio-Based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China
| | - Lu Li
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China.,State Key Laboratory of Bio-Based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China
| | - Haoyu Sun
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China.,State Key Laboratory of Bio-Based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China
| | - Zhen Li
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China.,State Key Laboratory of Bio-Based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China
| | - Zhengliang Qi
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China.
| | - Xinli Liu
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China. .,State Key Laboratory of Bio-Based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China.
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Genome-Wide Identification of Transcription Start Sites in Two Alphaproteobacteria, Rhodobacter sphaeroides 2.4.1 and Novosphingobium aromaticivorans DSM 12444. Microbiol Resour Announc 2020; 9:9/36/e00880-20. [PMID: 32883797 PMCID: PMC7471390 DOI: 10.1128/mra.00880-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Here, we report the genome-wide identification of transcription start sites (TSSs) from two Alphaproteobacteria grown under conditions that result in significant changes in gene expression. TSSs that were identified as present in one condition or both will be an important resource for future studies of these, and possibly other, Alphaproteobacteria. Here, we report the genome-wide identification of transcription start sites (TSSs) from two Alphaproteobacteria grown under conditions that result in significant changes in gene expression. TSSs that were identified as present in one condition or both will be an important resource for future studies of these, and possibly other, Alphaproteobacteria.
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Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism. mSystems 2019; 4:mSystems00297-18. [PMID: 30746495 PMCID: PMC6365646 DOI: 10.1128/msystems.00297-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/12/2019] [Indexed: 12/13/2022] Open
Abstract
Deoxyribose is one of the building blocks of DNA and is released when cells die and their DNA degrades. We identified a bacterium that can grow with deoxyribose as its sole source of carbon even though its genome does not contain any of the known genes for breaking down deoxyribose. By growing many mutants of this bacterium together on deoxyribose and using DNA sequencing to measure the change in the mutants’ abundance, we identified multiple protein-coding genes that are required for growth on deoxyribose. Based on the similarity of these proteins to enzymes of known function, we propose a 6-step pathway in which deoxyribose is oxidized and then cleaved. Diverse bacteria use a portion of this pathway to break down a related compound, deoxyribonate, which is a waste product of metabolism. Our study illustrates the utility of large-scale bacterial genetics to identify previously unknown metabolic pathways. Using genome-wide mutant fitness assays in diverse bacteria, we identified novel oxidative pathways for the catabolism of 2-deoxy-d-ribose and 2-deoxy-d-ribonate. We propose that deoxyribose is oxidized to deoxyribonate, oxidized to ketodeoxyribonate, and cleaved to acetyl coenzyme A (acetyl-CoA) and glyceryl-CoA. We have genetic evidence for this pathway in three genera of bacteria, and we confirmed the oxidation of deoxyribose to ketodeoxyribonate in vitro. In Pseudomonas simiae, the expression of enzymes in the pathway is induced by deoxyribose or deoxyribonate, while in Paraburkholderia bryophila and in Burkholderia phytofirmans, the pathway proceeds in parallel with the known deoxyribose 5-phosphate aldolase pathway. We identified another oxidative pathway for the catabolism of deoxyribonate, with acyl-CoA intermediates, in Klebsiella michiganensis. Of these four bacteria, only P. simiae relies entirely on an oxidative pathway to consume deoxyribose. The deoxyribose dehydrogenase of P. simiae is either nonspecific or evolved recently, as this enzyme is very similar to a novel vanillin dehydrogenase from Pseudomonas putida that we identified. So, we propose that these oxidative pathways evolved primarily to consume deoxyribonate, which is a waste product of metabolism. IMPORTANCE Deoxyribose is one of the building blocks of DNA and is released when cells die and their DNA degrades. We identified a bacterium that can grow with deoxyribose as its sole source of carbon even though its genome does not contain any of the known genes for breaking down deoxyribose. By growing many mutants of this bacterium together on deoxyribose and using DNA sequencing to measure the change in the mutants’ abundance, we identified multiple protein-coding genes that are required for growth on deoxyribose. Based on the similarity of these proteins to enzymes of known function, we propose a 6-step pathway in which deoxyribose is oxidized and then cleaved. Diverse bacteria use a portion of this pathway to break down a related compound, deoxyribonate, which is a waste product of metabolism. Our study illustrates the utility of large-scale bacterial genetics to identify previously unknown metabolic pathways.
