Microbial-derived soil organic matter (SOM), or necromass, is an important source of SOM and is s... more Microbial-derived soil organic matter (SOM), or necromass, is an important source of SOM and is sensitive to climate warming. Soil classification systems consider soil physicochemical properties that influence SOM, hinting at the potential utility of incorporating classification systems in soil carbon (C) projections. Currently, there is no consensus on climate warming effects on necromass and if these responses vary across reference soil groups. To estimate the vulnerability of necromass to climate warming, we performed a meta-analysis of publications examining in situ experimental soil warming effects on microbial necromass via amino sugar analysis. We built generalized linear models (GLM) to explore if soil groups and warming methodologies can be used to predict necromass stocks. Our results showed that warming effect sizes on necromass were not uniform across reference soil groups. Specifically, warming effect sizes were generally positive in permafrost soils but negative in cal...
<p>Venn diagrams of differentially expressed genes, where <b>(A)</b> green circ... more <p>Venn diagrams of differentially expressed genes, where <b>(A)</b> green circles indicate number of total genes are up-regulated each time point, and <b>(B)</b> red circles indicate number of total genes were down-regulated each time point. EE indicates cells analyzed in early exponential phase, ME, mid-exponential phase and ES, early stationary phase, where actual times of sampling each cell population is indicated in the methods as well as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0186440#pone.0186440.g001" target="_blank">Fig 1A</a>. <b>(C)</b> Changes in the gene profile as a result of lignin exposure in early exponential phase, mid-exponential and early stationary phase of growth. In the right side of each chart (blue), number of genes with increased relative abundance, and in the left side (red), number of genes with lower relative abundance. The genes are grouped according to functional class as defined by COG annotation.</p
Soils are the largest repository of organic carbon (C) in the terrestrial biosphere and represent... more Soils are the largest repository of organic carbon (C) in the terrestrial biosphere and represent an important source of CO2 to the atmosphere. Microbes are key drivers of C cycling and exhibit a large range in C use efficiency (CUE), the fraction of substrate C incorporated into biomass per substrate assimilated. While small changes in CUE can have profound effects on soil CO2 flux, our understanding of the intersection of genomic and abiotic factors driving soil CUE dynamics is still very limited. This research couples two culture collections of fungi and bacteria isolated from a long-term soil warming experiment at Harvard Forest, where soils have been heated 5C above ambient for 26 years. We have over a decade of field measurements of C cycling and microbial community analyses using metagenomics and metatranscriptomics. Because microbial feedbacks to the environment are regulated at the organismic level, the foundation of this research is the physiology and genomics of CUE among isolates that we have determined to be either dominant in our soil system, sensitive to climate change factors, or both. Experiments using artificial soil, lab incubations of field-collected soil, and a field manipulation will validate potential omics-informed, novel genomic markers to be used as proxies for CUE in models. Towards our first goal of defining genomic markers of CUE response to environmental change, we have been defining the physiological response of bacterial and fungal isolates to changes in substrate and temperature in the lab. The CUE of fifteen soil bacteria covering six phyla is being evaluated under three temperatures and up to four C sources, with a similar study being conducted for fungi. Both bacterial and fungal isolates show diverse temperature responses, with some bacterial isolates showing reduced efficiency at higher temperatures while others showed no change or an increase. An exploratory analysis determined that bacterial genomes enriched in energy generation and metabolism tended to show a decrease in CUE on glucose at higher temperatures, while those relatively depleted in these genes tended to show an increase. This analysis was facilitated by computational tools generated by our group for automating steps in multigene phylogenetic tree production and will be followed up in the upcoming year with the development and calculation of metrics for metabolic complexity correlated with CUE. For objective 2, we have finalized method development for measuring microbial growth and CUE in soil using a novel, substrate-free approach with O-H2O. This method was found to be more sensitive and interpretable than traditional C approaches. Cultivation of select fungal and bacterial isolates and of simplified soil-derived microbial consortia in artificial soil shows a promising route for linking the liquid-culture-based evaluation of genomic markers of CUE sensitivity in natural soils. A qPCR-based approach