1
|
Sarkar S, Kazarina A, Hansen PM, Ward K, Hargreaves C, Reese N, Ran Q, Kessler W, de Souza LF, Loecke TD, Sarto MVM, Rice CW, Zeglin LH, Sikes BA, Lee ST. Ammonia-oxidizing archaea and bacteria differentially contribute to ammonia oxidation in soil under precipitation gradients and land legacy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566028. [PMID: 37987001 PMCID: PMC10659370 DOI: 10.1101/2023.11.08.566028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Background Global change has accelerated the nitrogen cycle. Soil nitrogen stock degradation by microbes leads to the release of various gases, including nitrous oxide (N2O), a potent greenhouse gas. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) participate in the soil nitrogen cycle, producing N2O. There are outstanding questions regarding the impact of environmental processes such as precipitation and land use legacy on AOA and AOB structurally, compositionally, and functionally. To answer these questions, we analyzed field soil cores and soil monoliths under varying precipitation profiles and land legacies. Results We resolved 28 AOA and AOB metagenome assembled genomes (MAGs) and found that they were significantly higher in drier environments and differentially abundant in different land use legacies. We further dissected AOA and AOB functional potentials to understand their contribution to nitrogen transformation capabilities. We identified the involvement of stress response genes, differential metabolic functional potentials, and subtle population dynamics under different environmental parameters for AOA and AOB. We observed that AOA MAGs lacked a canonical membrane-bound electron transport chain and F-type ATPase but possessed A/A-type ATPase, while AOB MAGs had a complete complex III module and F-type ATPase, suggesting differential survival strategies of AOA and AOB. Conclusions The outcomes from this study will enable us to comprehend how drought-like environments and land use legacies could impact AOA- and AOB-driven nitrogen transformations in soil.
Collapse
Affiliation(s)
- Soumyadev Sarkar
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Anna Kazarina
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Paige M. Hansen
- PMH Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado USA
| | - Kaitlyn Ward
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | | | - Nicholas Reese
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Qinghong Ran
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Willow Kessler
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Ligia F.T. de Souza
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Terry D. Loecke
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
- Environmental Studies Program, University of Kansas, Lawrence, Kansas, USA
| | | | - Charles W. Rice
- Department of Agronomy, Kansas State University, Manhattan, Kansas, USA
| | - Lydia H. Zeglin
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Benjamin A. Sikes
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
| | - Sonny T.M. Lee
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| |
Collapse
|
2
|
Park MJ, Kim YJ, Park M, Yu J, Namirimu T, Roh YR, Kwon KK. Establishment of Genome Based Criteria for Classification of the Family Desulfovibrionaceae and Proposal of Two Novel Genera, Alkalidesulfovibrio gen. nov. and Salidesulfovibrio gen. nov. Front Microbiol 2022; 13:738205. [PMID: 35694308 PMCID: PMC9174804 DOI: 10.3389/fmicb.2022.738205] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 04/11/2022] [Indexed: 01/14/2023] Open
Abstract
Bacteria in the Desulfovibrionaceae family, which contribute to S element turnover as sulfate-reducing bacteria (SRB) and disproportionation of partially oxidized sulfoxy anions, have been extensively investigated since the importance of the sulfur cycle emerged. Novel species belonging to this taxon are frequently reported, because they exist in various environments and are easy to culture using established methods. Due to the rapid expansion of the taxon, correction and reclassification have been conducted. The development of high-throughput sequencing facilitated rapid expansion of genome sequence database. Genome-based criteria, based on these databases, proved to be potential classification standard by overcoming the limitations of 16S rRNA-based phylogeny. Although standards methods for taxogenomics are being established, the addition of a novel genus requires extensive calculations with taxa, including many species, such as Desulfovibrionaceae. Thus, the genome-based criteria for classification of Desulfovibrionaceae were established and validated in this study. The average amino-acid identity (AAI) cut-off value, 63.43 ± 0.01, was calculated to be an appropriate criterion for genus delineation of the family Desulfovibrionaceae. By applying the AAI cut-off value, 88 genomes of the Desulfovibrionaceae were divided into 27 genera, which follows the core gene phylogeny results. In this process, two novel genera (Alkalidesulfovibrio and Salidesulfovibrio) and one former invalid genus (“Psychrodesulfovibrio”) were officially proposed. Further, by applying the 95–96% average nucleotide identity (ANI) standard and the 70% digital DNA–DNA hybridization standard values for species delineation of strains that were classified as the same species, five strains have the potential to be newly classified. After verifying that the classification was appropriately performed through relative synonymous codon usage analysis, common characteristics were listed by group. In addition, by detecting metal resistance related genes via in silico analysis, it was confirmed that most strains display metal tolerance.
