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Pold G, Bonilla-Rosso G, Saghaï A, Strous M, Jones CM, Hallin S. Phylogenetics and environmental distribution of nitric oxide-forming nitrite reductases reveal their distinct functional and ecological roles. ISME Communications 2024; 4:ycae020. [PMID: 38584645 PMCID: PMC10999283 DOI: 10.1093/ismeco/ycae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/16/2024] [Accepted: 01/29/2024] [Indexed: 04/09/2024]
Abstract
The two evolutionarily unrelated nitric oxide-producing nitrite reductases, NirK and NirS, are best known for their redundant role in denitrification. They are also often found in organisms that do not perform denitrification. To assess the functional roles of the two enzymes and to address the sequence and structural variation within each, we reconstructed robust phylogenies of both proteins with sequences recovered from 6973 isolate and metagenome-assembled genomes and identified 32 well-supported clades of structurally distinct protein lineages. We then inferred the potential niche of each clade by considering other functional genes of the organisms carrying them as well as the relative abundances of each nir gene in 4082 environmental metagenomes across diverse aquatic, terrestrial, host-associated, and engineered biomes. We demonstrate that Nir phylogenies recapitulate ecology distinctly from the corresponding organismal phylogeny. While some clades of the nitrite reductase were equally prevalent across biomes, others had more restricted ranges. Nitrifiers make up a sizeable proportion of the nitrite-reducing community, especially for NirK in marine waters and dry soils. Furthermore, the two reductases showed distinct associations with genes involved in oxidizing and reducing other compounds, indicating that the NirS and NirK activities may be linked to different elemental cycles. Accordingly, the relative abundance and diversity of NirS versus NirK vary between biomes. Our results show the divergent ecological roles NirK and NirS-encoding organisms may play in the environment and provide a phylogenetic framework to distinguish the traits associated with organisms encoding the different lineages of nitrite reductases.
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Affiliation(s)
- Grace Pold
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Germán Bonilla-Rosso
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Aurélien Saghaï
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Marc Strous
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Christopher M Jones
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
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Saghaï A, Pold G, Jones CM, Hallin S. Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes. Nat Commun 2023; 14:8249. [PMID: 38086813 PMCID: PMC10716430 DOI: 10.1038/s41467-023-44022-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Nitrate ammonification is important for soil nitrogen retention. However, the ecology of ammonifiers and their prevalence compared with denitrifiers, being competitors for nitrate, are overlooked. Here, we screen 1 million genomes for nrfA and onr, encoding ammonifier nitrite reductases. About 40% of ammonifier assemblies carry at least one denitrification gene and show higher potential for nitrous oxide production than consumption. We then use a phylogeny-based approach to recruit gene fragments of nrfA, onr and denitrification nitrite reductase genes (nirK, nirS) in 1861 global terrestrial metagenomes. nrfA outnumbers the nearly negligible onr counts in all biomes, but denitrification genes dominate, except in tundra. Random forest modelling teases apart the influence of the soil C/N on nrfA-ammonifier vs denitrifier abundance, showing an effect of nitrate rather than carbon content. This study demonstrates the multiple roles nitrate ammonifiers play in nitrogen cycling and identifies factors ultimately controlling the fate of soil nitrate.
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Affiliation(s)
- Aurélien Saghaï
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| | - Grace Pold
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| | - Christopher M Jones
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| | - Sara Hallin
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden.
