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Novak V, Andeer PF, Bowen BP, Ding Y, Zhalnina K, Hofmockel KS, Tomaka C, Harwood TV, van Winden MCM, Golini AN, Kosina SM, Northen TR. Reproducible growth of Brachypodium in EcoFAB 2.0 reveals that nitrogen form and starvation modulate root exudation. Sci Adv 2024; 10:eadg7888. [PMID: 38170767 PMCID: PMC10776018 DOI: 10.1126/sciadv.adg7888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024]
Abstract
Understanding plant-microbe interactions requires examination of root exudation under nutrient stress using standardized and reproducible experimental systems. We grew Brachypodium distachyon hydroponically in fabricated ecosystem devices (EcoFAB 2.0) under three inorganic nitrogen forms (nitrate, ammonium, and ammonium nitrate), followed by nitrogen starvation. Analyses of exudates with liquid chromatography-tandem mass spectrometry, biomass, medium pH, and nitrogen uptake showed EcoFAB 2.0's low intratreatment data variability. Furthermore, the three inorganic nitrogen forms caused differential exudation, generalized by abundant amino acids-peptides and alkaloids. Comparatively, nitrogen deficiency decreased nitrogen-containing compounds but increased shikimates-phenylpropanoids. Subsequent bioassays with two shikimates-phenylpropanoids (shikimic and p-coumaric acids) on soil bacteria or Brachypodium seedlings revealed their distinct capacity to regulate both bacterial and plant growth. Our results suggest that (i) Brachypodium alters exudation in response to nitrogen status, which can affect rhizobacterial growth, and (ii) EcoFAB 2.0 is a valuable standardized plant research tool.
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Affiliation(s)
- Vlastimil Novak
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Peter F. Andeer
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Benjamin P. Bowen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yezhang Ding
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kateryna Zhalnina
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kirsten S. Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Connor Tomaka
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Thomas V. Harwood
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Amber N. Golini
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Suzanne M. Kosina
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Trent R. Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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2
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Acharya SM, Yee MO, Diamond S, Andeer PF, Baig NF, Aladesanmi OT, Northen TR, Banfield JF, Chakraborty R. Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots. ISME Commun 2023; 3:54. [PMID: 37280433 PMCID: PMC10244434 DOI: 10.1038/s43705-023-00265-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 05/18/2023] [Accepted: 05/24/2023] [Indexed: 06/08/2023]
Abstract
For a deeper and comprehensive understanding of the composition and function of rhizosphere microbiomes, we need to focus at the scale of individual roots in standardized growth containers. Root exudation patterns are known to vary along distinct parts of the root even in juvenile plants giving rise to spatially distinct microbial niches. To address this, we analyzed the microbial community from two spatially distinct zones of the developing primary root (tip and base) in young Brachypodium distachyon grown in natural soil using standardized fabricated ecosystems known as EcoFABs as well as in more conventional pot and tubes. 16S rRNA based community analysis showed a strong rhizosphere effect resulting in significant enrichment of several OTUs belonging to Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. However, microbial community composition did not differ between root tips and root base or across different growth containers. Functional analysis of bulk metagenomics revealed significant differences between root tips and bulk soil. The genes associated with different metabolic pathways and root colonization were enriched in root tips. On the other hand, genes associated with nutrient-limitation and environmental stress were prominent in the bulk soil compared to root tips, implying the absence of easily available, labile carbon and nutrients in bulk soil relative to roots. Such insights into the relationships between developing root and microbial communities are critical for judicious understanding of plant-microbe interactions in early developmental stages of plants.
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Affiliation(s)
- Shwetha M Acharya
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mon Oo Yee
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Spencer Diamond
- Department of Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA
| | - Peter F Andeer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nameera F Baig
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Omolara T Aladesanmi
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA
| | - Romy Chakraborty
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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3
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Wang Y, Wilhelm RC, Swenson TL, Silver A, Andeer PF, Golini A, Kosina SM, Bowen BP, Buckley DH, Northen TR. Substrate Utilization and Competitive Interactions Among Soil Bacteria Vary With Life-History Strategies. Front Microbiol 2022; 13:914472. [PMID: 35756023 PMCID: PMC9225577 DOI: 10.3389/fmicb.2022.914472] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
Microorganisms have evolved various life-history strategies to survive fluctuating resource conditions in soils. However, it remains elusive how the life-history strategies of microorganisms influence their processing of organic carbon, which may affect microbial interactions and carbon cycling in soils. Here, we characterized the genomic traits, exometabolite profiles, and interactions of soil bacteria representing copiotrophic and oligotrophic strategists. Isolates were selected based on differences in ribosomal RNA operon (rrn) copy number, as a proxy for life-history strategies, with pairs of “high” and “low” rrn copy number isolates represented within the Micrococcales, Corynebacteriales, and Bacillales. We found that high rrn isolates consumed a greater diversity and amount of substrates than low rrn isolates in a defined growth medium containing common soil metabolites. We estimated overlap in substrate utilization profiles to predict the potential for resource competition and found that high rrn isolates tended to have a greater potential for competitive interactions. The predicted interactions positively correlated with the measured interactions that were dominated by negative interactions as determined through sequential growth experiments. This suggests that resource competition was a major force governing interactions among isolates, while cross-feeding of metabolic secretion likely contributed to the relatively rare positive interactions observed. By connecting bacterial life-history strategies, genomic features, and metabolism, our study advances the understanding of the links between bacterial community composition and the transformation of carbon in soils.