Collapse
Affiliation(s)
- Mi-Jeong Park
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Yun Jae Kim
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
| | - Myeongkyu Park
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
| | - Jihyun Yu
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Teddy Namirimu
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Yoo-Rim Roh
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Kae Kyoung Kwon
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
- *Correspondence: Kae Kyoung Kwon,
| |
Collapse
|
3
|
Namirimu T, Yang JA, Yang SH, Yu J, Kim YJ, Kwon KK. Proteiniclasticum aestuarii sp. nov., isolated from tidal flat sediment, and emended descriptions of the genus Proteiniclasticum and Proteiniclasticum ruminis. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005275] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterium, designated SCR006T, was isolated from tidal flat sediment from Suncheon Bay, Republic of Korea. Cells of strain SCR006T were strictly anaerobic, motile cocci, Gram-reaction-negative, and catalase- and oxidase-negative. Growth was observed at 4–41 °C (optimum, 34–37 °C), at pH 6.5–10.0 (optimum, pH 7.0–7.5) and in presence of 0–8 % NaCl (optimum, 0–2 %). Fermentation products of peptone–yeast–glucose medium were acetate and ethanol. Results of phylogenetic analyses based on 16S rRNA gene sequences indicated that strain SCR006T had high sequence similarity to
Proteiniclasticum ruminis
D3RC-2T (97.9 %), followed by
Youngiibacter multivorans
DSM 6139T (95.9 %) and
Youngiibacter fragilis
232.1T (95.0 %). The average nucleotide identity value between strain SCR006T and
P. ruminis
DSM 24773T was 72.7 %, which strongly supported that strain SCR006T reresents a novel species within the genus
Proteiniclasticum
. The major cellular fatty acids are iso-C15 : 0 (27.2 %) and anteiso-C15 : 0 (16.9 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unidentified phospholipids, an unidentified aminolipid and five unidentified lipids. The genomic size was 3.2 Mb with genomic DNA G+C content of 45.6 mol%. The results of 16S rRNA-based and genome-based phylogenetic tree analyses indicated that SCR006T should be assigned to the genus
Proteiniclasticum
. Strain SCR006T could be distinguished from
P. ruminis
D3RC-2T by its growth conditions, cell morphology and genomic characteristics. Based on the phenotypic, phylogenetic, genomic and chemotaxonomic features, strain SCR006T represents a novel species, for which the name Proteiniclasticum aestuarii sp. nov. is proposed, with the type strain SCR006T (=KCTC 25245T= JCM 34531T)
Collapse
Affiliation(s)
- Teddy Namirimu
- Major of Applied Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Jhung-Ahn Yang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Sung-Hyun Yang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Jihyun Yu
- Major of Applied Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Yun Jae Kim
- Major of Applied Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Kae Kyoung Kwon
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
- Major of Applied Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
| |
Collapse
|
4
|
Chaudhari NM, Overholt WA, Figueroa-Gonzalez PA, Taubert M, Bornemann TLV, Probst AJ, Hölzer M, Marz M, Küsel K. The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers. ENVIRONMENTAL MICROBIOME 2021; 16:24. [PMID: 34906246 PMCID: PMC8672522 DOI: 10.1186/s40793-021-00395-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/03/2021] [Indexed: 05/16/2023]
Abstract