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Bösch Y, Pold G, Saghaï A, Karlsson M, Jones CM, Hallin S. Distribution and Environmental Drivers of Fungal Denitrifiers in Global Soils. Microbiol Spectr 2023; 11:e0006123. [PMID: 37222601 PMCID: PMC10269876 DOI: 10.1128/spectrum.00061-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/05/2023] [Indexed: 05/25/2023] Open
Abstract
The microbial process of denitrification is the primary source of the greenhouse gas nitrous oxide (N2O) from terrestrial ecosystems. Fungal denitrifiers, unlike many bacteria, lack the N2O reductase, and thereby are sources of N2O. Still, their diversity, global distribution, and environmental determinants, as well as their relative importance, compared to bacterial and archaeal denitrifiers, remain unresolved. Employing a phylogenetically informed approach to analyze 1,980 global soil and rhizosphere metagenomes for the denitrification marker gene nirK, which codes for the copper dependent nitrite reductase in denitrification, we show that fungal denitrifiers are sparse, yet cosmopolitan and that they are dominated by saprotrophs and pathogens. Few showed biome-specific distribution patterns, although members of the Fusarium oxysporum species complex, which are known to produce substantial amounts of N2O, were proportionally more abundant and diverse in the rhizosphere than in other biomes. Fungal denitrifiers were most frequently detected in croplands, but they were most abundant in forest soils when normalized to metagenome size. Nevertheless, the overwhelming dominance of bacterial and archaeal denitrifiers suggests a much lower fungal contribution to N2O emissions than was previously estimated. In relative terms, they could play a role in soils that are characterized by a high carbon to nitrogen ratio and a low pH, especially in the tundra as well as in boreal and temperate coniferous forests. Because global warming predicts the proliferation of fungal pathogens, the prevalence of potential plant pathogens among fungal denitrifiers and the cosmopolitan distribution of these organisms suggest that fungal denitrifier abundance may increase in terrestrial ecosystems. IMPORTANCE Fungal denitrifiers, in contrast to their bacterial counterparts, are a poorly studied functional group within the nitrogen cycle, even though they produce the greenhouse gas N2O. To curb soil N2O emissions, a better understanding of their ecology and distribution in soils from different ecosystems is needed. Here, we probed a massive amount of DNA sequences and corresponding soil data from a large number of samples that represented the major soil environments for a broad understanding of fungal denitrifier diversity at the global scale. We show that fungal denitrifiers are predominantly cosmopolitan saprotrophs and opportunistic pathogens. Fungal denitrifiers constituted, on average, 1% of the total denitrifier community. This suggests that earlier estimations of fungal denitrifier abundance, and, thereby, it is also likely that the contributions of fungal denitrifiers to N2O emissions have been overestimated. Nevertheless, with many fungal denitrifiers being plant pathogens, they could become increasingly relevant, as soilborne pathogenic fungi are predicted to increase with ongoing climate change.
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Affiliation(s)
- Yvonne Bösch
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| | - Grace Pold
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| | - Aurélien Saghaï
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| | - Magnus Karlsson
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| | - Christopher M. Jones
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| | - Sara Hallin
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
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Domeignoz-Horta LA, Pold G, Erb H, Sebag D, Verrecchia E, Northen T, Louie K, Eloe-Fadrosh E, Pennacchio C, Knorr MA, Frey SD, Melillo JM, DeAngelis KM. Substrate availability and not thermal acclimation controls microbial temperature sensitivity response to long-term warming. Glob Chang Biol 2023; 29:1574-1590. [PMID: 36448874 DOI: 10.1111/gcb.16544] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/18/2022] [Indexed: 05/28/2023]
Abstract
Microbes are responsible for cycling carbon (C) through soils, and predicted changes in soil C stocks under climate change are highly sensitive to shifts in the mechanisms assumed to control the microbial physiological response to warming. Two mechanisms have been suggested to explain the long-term warming impact on microbial physiology: microbial thermal acclimation and changes in the quantity and quality of substrates available for microbial metabolism. Yet studies disentangling these two mechanisms are lacking. To resolve the drivers of changes in microbial physiology in response to long-term warming, we sampled soils from 13- and 28-year-old soil warming experiments in different seasons. We performed short-term laboratory incubations across a range of temperatures to measure the relationships between temperature sensitivity of physiology (growth, respiration, carbon use efficiency, and extracellular enzyme activity) and the chemical composition of soil organic matter. We observed apparent thermal acclimation of microbial respiration, but only in summer, when warming had exacerbated the seasonally-induced, already small dissolved organic matter pools. Irrespective of warming, greater quantity and quality of soil carbon increased the extracellular enzymatic pool and its temperature sensitivity. We propose that fresh litter input into the system seasonally cancels apparent thermal acclimation of C-cycling processes to decadal warming. Our findings reveal that long-term warming has indirectly affected microbial physiology via reduced C availability in this system, implying that earth system models including these negative feedbacks may be best suited to describe long-term warming effects on these soils.