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Affiliation(s)
- Ying Wang
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Roland C Wilhelm
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Tami L Swenson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Anita Silver
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Peter F Andeer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Amber Golini
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Suzanne M Kosina
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States.,Department of Microbiology, Cornell University, Ithaca, NY, United States
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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4
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de Raad M, Li YV, Kuehl JV, Andeer PF, Kosina SM, Hendrickson A, Saichek NR, Golini AN, Han LZ, Wang Y, Bowen BP, Deutschbauer AM, Arkin AP, Chakraborty R, Northen TR. A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria. Front Microbiol 2022; 13:855331. [PMID: 35694313 PMCID: PMC9174792 DOI: 10.3389/fmicb.2022.855331] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Exometabolomics is an approach to assess how microorganisms alter, or react to their environments through the depletion and production of metabolites. It allows the examination of how soil microbes transform the small molecule metabolites within their environment, which can be used to study resource competition and cross-feeding. This approach is most powerful when used with defined media that enable tracking of all metabolites. However, microbial growth media have traditionally been developed for the isolation and growth of microorganisms but not metabolite utilization profiling through Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS). Here, we describe the construction of a defined medium, the Northen Lab Defined Medium (NLDM), that not only supports the growth of diverse soil bacteria but also is defined and therefore suited for exometabolomic experiments. Metabolites included in NLDM were selected based on their presence in R2A medium and soil, elemental stoichiometry requirements, as well as knowledge of metabolite usage by different bacteria. We found that NLDM supported the growth of 108 of the 110 phylogenetically diverse (spanning 36 different families) soil bacterial isolates tested and all of its metabolites were trackable through LC–MS/MS analysis. These results demonstrate the viability and utility of the constructed NLDM medium for growing and characterizing diverse microbial isolates and communities.
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Affiliation(s)
- Markus de Raad
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Yifan V. Li
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jennifer V. Kuehl
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Peter F. Andeer
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Suzanne M. Kosina
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Andrew Hendrickson
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Nicholas R. Saichek
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Amber N. Golini
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - La Zhen Han
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Ying Wang
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Benjamin P. Bowen
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Adam M. Deutschbauer
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Adam P. Arkin
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Romy Chakraborty
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Trent R. Northen
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
- Lawrence Berkeley National Laboratory, Joint Genome Institute, Berkeley, CA, United States
- *Correspondence: Trent R. Northen,
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5
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Diamond S, Andeer PF, Li Z, Crits-Christoph A, Burstein D, Anantharaman K, Lane KR, Thomas BC, Pan C, Northen TR, Banfield JF. Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms. Nat Microbiol 2019; 4:1356-1367. [PMID: 31110364 PMCID: PMC6784897 DOI: 10.1038/s41564-019-0449-y] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/03/2019] [Indexed: 12/15/2022]
Abstract
Soil microbial activity drives the carbon and nitrogen cycles and is an important determinant of atmospheric trace gas turnover, yet most soils are dominated by microorganisms with unknown metabolic capacities. Even Acidobacteria, among the most abundant bacteria in soil, remain poorly characterized, and functions across groups such as Verrucomicrobia, Gemmatimonadetes, Chloroflexi and Rokubacteria are understudied. Here, we have resolved 60 metagenomic and 20 proteomic data sets from a Mediterranean grassland soil ecosystem and recovered 793 near-complete microbial genomes from 18 phyla, representing around one-third of all microorganisms detected. Importantly, this enabled extensive genomics-based metabolic predictions for these communities. Acidobacteria from multiple previously unstudied classes have genomes that encode large enzyme complements for complex carbohydrate degradation. Alternatively, most microorganisms encode carbohydrate esterases that strip readily accessible methyl and acetyl groups from polymers like pectin and xylan, forming methanol and acetate, the availability of which could explain the high prevalence of C1 metabolism and acetate utilization in genomes. Microorganism abundances among samples collected at three soil depths and under natural and amended rainfall regimes indicate statistically higher associations of inorganic nitrogen metabolism and carbon degradation in deep and shallow soils, respectively. This partitioning decreased in samples under extended spring rainfall, indicating that long-term climate alteration can affect both carbon and nitrogen cycling. Overall, by leveraging natural and experimental gradients with genome-resolved metabolic profiles, we link microorganisms lacking prior genomic characterization to specific roles in complex carbon, C1, nitrate and ammonia transformations, and constrain factors that impact their distributions in soil.