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Lambrecht SJ, Wahlig JML, Steglich C. The GntR family transcriptional regulator PMM1637 regulates the highly conserved cyanobacterial sRNA Yfr2 in marine picocyanobacteria. DNA Res 2019; 25:489-497. [PMID: 29901694 PMCID: PMC6191309 DOI: 10.1093/dnares/dsy019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/14/2018] [Indexed: 11/21/2022] Open
Abstract
Prochlorococcus is a marine picocyanobacterium with a streamlined genome that is adapted to different ecological niches in the oligotrophic oceans. There are currently >20 regulatory small RNAs (sRNAs) that have been identified in the model strain Prochlorococcus MED4. While most of these sRNAs are ecotype-specific, sRNA homologs of Yfr1 and of the Yfr2 family are widely found throughout the cyanobacterial phylum. Although they were identified 13 yrs ago, the functions of Yfr1 and Yfr2 have remained unknown. We observed a strong induction of two Yfr2 sRNA homologs of Prochlorococcus MED4 during high light stress and nitrogen starvation. Several Prochlorococcus and marine Synechococcus yfr2 promoter regions contain a conserved motif we named CGRE1 (cyanobacterial GntR family transcriptional regulator responsive element 1). Using the conserved promoter region as bait in a DNA affinity pull-down assay we identified the GntR family transcriptional regulator PMM1637 as a binding partner. Similar to Yfr2, homologs of PMM1637 are universally and exclusively found in cyanobacteria. We suggest that PMM1637 governs the induction of gene expression of Yfr2 homologs containing CGRE1 in their promoters under nitrogen-depleted and high-light stress conditions.
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Affiliation(s)
- S Joke Lambrecht
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - J Mascha L Wahlig
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - Claudia Steglich
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
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A Key Regulator of the Glycolytic and Gluconeogenic Central Metabolic Pathways in Sinorhizobium meliloti. Genetics 2017; 207:961-974. [PMID: 28851745 DOI: 10.1534/genetics.117.300212] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 08/24/2017] [Indexed: 01/22/2023] Open
Abstract
The order Rhizobiales contains numerous agriculturally, biotechnologically, and medically important bacteria, including the rhizobia, and the genera Agrobacterium, Brucella, and Methylobacterium, among others. These organisms tend to be metabolically versatile, but there has been relatively little investigation into the regulation of their central carbon metabolic pathways. Here, RNA-sequencing and promoter fusion data are presented to show that the PckR protein is a key regulator of central carbon metabolism in Sinorhizobium meliloti; during growth with gluconeogenic substrates, PckR represses expression of the complete Entner-Doudoroff glycolytic pathway and induces expression of the pckA and fbaB gluconeogenic genes. Electrophoretic mobility shift assays indicate that PckR binds an imperfect palindromic sequence that overlaps the promoter or transcriptional start site in the negatively regulated promoters, or is present in tandem upstream the promoter motifs in the positively regulated promoters. Genetic and in vitro electrophoretic mobility shift assay experiments suggest that elevated concentrations of a PckR effector ligand results in the dissociation of PckR from its target binding site, and evidence is presented that suggests phosphoenolpyruvate may function as the effector. Characterization of missense pckR alleles identified three conserved residues important for increasing the affinity of PckR for its cognate effector molecule. Bioinformatics analyses illustrates that PckR is limited to a narrow phylogenetic range consisting of the Rhizobiaceae, Phyllobacteriaceae, Brucellaceae, and Bartonellaceae families. These data provide novel insights into the regulation of the core carbon metabolic pathways of this pertinent group of α-proteobacteria.