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Affiliation(s)
- Luiz A Domeignoz-Horta
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Grace Pold
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Hailey Erb
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - David Sebag
- IFP Energies Nouvelles, Rueil-Malmaison, France
- Faculty of Geosciences and the Environment, Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Eric Verrecchia
- Faculty of Geosciences and the Environment, Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Trent Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Katherine Louie
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Emiley Eloe-Fadrosh
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Christa Pennacchio
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Melissa A Knorr
- School of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Serita D Frey
- School of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Jerry M Melillo
- The Ecosystems Center, Marine Biological Laboratories, Woods Hole, Massachusetts, USA
| | - Kristen M DeAngelis
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
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Pold G, Baillargeon N, Lepe A, Rastetter EB, Sistla SA. Warming effects on arctic tundra biogeochemistry are limited but habitat‐dependent: a meta‐analysis. Ecosphere 2021. [DOI: 10.1002/ecs2.3777] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Grace Pold
- Natural Resources Management & Environmental Sciences College of Agriculture, Food & Environmental Sciences California Polytechnic State University San Luis Obispo California USA
| | - Natalie Baillargeon
- Smith College Northampton Massachusetts USA
- Woodwell Climate Research Center Woods Hole Massachusetts USA
| | - Adan Lepe
- Amherst College Amherst Massachusetts USA
| | - Edward B. Rastetter
- Marine Biological Laboratories The Ecosystems Center Woods Hole Massachusetts USA
| | - Seeta A. Sistla
- Natural Resources Management & Environmental Sciences College of Agriculture, Food & Environmental Sciences California Polytechnic State University San Luis Obispo California USA
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Domeignoz-Horta LA, Pold G, Liu XJA, Frey SD, Melillo JM, DeAngelis KM. Microbial diversity drives carbon use efficiency in a model soil. Nat Commun 2020; 11:3684. [PMID: 32703952 PMCID: PMC7378083 DOI: 10.1038/s41467-020-17502-z] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [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: 12/18/2019] [Accepted: 06/19/2020] [Indexed: 02/01/2023] Open
Abstract
Empirical evidence for the response of soil carbon cycling to the combined effects of warming, drought and diversity loss is scarce. Microbial carbon use efficiency (CUE) plays a central role in regulating the flow of carbon through soil, yet how biotic and abiotic factors interact to drive it remains unclear. Here, we combine distinct community inocula (a biotic factor) with different temperature and moisture conditions (abiotic factors) to manipulate microbial diversity and community structure within a model soil. While community composition and diversity are the strongest predictors of CUE, abiotic factors modulated the relationship between diversity and CUE, with CUE being positively correlated with bacterial diversity only under high moisture. Altogether these results indicate that the diversity × ecosystem-function relationship can be impaired under non-favorable conditions in soils, and that to understand changes in soil C cycling we need to account for the multiple facets of global changes.
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Affiliation(s)
| | - Grace Pold
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Xiao-Jun Allen Liu
- Department of Microbiology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Serita D Frey
- School of Natural Resources and the Environment, University of New Hampshire, Durham, NH, 03824, USA
| | - Jerry M Melillo
- The Ecosystems Center, Marine Biological Laboratories, Woods Hole, MA, 02543, USA
| | - Kristen M DeAngelis
- Department of Microbiology, University of Massachusetts, Amherst, MA, 01003, USA.
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Pold G, Domeignoz-Horta LA, Morrison EW, Frey SD, Sistla SA, DeAngelis KM. Carbon Use Efficiency and Its Temperature Sensitivity Covary in Soil Bacteria. mBio 2020; 11:e02293-19. [PMID: 31964725 PMCID: PMC6974560 DOI: 10.1128/mbio.02293-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/02/2019] [Indexed: 01/11/2023] Open
Abstract
The strategy that microbial decomposers take with respect to using substrate for growth versus maintenance is one essential biological determinant of the propensity of carbon to remain in soil. To quantify the environmental sensitivity of this key physiological trade-off, we characterized the carbon use efficiency (CUE) of 23 soil bacterial isolates across seven phyla at three temperatures and with up to four substrates. Temperature altered CUE in both an isolate-specific manner and a substrate-specific manner. We searched for genes correlated with the temperature sensitivity of CUE on glucose and deemed those functional genes which were similarly correlated with CUE on other substrates to be validated as markers of CUE. Ultimately, we did not identify any such robust functional gene markers of CUE or its temperature sensitivity. However, we found a positive correlation between rRNA operon copy number and CUE, opposite what was expected. We also found that inefficient taxa increased their CUE with temperature, while those with high CUE showed a decrease in CUE with temperature. Together, our results indicate that CUE is a flexible parameter within bacterial taxa and that the temperature sensitivity of CUE is better explained by observed physiology than by genomic composition across diverse taxa. We conclude that the bacterial CUE response to temperature and substrate is more variable than previously thought.IMPORTANCE Soil microbes respond to environmental change by altering how they allocate carbon to growth versus respiration-or carbon use efficiency (CUE). Ecosystem and Earth System models, used to project how global soil C stocks will continue to respond to the climate crisis, often assume that microbes respond homogeneously to changes in the environment. In this study, we quantified how CUE varies with changes in temperature and substrate quality in soil bacteria and evaluated why CUE characteristics may differ between bacterial isolates and in response to altered growth conditions. We found that bacterial taxa capable of rapid growth were more efficient than those limited to slow growth and that taxa with high CUE were more likely to become less efficient at higher temperatures than those that were less efficient to begin with. Together, our results support the idea that the CUE temperature response is constrained by both growth rate and CUE and that this partly explains how bacteria acclimate to a warming world.