BACKGROUND The highly diverse Cand. Patescibacteria are predicted to have minimal biosynthetic and metabolic pathways, which hinders understanding of how their populations differentiate in response to environmental drivers or host organisms. Their mechanisms employed to cope with oxidative stress are largely unknown. Here, we utilized genome-resolved metagenomics to investigate the adaptive genome repertoire of Patescibacteria in oxic and anoxic groundwaters, and to infer putative host ranges. RESULTS Within six groundwater wells, Cand. Patescibacteria was the most dominant (up to 79%) super-phylum across 32 metagenomes sequenced from DNA retained on 0.2 and 0.1 µm filters after sequential filtration. Of the reconstructed 1275 metagenome-assembled genomes (MAGs), 291 high-quality MAGs were classified as Cand. Patescibacteria. Cand. Paceibacteria and Cand. Microgenomates were enriched exclusively in the 0.1 µm fractions, whereas candidate division ABY1 and Cand. Gracilibacteria were enriched in the 0.2 µm fractions. On average, Patescibacteria enriched in the smaller 0.1 µm filter fractions had 22% smaller genomes, 13.4% lower replication measures, higher proportion of rod-shape determining proteins, and of genomic features suggesting type IV pili mediated cell-cell attachments. Near-surface wells harbored Patescibacteria with higher replication rates than anoxic downstream wells characterized by longer water residence time. Except prevalence of superoxide dismutase genes in Patescibacteria MAGs enriched in oxic groundwaters (83%), no major metabolic or phylogenetic differences were observed. The most abundant Patescibacteria MAG in oxic groundwater encoded a nitrate transporter, nitrite reductase, and F-type ATPase, suggesting an alternative energy conservation mechanism. Patescibacteria consistently co-occurred with one another or with members of phyla Nanoarchaeota, Bacteroidota, Nitrospirota, and Omnitrophota. Among the MAGs enriched in 0.2 µm fractions,, only 8% Patescibacteria showed highly significant one-to-one correlation, mostly with Omnitrophota. Motility and transport related genes in certain Patescibacteria were highly similar to genes from other phyla (Omnitrophota, Proteobacteria and Nanoarchaeota). CONCLUSION Other than genes to cope with oxidative stress, we found little genomic evidence for niche adaptation of Patescibacteria to oxic or anoxic groundwaters. Given that we could detect specific host preference only for a few MAGs, we speculate that the majority of Patescibacteria is able to attach multiple hosts just long enough to loot or exchange supplies.
Collapse
Affiliation(s)
- Narendrakumar M. Chaudhari
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Will A. Overholt
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Perla Abigail Figueroa-Gonzalez
- Department for Chemistry, Environmental Microbiology and Biotechnology, Group for Aquatic Microbial Ecology (GAME), University Duisburg-Essen, Essen, Germany
| | - Martin Taubert
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Till L. V. Bornemann
- Department for Chemistry, Environmental Microbiology and Biotechnology, Group for Aquatic Microbial Ecology (GAME), University Duisburg-Essen, Essen, Germany
| | - Alexander J. Probst
- Department for Chemistry, Environmental Microbiology and Biotechnology, Group for Aquatic Microbial Ecology (GAME), University Duisburg-Essen, Essen, Germany
| | - Martin Hölzer
- RNA Bioinformatics and High Throughput Analysis, Friedrich Schiller University, Jena, Germany
- European Virus Bioinformatics Center, Friedrich Schiller University, Jena, Germany
- Present Address: Methodology and Research Infrastructure, MF1 Bioinformatics, Robert Koch Institute, Berlin, Germany
| | - Manja Marz