is being developed to estimate fungal and bacterial biomass and growth in artificial soil, and we have begun to use it to evaluate CUE of bacteria under a range of temperatures and moistures. Expansion of results to natural soil communities and the consortia will enable us to independently validate genomic markers of efficiency identified in isolates. In pursuit of objective 3, the data derived from the field and microbial laboratory studies will be used to improve model parameterization of terrestrial system responses to environmental change. Incorporating the range of CUE temperature sensitivities observed in bacterial isolates into the litter decomposition model DEMENT confirms that predicted soil C stock response to warming is highly sensitive to this parameter. Continued work to refine the “soil” version of this model with organo-mineral interactions will enable predictions of slower-cycling soil C pools. We will also incorporate the genomics-informed data on microbial CUE combined with field measurements from a long-term warming and warming × nitrogen study into a stoichiometrically-coupled, acclimating microbe-plant-soil model (SCAMPS) that aggregates microbial dynamics at the community-scale and compare these simulations with the guild-based microbial models (DEMENT and MIMICS). Understanding the genes, metabolic pathways, and phylogenetic signals associated with microbial CUE that drive soil community responses to key global change drivers will provide a stronger basis for modeling soil C dynamics and climate-C feedbacks. Our research will establish a path by which new and extant -omics datasets may be integrated into ecosystem models. These new proxies should create greater power to infer the sensitivity of CUE to environmental dynamics and the tendency of CUE to change and adapt over long times. Publications related to this research 1. Grace Pold, Erin M. Conlon, Marcel Huntemann, Manoj Pillay, Natalia Mikhailova, Dimitrios Stamatis, T.B.K. Reddy, Chris Daum, Nicole Shapiro, Nikos Kyrpides, Tanja…
More than two decades of experimental soil warming in the Prospect Hill tract of the Harvard Fore... more More than two decades of experimental soil warming in the Prospect Hill tract of the Harvard Forest has revealed non-linear soil respiration (HF005) and soil carbon loss patterns (Melillo et al., Science, 2017). The datasets here were collected to evaluate how the quantity and quality of soil carbon has been affected by 5C warming, and to assess the role that altered extracellular enzyme allocation may play in this. We collected soils over the 2014 growing season, after 23 years of soil warming. We confirmed previous results that warming had depleted the soil of organic matter, and this was accompanied by an overall decrease in microbial biomass particularly apparent in the forest floor in the fall. Using pyrolysis-GCMS, we found that the relative abundance of soil organic matter compound classes was unaffected by warming in the upper organic horizon ("forest floor"). However, lipids increased in relative abundance to the detriment of polysaccharides and lignin in the uppe...
Soil microbial carbon use efficiency (CUE) is a combination of growth and respiration, which may ... more Soil microbial carbon use efficiency (CUE) is a combination of growth and respiration, which may respond differently to climate change depending on physical protection of soil carbon (C) and its availability to microbes. In a mid-latitude hardwood forest in central Massachusetts, 27 years of soil warming (+5 ◦C) has resulted in C loss and altered soil organic matter (SOM) quality, yet the underlying mechanisms remain unclear. Here, we hypothesized that long-term warming reduces physical aggregate protection of SOM, microbial CUE, and its temperature sensitivity. Soil was separated into macroaggregate (250–2000 μm) and microaggregate (less than 250 μm) fractions, and CUE was measured with 18O-enriched water in samples incubated at 15 and 25 ◦C for 24 h. We found that long-term warming reduced soil C and nitrogen concentrations and extracellular enzyme activity in macroaggregates, but did not affect physical protection of SOM. Long-term warming showed little effect on CUE or microbial...
As Earth's climate warms, soil carbon pools and the microbes that process them may change, al... more As Earth's climate warms, soil carbon pools and the microbes that process them may change, altering the way in which carbon is recycled in soil. We used bacterial cultivation to evaluate the hypothesis that experimentally raising soil temperatures by 5°C for 20 years increased the potential for temperate forest soil microbial communities to degrade carbohydrates. A greater proportion of the 295 bacteria from 6 phyla (10 classes, 14 orders, and 34 families) isolated from heated plots in the 20-year experiment were able to depolymerize cellulose and xylan than bacterial isolates from control soils. These findings indicate that the enrichment of bacteria capable of degrading carbohydrates could be important for accelerated carbon cycling in a warmer world. Data for the isolates from the Harvard Forest culturing project is archived at https://osf.io/ahb2v/.