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Affiliation(s)
- Grace Pold
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Luiz A Domeignoz-Horta
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Eric W Morrison
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Serita D Frey
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Seeta A Sistla
- Natural Resources Management and Environmental Sciences, California Polytechnic State University, San Luis Obispo, California, USA
| | - Kristen M DeAngelis
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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Melillo JM, Frey SD, DeAngelis KM, Werner WJ, Bernard MJ, Bowles FP, Pold G, Knorr MA, Grandy AS. Long-term pattern and magnitude of soil carbon feedback to the climate system in a warming world. Science 2017; 358:101-105. [DOI: 10.1126/science.aan2874] [Citation(s) in RCA: 350] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/23/2017] [Indexed: 11/02/2022]
Abstract
In a 26-year soil warming experiment in a mid-latitude hardwood forest, we documented changes in soil carbon cycling to investigate the potential consequences for the climate system. We found that soil warming results in a four-phase pattern of soil organic matter decay and carbon dioxide fluxes to the atmosphere, with phases of substantial soil carbon loss alternating with phases of no detectable loss. Several factors combine to affect the timing, magnitude, and thermal acclimation of soil carbon loss. These include depletion of microbially accessible carbon pools, reductions in microbial biomass, a shift in microbial carbon use efficiency, and changes in microbial community composition. Our results support projections of a long-term, self-reinforcing carbon feedback from mid-latitude forests to the climate system as the world warms.
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Smith NG, Pold G, Goranson C, Dukes JS. Characterizing the drivers of seedling leaf gas exchange responses to warming and altered precipitation: indirect and direct effects. AoB Plants 2016; 8:plw066. [PMID: 27658816 PMCID: PMC5091920 DOI: 10.1093/aobpla/plw066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/02/2016] [Indexed: 05/29/2023]
Abstract
Anthropogenic forces are projected to lead to warmer temperatures and altered precipitation patterns globally. The impact of these climatic changes on the uptake of carbon by the land surface will, in part, determine the rate and magnitude of these changes. However, there is a great deal of uncertainty in how terrestrial ecosystems will respond to climate in the future. Here, we used a fully factorial warming (four levels) by precipitation (three levels) manipulation experiment in an old-field ecosystem in the northeastern USA to examine the impact of climatic changes on leaf carbon exchange in five species of deciduous tree seedlings. We found that photosynthesis generally increased in response to increasing precipitation and decreased in response to warming. Respiration was less sensitive to the treatments. The net result was greater leaf carbon uptake in wetter and cooler conditions across all species. Structural equation modelling revealed the primary pathway through which climate impacted leaf carbon exchange. Net photosynthesis increased with increasing stomatal conductance and photosynthetic enzyme capacity (Vcmax), and decreased with increasing respiration of leaves. Soil moisture and leaf temperature at the time of measurement most heavily influenced these primary drivers of net photosynthesis. Leaf respiration increased with increasing soil moisture, leaf temperature, and photosynthetic supply of substrates. Counter to the soil moisture response, respiration decreased with increasing precipitation amount, indicating that the response to short- (i.e. soil moisture) versus long-term (i.e. precipitation amount) water stress differed, possibly as a result of changes in the relative amounts of growth and maintenance demand for respiration over time. These data (>500 paired measurements of light and dark leaf gas exchange), now publicly available, detail the pathways by which climate can impact leaf gas exchange and could be useful for testing assumptions in land surface models.