- RNA Bioinformatics and High Throughput Analysis, Friedrich Schiller University, Jena, Germany
- European Virus Bioinformatics Center, Friedrich Schiller University, Jena, Germany
- FLI Leibniz Institute for Age Research, Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| |
Collapse
|
5
|
Kim H, Park T, Kwon I, Seo J. Specific inhibition of Streptococcus bovis by endolysin LyJH307 supplementation shifts the rumen microbiota and metabolic pathways related to carbohydrate metabolism. J Anim Sci Biotechnol 2021; 12:93. [PMID: 34344466 PMCID: PMC8335910 DOI: 10.1186/s40104-021-00614-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023] Open
Abstract
Background Endolysins, the bacteriophage-originated peptidoglycan hydrolases, are a promising replacement for antibiotics due to immediate lytic activity and no antibiotic resistance. The objectives of this study were to investigate the lytic activity of endolysin LyJH307 against S. bovis and to explore changes in rumen fermentation and microbiota in an in vitro system. Two treatments were used: 1) control, corn grain without LyJH307; and 2) LyJH307, corn grain with LyJH307 (4 U/mL). An in vitro fermentation experiment was performed using mixture of rumen fluid collected from two cannulated Holstein steers (450 ± 30 kg) and artificial saliva buffer mixed as 1:3 ratio for 12 h incubation time. In vitro dry matter digestibility, pH, volatile fatty acids, and lactate concentration were estimated at 12 h, and the gas production was measured at 6, 9, and 12 h. The rumen bacterial community was analyzed using 16S rRNA amplicon sequencing. Results LyJH307 supplementation at 6 h incubation markedly decreased the absolute abundance of S. bovis (approximately 70% compared to control, P = 0.0289) and increased ruminal pH (P = 0.0335) at the 12 h incubation. The acetate proportion (P = 0.0362) was significantly increased after LyJH307 addition, whereas propionate (P = 0.0379) was decreased. LyJH307 supplementation increased D-lactate (P = 0.0340) without any change in L-lactate concentration (P > 0.10). There were no significant differences in Shannon’s index, Simpson’s index, Chao1 estimates, and evenness (P > 0.10). Based on Bray-Curtis dissimilarity matrices, the LyJH307 affected the overall shift in microbiota (P = 0.097). LyJH307 supplementation induced an increase of 11 genera containing Lachnoclostridium, WCHB1–41, unclassified genus Selenomonadaceae, Paraprevotella, vadinBE97, Ruminococcus gauvreauii group, Lactobacillus, Anaerorhabdus furcosa group, Victivallaceae, Desulfuromonadaceae, and Sediminispirochaeta. The predicted functional features represented by the Kyoto Encyclopedia of Genes and Genomes pathways were changed by LyJH307 toward a decrease of carbohydrate metabolism. Conclusions LyJH307 caused a reduction of S. bovis and an increase of pH with shifts in minor microbiota and its metabolic pathways related to carbohydrate metabolism. This study provides the first insight into the availability of endolysin as a specific modulator for rumen and shows the possibility of endolysin degradation by rumen microbiota. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-021-00614-x.
Collapse
Affiliation(s)
- Hanbeen Kim
- Department of Animal Science, Life and Industry Convergence Research Institute, Pusan National University, 1268-50 Samrangjin-ro, Miryang, 50463, Republic of Korea
| | - Tansol Park
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea
| | | | - Jakyeom Seo
- Department of Animal Science, Life and Industry Convergence Research Institute, Pusan National University, 1268-50 Samrangjin-ro, Miryang, 50463, Republic of Korea.