The acceleration of global warming due to terrestrial carbon (C)-cycle feedbacks is likely to be ... more The acceleration of global warming due to terrestrial carbon (C)-cycle feedbacks is likely to be an important, though poorly defined, component of future climate change. Both the sign and magnitude of these feedbacks in the real Earth system are still highly uncertain due to gaps in basic understanding of terrestrial ecosystem processes. This research takes advantage of an ongoing long-term soil warming experiment in which soils at the Harvard Forest LTER in Massachusetts have been heated for 24 years. By examining this long-term climate warming manipulation, this research targets two of the biggest questions in soil carbon response to climate warming: how will carbon use efficiency and physical protection of carbon altered in a warming world?
Background/Question/Methods Application of the existing theoretical frameworks of macro-organisma... more Background/Question/Methods Application of the existing theoretical frameworks of macro-organismal community ecology to complex microbial communities promises to provide a structure and clarity to otherwise huge and overwhelmingly complex sets of data. For many years, analysis of naturally-occurring microbial communities was limited by inability to identify prokaryotes and associate functional roles with populations. Rapid expansion of technology for analysis of community metagenomes now enables microbial ecologists to more comprehensively and realistically describe microbial communities. Two case studies using molecular characterization demonstrate the potentials and the pitfalls of soil microbial community analysis: one based on 16S RNA and the other on functional genes and transcripts. Results/Conclusions In the first study, trajectories of subsurface bacterial assemblages receiving carbon augmentation were followed using data from high density microarray analyses. Ordination ana...
Background/Question/Methods Soils store more carbon than the vegetation and atmosphere combined, ... more Background/Question/Methods Soils store more carbon than the vegetation and atmosphere combined, yet we still know relatively little about how the soil microbes mediating the formation and loss of organic matter in the pedosphere will respond to elevated global temperatures. After 20+ years of experimental 5°C warming in mixed deciduous stands at the Harvard Forest in central Massachusetts, it is clear that purely kinetic or substrate availability effects cannot explain observed changes in soil respiration, and that adaptation of the bacterial community is likely to play a role. Specifically, a previously-observed decrease in the fungal:bacterial ratio and increased bacterial diversity with warming at this site indicate that bacteria may be playing an increasingly important role in recalcitrant carbon decomposition. Here we set out to more directly evaluate this hypothesis by incubating unamended or lignin-baited Bio-Sep beads, an inert porous medium, at two depths in the organic ho...
Background/Question/Methods Earth's climate is warming, and if increased temperature accelera... more Background/Question/Methods Earth's climate is warming, and if increased temperature accelerates SOM decomposition then carbon (C) stored in soils will transfer to the atmosphere, resulting in a self-reinforcing (positive) feedback to the climate system. Though soil microbes are major drivers of soil C cycling, we lack an understanding of how long-term warming affects them. Ongoing field studies in the Harvard Forest (Petersham, MA) have experienced 5°C above ambient soil temperatures at three replicated sites for 5, 8 and 20 years, which now correspond to three distinct phases of CO2 emissions observed in the oldest field study site. Previous studies have suggested warming-induced decreasing abundance of fungi and adaptation of microbial communities to more efficiently decompose recalcitrant soil C in these sites. To analyze changing diversity among bacterial communities, we sequenced the 16S ribosomal RNA genes using Illumina technology and performed quantitative PCR to unders...