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Affiliation(s)
- Spencer Diamond
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - Peter F Andeer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zhou Li
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - David Burstein
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Karthik Anantharaman
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Katherine R Lane
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - Chongle Pan
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
- School of Computer Science and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA.
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.
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6
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Estes ER, Andeer PF, Nordlund D, Wankel SD, Hansel CM. Biogenic manganese oxides as reservoirs of organic carbon and proteins in terrestrial and marine environments. Geobiology 2017; 15:158-172. [PMID: 27396696 DOI: 10.1111/gbi.12195] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 05/02/2016] [Indexed: 05/29/2023]
Abstract
Manganese (Mn) oxides participate in a range of interactions with organic carbon (OC) that can lead to either carbon degradation or preservation. Here, we examine the abundance and composition of OC associated with biogenic and environmental Mn oxides to elucidate the role of Mn oxides as a reservoir for carbon and their potential for selective partitioning of particular carbon species. Mn oxides precipitated in natural brackish waters and by Mn(II)-oxidizing marine bacteria and terrestrial fungi harbor considerable levels of organic carbon (4.1-17.0 mol OC per kg mineral) compared to ferromanganese cave deposits which contain 1-2 orders of magnitude lower OC. Spectroscopic analyses indicate that the chemical composition of Mn oxide-associated OC from microbial cultures is homogeneous with bacterial Mn oxides hosting primarily proteinaceous carbon and fungal Mn oxides containing both protein- and lipopolysaccharide-like carbon. The bacterial Mn oxide-hosted proteins are involved in both Mn(II) oxidation and metal binding by these bacterial species and could be involved in the mineral nucleation process as well. By comparison, the composition of OC associated with Mn oxides formed in natural settings (brackish waters and particularly in cave ferromanganese rock coatings) is more spatially and chemically heterogeneous. Cave Mn oxide-associated organic material is enriched in aliphatic C, which together with the lower carbon concentrations, points to more extensive microbial or mineral processing of carbon in this system relative to the other systems examined in this study, and as would be expected in oligotrophic cave environments. This study highlights Mn oxides as a reservoir for carbon in varied environments. The presence and in some cases dominance of proteinaceous carbon within the biogenic and natural Mn oxides may contribute to preferential preservation of proteins in sediments and dominance of protein-dependent metabolisms in the subsurface biosphere.
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Affiliation(s)
- E R Estes
- Department of Marine Chemistry and Geochemistry, MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - P F Andeer
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - D Nordlund
- Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA
| | - S D Wankel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - C M Hansel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
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7
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Butterfield CN, Li Z, Andeer PF, Spaulding S, Thomas BC, Singh A, Hettich RL, Suttle KB, Probst AJ, Tringe SG, Northen T, Pan C, Banfield JF. Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone. PeerJ 2016; 4:e2687. [PMID: 27843720 PMCID: PMC5103831 DOI: 10.7717/peerj.2687] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/14/2016] [Indexed: 01/03/2023] Open
Abstract
Annually, half of all plant-derived carbon is added to soil where it is microbially respired to CO2. However, understanding of the microbiology of this process is limited because most culture-independent methods cannot link metabolic processes to the organisms present, and this link to causative agents is necessary to predict the results of perturbations on the system. We collected soil samples at two sub-root depths (10–20 cm and 30–40 cm) before and after a rainfall-driven nutrient perturbation event in a Northern California grassland that experiences a Mediterranean climate. From ten samples, we reconstructed 198 metagenome-assembled genomes that represent all major phylotypes. We also quantified 6,835 proteins and 175 metabolites and showed that after the rain event the concentrations of many sugars and amino acids approach zero at the base of the soil profile. Unexpectedly, the genomes of novel members of the Gemmatimonadetes and Candidate Phylum Rokubacteria phyla encode pathways for methylotrophy. We infer that these abundant organisms contribute substantially to carbon turnover in the soil, given that methylotrophy proteins were among the most abundant proteins in the proteome. Previously undescribed Bathyarchaeota and Thermoplasmatales archaea are abundant in deeper soil horizons and are inferred to contribute appreciably to aromatic amino acid degradation. Many of the other bacteria appear to breakdown other components of plant biomass, as evidenced by the prevalence of various sugar and amino acid transporters and corresponding hydrolyzing machinery in the proteome. Overall, our work provides organism-resolved insight into the spatial distribution of bacteria and archaea whose activities combine to degrade plant-derived organics, limiting the transport of methanol, amino acids and sugars into underlying weathered rock. The new insights into the soil carbon cycle during an intense period of carbon turnover, including biogeochemical roles to previously little known soil microbes, were made possible via the combination of metagenomics, proteomics, and metabolomics.