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Affiliation(s)
- Nicholas G Smith
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA Department of Biological Sciences, Purdue University, West Lafayette, IN, USA Purdue Climate Change Research Center, Purdue University, West Lafayette, IN, USA
| | - Grace Pold
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | - Carol Goranson
- Department of Biology, University of Massachusetts, Boston, MA, USA
| | - Jeffrey S Dukes
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA Department of Biological Sciences, Purdue University, West Lafayette, IN, USA Purdue Climate Change Research Center, Purdue University, West Lafayette, IN, USA Department of Biology, University of Massachusetts, Boston, MA, USA
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Pold G, Melillo JM, DeAngelis KM. Two decades of warming increases diversity of a potentially lignolytic bacterial community. Front Microbiol 2015; 6:480. [PMID: 26042112 PMCID: PMC4438230 DOI: 10.3389/fmicb.2015.00480] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [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: 02/10/2015] [Accepted: 04/30/2015] [Indexed: 11/13/2022] Open
Abstract
As Earth's climate warms, the massive stores of carbon found in soil are predicted to become depleted, and leave behind a smaller carbon pool that is less accessible to microbes. At a long-term forest soil-warming experiment in central Massachusetts, soil respiration and bacterial diversity have increased, while fungal biomass and microbially-accessible soil carbon have decreased. Here, we evaluate how warming has affected the microbial community's capability to degrade chemically-complex soil carbon using lignin-amended BioSep beads. We profiled the bacterial and fungal communities using PCR-based methods and completed extracellular enzyme assays as a proxy for potential community function. We found that lignin-amended beads selected for a distinct community containing bacterial taxa closely related to known lignin degraders, as well as members of many genera not previously noted as capable of degrading lignin. Warming tended to drive bacterial community structure more strongly in the lignin beads, while the effect on the fungal community was limited to unamended beads. Of those bacterial operational taxonomic units (OTUs) enriched by the warming treatment, many were enriched uniquely on lignin-amended beads. These taxa may be contributing to enhanced soil respiration under warming despite reduced readily available C availability. In aggregate, these results suggest that there is genetic potential for chemically complex soil carbon degradation that may lead to extended elevated soil respiration with long-term warming.
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Affiliation(s)
- Grace Pold
- Microbiology Department, University of Massachusetts Amherst, MA, USA ; Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, MA, USA
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DeAngelis KM, Pold G, Topçuoğlu BD, van Diepen LTA, Varney RM, Blanchard JL, Melillo J, Frey SD. Long-term forest soil warming alters microbial communities in temperate forest soils. Front Microbiol 2015; 6:104. [PMID: 25762989 PMCID: PMC4327730 DOI: 10.3389/fmicb.2015.00104] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [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: 10/04/2014] [Accepted: 01/27/2015] [Indexed: 01/24/2023] Open
Abstract
Soil microbes are major drivers of soil carbon cycling, yet we lack an understanding of how climate warming will affect microbial communities. Three ongoing field studies at the Harvard Forest Long-term Ecological Research (LTER) site (Petersham, MA) have warmed soils 5°C above ambient temperatures for 5, 8, and 20 years. We used this chronosequence to test the hypothesis that soil microbial communities have changed in response to chronic warming. Bacterial community composition was studied using Illumina sequencing of the 16S ribosomal RNA gene, and bacterial and fungal abundance were assessed using quantitative PCR. Only the 20-year warmed site exhibited significant change in bacterial community structure in the organic soil horizon, with no significant changes in the mineral soil. The dominant taxa, abundant at 0.1% or greater, represented 0.3% of the richness but nearly 50% of the observations (sequences). Individual members of the Actinobacteria, Alphaproteobacteria and Acidobacteria showed strong warming responses, with one Actinomycete decreasing from 4.5 to 1% relative abundance with warming. Ribosomal RNA copy number can obfuscate community profiles, but is also correlated with maximum growth rate or trophic strategy among bacteria. Ribosomal RNA copy number correction did not affect community profiles, but rRNA copy number was significantly decreased in warming plots compared to controls. Increased bacterial evenness, shifting beta diversity, decreased fungal abundance and increased abundance of bacteria with low rRNA operon copy number, including Alphaproteobacteria and Acidobacteria, together suggest that more or alternative niche space is being created over the course of long-term warming.
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Affiliation(s)
| | - Grace Pold
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Begüm D Topçuoğlu
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Linda T A van Diepen
- Department of Natural Resources and the Environment, University of New Hampshire Durham, NH, USA
| | - Rebecca M Varney
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | | | | | - Serita D Frey
- Department of Natural Resources and the Environment, University of New Hampshire Durham, NH, USA
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