The highly weathered soils of upland humid tropical forests are characterized by rapidly fluctuat... more The highly weathered soils of upland humid tropical forests are characterized by rapidly fluctuating redox conditions, dominated by Fe-oxide mineralogy, and have relatively low sulfate availability. To assess how fluctuating redox conditions and accompanying biogeochemistry impact microbial community structure and function, we collected soil cores from the Luquillo LTER forest in Puerto Rico and incubated them for 32 days under
Microbial-derived soil organic matter (SOM), or necromass, is an important source of SOM and is s... more Microbial-derived soil organic matter (SOM), or necromass, is an important source of SOM and is sensitive to climate warming. Soil classification systems consider soil physicochemical properties that influence SOM, hinting at the potential utility of incorporating classification systems in soil carbon (C) projections. Currently, there is no consensus on climate warming effects on necromass and if these responses vary across reference soil groups. To estimate the vulnerability of necromass to climate warming, we performed a meta-analysis of publications examining in situ experimental soil warming effects on microbial necromass via amino sugar analysis. We built generalized linear models (GLM) to explore if soil groups and warming methodologies can be used to predict necromass stocks. Our results showed that warming effect sizes on necromass were not uniform across reference soil groups. Specifically, warming effect sizes were generally positive in permafrost soils but negative in cal...
<p>Venn diagrams of differentially expressed genes, where <b>(A)</b> green circ... more <p>Venn diagrams of differentially expressed genes, where <b>(A)</b> green circles indicate number of total genes are up-regulated each time point, and <b>(B)</b> red circles indicate number of total genes were down-regulated each time point. EE indicates cells analyzed in early exponential phase, ME, mid-exponential phase and ES, early stationary phase, where actual times of sampling each cell population is indicated in the methods as well as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0186440#pone.0186440.g001" target="_blank">Fig 1A</a>. <b>(C)</b> Changes in the gene profile as a result of lignin exposure in early exponential phase, mid-exponential and early stationary phase of growth. In the right side of each chart (blue), number of genes with increased relative abundance, and in the left side (red), number of genes with lower relative abundance. The genes are grouped according to functional class as defined by COG annotation.</p
Soils are the largest repository of organic carbon (C) in the terrestrial biosphere and represent... more Soils are the largest repository of organic carbon (C) in the terrestrial biosphere and represent an important source of CO2 to the atmosphere. Microbes are key drivers of C cycling and exhibit a large range in C use efficiency (CUE), the fraction of substrate C incorporated into biomass per substrate assimilated. While small changes in CUE can have profound effects on soil CO2 flux, our understanding of the intersection of genomic and abiotic factors driving soil CUE dynamics is still very limited. This research couples two culture collections of fungi and bacteria isolated from a long-term soil warming experiment at Harvard Forest, where soils have been heated 5C above ambient for 26 years. We have over a decade of field measurements of C cycling and microbial community analyses using metagenomics and metatranscriptomics. Because microbial feedbacks to the environment are regulated at the organismic level, the foundation of this research is the physiology and genomics of CUE among isolates that we have determined to be either dominant in our soil system, sensitive to climate change factors, or both. Experiments using artificial soil, lab incubations of field-collected soil, and a field manipulation will validate potential omics-informed, novel genomic markers to be used as proxies for CUE in models. Towards our first goal of defining genomic markers of CUE response to environmental change, we have been defining the physiological response of bacterial and fungal isolates to changes in substrate and temperature in the lab. The CUE of fifteen soil bacteria covering six phyla is being evaluated under three temperatures and up to four C sources, with a similar study being conducted for fungi. Both bacterial and fungal isolates show diverse temperature responses, with some bacterial isolates showing reduced efficiency at higher temperatures while others showed no change or an increase. An exploratory analysis determined that bacterial genomes enriched in energy generation and metabolism tended to show a decrease in CUE on glucose at higher temperatures, while those relatively depleted in these genes tended to show an increase. This analysis was facilitated by computational tools generated by our group for automating steps in multigene phylogenetic tree production and will be followed up in the upcoming year with the development and calculation of metrics for metabolic complexity correlated with CUE. For objective 2, we have finalized method development for measuring microbial growth and CUE in soil using a novel, substrate-free approach with O-H2O. This method was found to be more sensitive and interpretable than traditional C approaches. Cultivation