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Affiliation(s)
- Cristina N Butterfield
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | - Zhou Li
- Chemical Sciences Division, Oak Ridge National Laboratory , Oak Ridge , TN , Unites States
| | - Peter F Andeer
- Lawrence Berkeley National Laboratory , Berkeley , CA , United States
| | - Susan Spaulding
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | - Brian C Thomas
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | - Andrea Singh
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory , Oak Ridge , TN , Unites States
| | - Kenwyn B Suttle
- Department of Ecology and Evolutionary Biology, University of California , Santa Cruz , CA , United States
| | - Alexander J Probst
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | | | - Trent Northen
- Lawrence Berkeley National Laboratory , Berkeley , CA , United States
| | - Chongle Pan
- Chemical Sciences Division, Oak Ridge National Laboratory , Oak Ridge , TN , Unites States
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, United States; Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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8
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Andeer PF, Learman DR, McIlvin M, Dunn JA, Hansel CM. Extracellular haem peroxidases mediate Mn(II) oxidation in a marine Roseobacter bacterium via superoxide production. Environ Microbiol 2015; 17:3925-36. [PMID: 25923595 DOI: 10.1111/1462-2920.12893] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 04/24/2015] [Accepted: 04/25/2015] [Indexed: 12/20/2022]
Abstract
Manganese (Mn) oxides are among the strongest sorbents and oxidants in environmental systems. A number of biotic and abiotic pathways induce the oxidation of Mn(II) to Mn oxides. Here, we use a combination of proteomic analyses and activity assays, to identify the enzyme(s) responsible for extracellular superoxide-mediated Mn oxide formation by a bacterium within the ubiquitous Roseobacter clade. We show that animal haem peroxidases (AHPs) located on the outer membrane and within the secretome are responsible for Mn(II) oxidation. These novel peroxidases have previously been implicated in direct Mn(II) oxidation by phylogenetically diverse bacteria. Yet, we show that in this Roseobacter species, AHPs mediate Mn(II) oxidation not through a direct reaction but by producing superoxide and likely also by degrading hydrogen peroxide. These findings point to a eukaryotic-like oscillatory oxidative-peroxidative enzymatic cycle by these AHPs that leads to Mn oxide formation by this organism. AHP expression appears unaffected by Mn(II), yet the large energetic investment required to produce and secrete these enzymes points to an as yet unknown physiological function. These findings are further evidence that bacterial peroxidases and secreted enzymes, in general, are unappreciated controls on the cycling of metals and reactive oxygen species (ROS), and by extension carbon, in natural systems.
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Affiliation(s)
- Peter F Andeer
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, 266 Woods Hole Rd MS# 52, Woods Hole, MA, 02543, USA
| | - Deric R Learman
- Department of Biology, Earth and Atmospheric Science, 190 Brooks Hall, Mt. Pleasant, MI, 48859, USA
| | - Matt McIlvin
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, 266 Woods Hole Rd MS# 52, Woods Hole, MA, 02543, USA
| | - James A Dunn
- Department of Biology, Earth and Atmospheric Science, 190 Brooks Hall, Mt. Pleasant, MI, 48859, USA
| | - Colleen M Hansel
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, 266 Woods Hole Rd MS# 52, Woods Hole, MA, 02543, USA
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9
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Abstract
Superoxide and other reactive oxygen species (ROS) originate from several natural sources and profoundly influence numerous elemental cycles, including carbon and trace metals. In the deep ocean, the permanent absence of light precludes currently known ROS sources, yet ROS production mysteriously occurs. Here, we show that taxonomically and ecologically diverse heterotrophic bacteria from aquatic and terrestrial environments are a vast, unrecognized, and light-independent source of superoxide, and perhaps other ROS derived from superoxide. Superoxide production by a model bacterium within the ubiquitous Roseobacter clade involves an extracellular oxidoreductase that is stimulated by the reduced form of nicotinamide adenine dinucleotide (NADH), suggesting a surprising homology with eukaryotic organisms. The consequences of ROS cycling in immense aphotic zones representing key sites of nutrient regeneration and carbon export must now be considered, including potential control of carbon remineralization and metal bioavailability.
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Affiliation(s)
- Julia M Diaz
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
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