| |
Collapse
|
6
|
Lovio-Fragoso JP, de Jesús-Campos D, López-Elías JA, Medina-Juárez LÁ, Fimbres-Olivarría D, Hayano-Kanashiro C. Biochemical and Molecular Aspects of Phosphorus Limitation in Diatoms and Their Relationship with Biomolecule Accumulation. BIOLOGY 2021; 10:biology10070565. [PMID: 34206287 PMCID: PMC8301168 DOI: 10.3390/biology10070565] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/31/2021] [Accepted: 06/09/2021] [Indexed: 11/24/2022]
Abstract
Simple Summary Phosphorus (P) is a key nutrient involved in the transfer of energy and the synthesis of several cellular components. It has been reported that P limitation in diatoms induces the synthesis of biomolecules and the accumulation of storage compounds, such as pigments, carbohydrates and lipids, with diverse biological activities, which can be used in diverse biotechnological applications. However, the molecular and biochemical mechanisms related to how diatoms cope with P deficiency are not clear, and research into this has been limited to a few species. The integration of results obtained from omics sciences could provide a broad understanding of the response of diatoms to P limitation, and the information obtained could help to solve challenges such as biomass production, by-products yield and genetic improvement of strains. Abstract Diatoms are the most abundant group of phytoplankton, and their success lies in their significant adaptation ability to stress conditions, such as nutrient limitation. Phosphorus (P) is a key nutrient involved in the transfer of energy and the synthesis of several cellular components. Molecular and biochemical mechanisms related to how diatoms cope with P deficiency are not clear, and research into this has been limited to a few species. Among the molecular responses that have been reported in diatoms cultured under P deficient conditions is the upregulation of genes encoding enzymes related to the transport, assimilation, remobilization and recycling of this nutrient. Regarding biochemical responses, due to the reduction of the requirements for carbon structures for the synthesis of proteins and phospholipids, more CO2 is fixed than is consumed by the Calvin cycle. To deal with this excess, diatoms redirect the carbon flow toward the synthesis of storage compounds such as triacylglycerides and carbohydrates, which are excreted as extracellular polymeric substances. This review aimed to gather all current knowledge regarding the biochemical and molecular mechanisms of diatoms related to managing P deficiency in order to provide a wider insight into and understanding of their responses, as well as the metabolic pathways affected by the limitation of this nutrient.
Collapse
|
7
|
Murphy CL, Biggerstaff J, Eichhorn A, Ewing E, Shahan R, Soriano D, Stewart S, VanMol K, Walker R, Walters P, Elshahed MS, Youssef NH. Genomic characterization of three novel Desulfobacterota classes expand the metabolic and phylogenetic diversity of the phylum. Environ Microbiol 2021; 23:4326-4343. [PMID: 34056821 DOI: 10.1111/1462-2920.15614] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 12/01/2022]
Abstract
We report on the genomic characterization of three novel classes in the phylum Desulfobacterota. One class (proposed name Candidatus 'Anaeroferrophillalia') was characterized by heterotrophic growth capacity, either fermentatively or utilizing polysulfide, tetrathionate or thiosulfate as electron acceptors. In the absence of organic carbon sources, autotrophic growth via the Wood-Ljungdahl (WL) pathway and using hydrogen or Fe(II) as an electron donor is also inferred for members of the 'Anaeroferrophillalia'. The second class (proposed name Candidatus 'Anaeropigmentia') was characterized by its capacity for growth at low oxygen concentration, and the capacity to synthesize the methyl/alkyl carrier CoM, an ability that is prevalent in the archaeal but rare in the bacterial domain. Pigmentation is inferred from the capacity for carotenoid (lycopene) production. The third class (proposed name Candidatus 'Zymogenia') was characterized by fermentative heterotrophic growth capacity, broad substrate range and the adaptation of some of its members to hypersaline habitats. Analysis of the distribution pattern of all three classes showed their occurrence as rare community members in multiple habitats, with preferences for anaerobic terrestrial, freshwater and marine environments over oxygenated (e.g. pelagic ocean and agricultural land) settings. Special preference for some members of the class Candidatus 'Zymogenia' for hypersaline environments such as hypersaline microbial mats and lagoons was observed.