of select fungal and bacterial isolates and of simplified soil-derived microbial consortia in artificial soil shows a promising route for linking the liquid-culture-based evaluation of genomic markers of CUE sensitivity in natural soils. A qPCR-based approach is being developed to estimate fungal and bacterial biomass and growth in artificial soil, and we have begun to use it to evaluate CUE of bacteria under a range of temperatures and moistures. Expansion of results to natural soil communities and the consortia will enable us to independently validate genomic markers of efficiency identified in isolates. In pursuit of objective 3, the data derived from the field and microbial laboratory studies will be used to improve model parameterization of terrestrial system responses to environmental change. Incorporating the range of CUE temperature sensitivities observed in bacterial isolates into the litter decomposition model DEMENT confirms that predicted soil C stock response to warming is highly sensitive to this parameter. Continued work to refine the “soil” version of this model with organo-mineral interactions will enable predictions of slower-cycling soil C pools. We will also incorporate the genomics-informed data on microbial CUE combined with field measurements from a long-term warming and warming × nitrogen study into a stoichiometrically-coupled, acclimating microbe-plant-soil model (SCAMPS) that aggregates microbial dynamics at the community-scale and compare these simulations with the guild-based microbial models (DEMENT and MIMICS). Understanding the genes, metabolic pathways, and phylogenetic signals associated with microbial CUE that drive soil community responses to key global change drivers will provide a stronger basis for modeling soil C dynamics and climate-C feedbacks. Our research will establish a path by which new and extant -omics datasets may be integrated into ecosystem models. These new proxies should create greater power to infer the sensitivity of CUE to environmental dynamics and the tendency of CUE to change and adapt over long times. Publications related to this research 1. Grace Pold, Erin M. Conlon, Marcel Huntemann, Manoj Pillay, Natalia Mikhailova, Dimitrios Stamatis, T.B.K. Reddy, Chris Daum, Nicole Shapiro, Nikos Kyrpides, Tanja…
More than two decades of experimental soil warming in the Prospect Hill tract of the Harvard Fore... more More than two decades of experimental soil warming in the Prospect Hill tract of the Harvard Forest has revealed non-linear soil respiration (HF005) and soil carbon loss patterns (Melillo et al., Science, 2017). The datasets here were collected to evaluate how the quantity and quality of soil carbon has been affected by 5C warming, and to assess the role that altered extracellular enzyme allocation may play in this. We collected soils over the 2014 growing season, after 23 years of soil warming. We confirmed previous results that warming had depleted the soil of organic matter, and this was accompanied by an overall decrease in microbial biomass particularly apparent in the forest floor in the fall. Using pyrolysis-GCMS, we found that the relative abundance of soil organic matter compound classes was unaffected by warming in the upper organic horizon ("forest floor"). However, lipids increased in relative abundance to the detriment of polysaccharides and lignin in the uppe...
Soil microbial carbon use efficiency (CUE) is a combination of growth and respiration, which may ... more Soil microbial carbon use efficiency (CUE) is a combination of growth and respiration, which may respond differently to climate change depending on physical protection of soil carbon (C) and its availability to microbes. In a mid-latitude hardwood forest in central Massachusetts, 27 years of soil warming (+5 ◦C) has resulted in C loss and altered soil organic matter (SOM) quality, yet the underlying mechanisms remain unclear. Here, we hypothesized that long-term warming reduces physical aggregate protection of SOM, microbial CUE, and its temperature sensitivity. Soil was separated into macroaggregate (250–2000 μm) and microaggregate (less than 250 μm) fractions, and CUE was measured with 18O-enriched water in samples incubated at 15 and 25 ◦C for 24 h. We found that long-term warming reduced soil C and nitrogen concentrations and extracellular enzyme activity in macroaggregates, but did not affect physical protection of SOM. Long-term warming showed little effect on CUE or microbial...
As Earth's climate warms, soil carbon pools and the microbes that process them may change, al... more As Earth's climate warms, soil carbon pools and the microbes that process them may change, altering the way in which carbon is recycled in soil. We used bacterial cultivation to evaluate the hypothesis that experimentally raising soil temperatures by 5°C for 20 years increased the potential for temperate forest soil microbial communities to degrade carbohydrates. A greater proportion of the 295 bacteria from 6 phyla (10 classes, 14 orders, and 34 families) isolated from heated plots in the 20-year experiment were able to depolymerize cellulose and xylan than bacterial isolates from control soils. These findings indicate that the enrichment of bacteria capable of degrading carbohydrates could be important for accelerated carbon cycling in a warmer world. Data for the isolates from the Harvard Forest culturing project is archived at https://osf.io/ahb2v/.