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Leyn SA, Maezato Y, Romine MF, Rodionov DA. Genomic Reconstruction of Carbohydrate Utilization Capacities in Microbial-Mat Derived Consortia. Front Microbiol 2017; 8:1304. [PMID: 28751880 PMCID: PMC5507952 DOI: 10.3389/fmicb.2017.01304] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/28/2017] [Indexed: 11/29/2022] Open
Abstract
Two nearly identical unicyanobacterial consortia (UCC) were previously isolated from benthic microbial mats that occur in a heliothermal saline lake in northern Washington State. Carbohydrates are a primary source of carbon and energy for most heterotrophic bacteria. Since CO2 is the only carbon source provided, the cyanobacterium must provide a source of carbon to the heterotrophs. Available genomic sequences for all members of the UCC provide opportunity to investigate the metabolic routes of carbon transfer between autotroph and heterotrophs. Here, we applied a subsystem-based comparative genomics approach to reconstruct carbohydrate utilization pathways and identify glycohydrolytic enzymes, carbohydrate transporters and pathway-specific transcriptional regulators in 17 heterotrophic members of the UCC. The reconstructed metabolic pathways include 800 genes, near a one-fourth of which encode enzymes, transporters and regulators with newly assigned metabolic functions resulting in discovery of novel functional variants of carbohydrate utilization pathways. The in silico analysis revealed the utilization capabilities for 40 carbohydrates and their derivatives. Two Halomonas species demonstrated the largest number of sugar catabolic pathways. Trehalose, sucrose, maltose, glucose, and beta-glucosides are the most commonly utilized saccharides in this community. Reconstructed regulons for global regulators HexR and CceR include central carbohydrate metabolism genes in the members of Gammaproteobacteria and Alphaproteobacteria, respectively. Genomics analyses were supplemented by experimental characterization of metabolic phenotypes in four isolates derived from the consortia. Measurements of isolate growth on the defined medium supplied with individual carbohydrates confirmed most of the predicted catabolic phenotypes. Not all consortia members use carbohydrates and only a few use complex polysaccharides suggesting a hierarchical carbon flow from cyanobacteria to each heterotroph. In summary, the genomics-based identification of carbohydrate utilization capabilities provides a basis for future experimental studies of carbon flow in UCC.
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Affiliation(s)
- Semen A Leyn
- Sanford-Burnham-Prebys Medical Discovery Institute, La JollaCA, United States.,A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of SciencesMoscow, Russia
| | - Yukari Maezato
- Biological Sciences Division, Pacific Northwest National Laboratory, RichlandWA, United States
| | - Margaret F Romine
- Biological Sciences Division, Pacific Northwest National Laboratory, RichlandWA, United States
| | - Dmitry A Rodionov
- Sanford-Burnham-Prebys Medical Discovery Institute, La JollaCA, United States.,A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of SciencesMoscow, Russia
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Imam S, Schäuble S, Brooks AN, Baliga NS, Price ND. Data-driven integration of genome-scale regulatory and metabolic network models. Front Microbiol 2015; 6:409. [PMID: 25999934 PMCID: PMC4419725 DOI: 10.3389/fmicb.2015.00409] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 04/20/2015] [Indexed: 12/21/2022] Open
Abstract
Microbes are diverse and extremely versatile organisms that play vital roles in all ecological niches. Understanding and harnessing microbial systems will be key to the sustainability of our planet. One approach to improving our knowledge of microbial processes is through data-driven and mechanism-informed computational modeling. Individual models of biological networks (such as metabolism, transcription, and signaling) have played pivotal roles in driving microbial research through the years. These networks, however, are highly interconnected and function in concert-a fact that has led to the development of a variety of approaches aimed at simulating the integrated functions of two or more network types. Though the task of integrating these different models is fraught with new challenges, the large amounts of high-throughput data sets being generated, and algorithms being developed, means that the time is at hand for concerted efforts to build integrated regulatory-metabolic networks in a data-driven fashion. In this perspective, we review current approaches for constructing integrated regulatory-metabolic models and outline new strategies for future development of these network models for any microbial system.
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Affiliation(s)
- Saheed Imam
- Institute for Systems Biology Seattle, WA, USA
| | - Sascha Schäuble
- Institute for Systems Biology Seattle, WA, USA ; Jena University Language and Information Engineering Lab, Friedrich-Schiller-University Jena Jena, Germany
| | | | - Nitin S Baliga
- Institute for Systems Biology Seattle, WA, USA ; Departments of Biology and Microbiology, University of Washington Seattle, WA, USA ; Molecular and Cellular Biology Program, University of Washington Seattle, WA, USA ; Lawrence Berkeley National Lab Berkeley, CA, USA
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