Collapse
Affiliation(s)
- Chelsea L Murphy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - James Biggerstaff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Alexis Eichhorn
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Essences Ewing
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Ryan Shahan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Diana Soriano
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Sydney Stewart
- Department of Animal Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Kaitlynn VanMol
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Ross Walker
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Payton Walters
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| |
Collapse
|
8
|
Usai G, Cirrincione S, Re A, Manfredi M, Pagnani A, Pessione E, Mazzoli R. Clostridium cellulovorans metabolism of cellulose as studied by comparative proteomic approach. J Proteomics 2020; 216:103667. [DOI: 10.1016/j.jprot.2020.103667] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/31/2019] [Accepted: 01/22/2020] [Indexed: 12/15/2022]
|
9
|
Leavitt WD, Venceslau SS, Waldbauer J, Smith DA, Pereira IAC, Bradley AS. Proteomic and Isotopic Response of Desulfovibrio vulgaris to DsrC Perturbation. Front Microbiol 2019; 10:658. [PMID: 31031715 PMCID: PMC6470260 DOI: 10.3389/fmicb.2019.00658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 03/15/2019] [Indexed: 11/30/2022] Open
Abstract
Dissimilatory sulfate reduction is a microbial energy metabolism that can produce sulfur isotopic fractionations over a large range in magnitude. Calibrating sulfur isotopic fractionation in laboratory experiments allows for better interpretations of sulfur isotopes in modern sediments and ancient sedimentary rocks. The proteins involved in sulfate reduction are expressed in response to environmental conditions, and are collectively responsible for the net isotopic fractionation between sulfate and sulfide. We examined the role of DsrC, a key component of the sulfate reduction pathway, by comparing wildtype Desulfovibrio vulgaris DSM 644T to strain IPFG07, a mutant deficient in DsrC production. Both strains were cultivated in parallel chemostat reactors at identical turnover times and cell specific sulfate reduction rates. Under these conditions, sulfur isotopic fractionations between sulfate and sulfide of 17.3 ± 0.5‰ or 12.6 ± 0.5‰ were recorded for the wildtype or mutant, respectively. The enzymatic machinery that produced these different fractionations was revealed by quantitative proteomics. Results are consistent with a cellular-level response that throttled the supply of electrons and sulfur supply through the sulfate reduction pathway more in the mutant relative to the wildtype, independent of rate. We conclude that the smaller fractionation observed in the mutant strain is a consequence of sulfate reduction that proceeded at a rate that consumed a greater proportion of the strains overall capacity for sulfate reduction. These observations have consequences for models of sulfate reducer metabolism and how it yields different isotopic fractionations, notably, the role of DsrC in central energy metabolism.
Collapse
Affiliation(s)
- William D. Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, United States
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
- Department of Chemistry, Dartmouth College, Hanover, NH, United States
| | - Sofia S. Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Jacob Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, United States
| | - Derek A. Smith
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, United States
| | - Inês A. Cardoso Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Alexander S. Bradley
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, United States
- Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, United States
| |
Collapse
|
10
|
Abstract
Dissimilatory sulfate and sulfur reduction evolved billions of years ago and while the bacteria and archaea that use this unique metabolism employ a variety of electron donors, H(2) is most commonly used as the energy source. These prokaryotes use multiheme c-type proteins to shuttle electrons from electron donors, and electron transport complexes presumed to contain b-type hemoproteins contribute to proton charging of the membrane. Numerous sulfate and sulfur reducers use an alternate pathway for heme synthesis and, frequently, uniquely specific axial ligands are used to secure c-type heme to the protein. This review presents some of the types and functional activities of hemoproteins involved in these two dissimilatory reduction pathways.