The acceleration of global warming due to terrestrial carbon (C)-cycle feedbacks is likely to be ... more The acceleration of global warming due to terrestrial carbon (C)-cycle feedbacks is likely to be an important, though poorly defined, component of future climate change. Both the sign and magnitude of these feedbacks in the real Earth system are still highly uncertain due to gaps in basic understanding of terrestrial ecosystem processes. This research takes advantage of an ongoing long-term soil warming experiment in which soils at the Harvard Forest LTER in Massachusetts have been heated for 24 years. By examining this long-term climate warming manipulation, this research targets two of the biggest questions in soil carbon response to climate warming: how will carbon use efficiency and physical protection of carbon altered in a warming world?
Background/Question/Methods Application of the existing theoretical frameworks of macro-organisma... more Background/Question/Methods Application of the existing theoretical frameworks of macro-organismal community ecology to complex microbial communities promises to provide a structure and clarity to otherwise huge and overwhelmingly complex sets of data. For many years, analysis of naturally-occurring microbial communities was limited by inability to identify prokaryotes and associate functional roles with populations. Rapid expansion of technology for analysis of community metagenomes now enables microbial ecologists to more comprehensively and realistically describe microbial communities. Two case studies using molecular characterization demonstrate the potentials and the pitfalls of soil microbial community analysis: one based on 16S RNA and the other on functional genes and transcripts. Results/Conclusions In the first study, trajectories of subsurface bacterial assemblages receiving carbon augmentation were followed using data from high density microarray analyses. Ordination ana...
Background/Question/Methods Soils store more carbon than the vegetation and atmosphere combined, ... more Background/Question/Methods Soils store more carbon than the vegetation and atmosphere combined, yet we still know relatively little about how the soil microbes mediating the formation and loss of organic matter in the pedosphere will respond to elevated global temperatures. After 20+ years of experimental 5°C warming in mixed deciduous stands at the Harvard Forest in central Massachusetts, it is clear that purely kinetic or substrate availability effects cannot explain observed changes in soil respiration, and that adaptation of the bacterial community is likely to play a role. Specifically, a previously-observed decrease in the fungal:bacterial ratio and increased bacterial diversity with warming at this site indicate that bacteria may be playing an increasingly important role in recalcitrant carbon decomposition. Here we set out to more directly evaluate this hypothesis by incubating unamended or lignin-baited Bio-Sep beads, an inert porous medium, at two depths in the organic ho...
Background/Question/Methods Earth's climate is warming, and if increased temperature accelera... more Background/Question/Methods Earth's climate is warming, and if increased temperature accelerates SOM decomposition then carbon (C) stored in soils will transfer to the atmosphere, resulting in a self-reinforcing (positive) feedback to the climate system. Though soil microbes are major drivers of soil C cycling, we lack an understanding of how long-term warming affects them. Ongoing field studies in the Harvard Forest (Petersham, MA) have experienced 5°C above ambient soil temperatures at three replicated sites for 5, 8 and 20 years, which now correspond to three distinct phases of CO2 emissions observed in the oldest field study site. Previous studies have suggested warming-induced decreasing abundance of fungi and adaptation of microbial communities to more efficiently decompose recalcitrant soil C in these sites. To analyze changing diversity among bacterial communities, we sequenced the 16S ribosomal RNA genes using Illumina technology and performed quantitative PCR to unders...
The highly weathered soils of upland humid tropical forests are characterized by rapidly fluctuat... more The highly weathered soils of upland humid tropical forests are characterized by rapidly fluctuating redox conditions, dominated by Fe-oxide mineralogy, and have relatively low sulfate availability. To assess how fluctuating redox conditions and accompanying biogeochemistry impact microbial community structure and function, we collected soil cores from the Luquillo LTER forest in Puerto Rico and incubated them for 32 days under
Uploads