Collapse
|
11
|
Dubini A, Mus F, Seibert M, Grossman AR, Posewitz MC. Flexibility in anaerobic metabolism as revealed in a mutant of Chlamydomonas reinhardtii lacking hydrogenase activity. J Biol Chem 2009; 284:7201-13. [PMID: 19117946 PMCID: PMC2652310 DOI: 10.1074/jbc.m803917200] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Revised: 12/29/2008] [Indexed: 11/06/2022] Open
Abstract
The green alga Chlamydomonas reinhardtii has a network of fermentation pathways that become active when cells acclimate to anoxia. Hydrogenase activity is an important component of this metabolism, and we have compared metabolic and regulatory responses that accompany anaerobiosis in wild-type C. reinhardtii cells and a null mutant strain for the HYDEF gene (hydEF-1 mutant), which encodes an [FeFe] hydrogenase maturation protein. This mutant has no hydrogenase activity and exhibits elevated accumulation of succinate and diminished production of CO2 relative to the parental strain during dark, anaerobic metabolism. In the absence of hydrogenase activity, increased succinate accumulation suggests that the cells activate alternative pathways for pyruvate metabolism, which contribute to NAD(P)H reoxidation, and continued glycolysis and fermentation in the absence of O2. Fermentative succinate production potentially proceeds via the formation of malate, and increases in the abundance of mRNAs encoding two malate-forming enzymes, pyruvate carboxylase and malic enzyme, are observed in the mutant relative to the parental strain following transfer of cells from oxic to anoxic conditions. Although C. reinhardtii has a single gene encoding pyruvate carboxylase, it has six genes encoding putative malic enzymes. Only one of the malic enzyme genes, MME4, shows a dramatic increase in expression (mRNA abundance) in the hydEF-1 mutant during anaerobiosis. Furthermore, there are marked increases in transcripts encoding fumarase and fumarate reductase, enzymes putatively required to convert malate to succinate. These results illustrate the marked metabolic flexibility of C. reinhardtii and contribute to the development of an informed model of anaerobic metabolism in this and potentially other algae.
Collapse
Affiliation(s)
- Alexandra Dubini
- Environmental Science and Engineering Division, Colorado School of Mines, Golden, Colorado 80401, USA
| | | | | | | | | |
Collapse
|
12
|
Saitoh T, Tachibana Y, Higuchi Y, Hori H, Akutsu H. Correlation between thegTensors and the Nonplanarity of Porphyrin Rings inDesulfovibrio vulgarisMiyazaki F Cytochromec3, Studied by Single Crystal EPR. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2004. [DOI: 10.1246/bcsj.77.357] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
13
|
Harada E, Fukuoka Y, Ohmura T, Fukunishi A, Kawai G, Fujiwara T, Akutsu H. Redox-coupled conformational alternations in cytochrome c(3) from D. vulgaris Miyazaki F on the basis of its reduced solution structure. J Mol Biol 2002; 319:767-78. [PMID: 12054869 DOI: 10.1016/s0022-2836(02)00367-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Heteronuclear NMR spectroscopy was performed to determine the solution structure of (15)N-labeled ferrocytochrome c(3) from Desulfovibrio vulgaris Miyazaki F (DvMF). Although the folding of the reduced cytochrome c(3) in solution was similar to that of the oxidized one in the crystal structure, the region involving hemes 1 and 2 was different. The redox-coupled conformational change is consistent with the reported solution structure of D. vulgaris Hildenborough ferrocytochrome c(3), but is different from those of other cytochromes c(3). The former is homologous with DvMF cytochrome c(3) in amino acid sequence. Small displacements of hemes 1 and 2 relative to hemes 3 and 4 were observed. This observation is consistent with the unusual behavior of the 2(1)CH(3) signal of heme 3 reported previously. As shown by the (15)N relaxation parameters of the backbone, a region between hemes 1 and 2 has more flexibility than the other regions. The results of this work strongly suggest that the cooperative reduction of hemes 1 and 2 is based on the conformational changes of the C-13 propionate of heme 1 and the aromatic ring of Tyr43, and the interaction between His34 and His 35 through covalent and coordination bonds.
Collapse
Affiliation(s)
- Erisa Harada
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | | | | | | | | | | | | |
Collapse
|