Microbial carbon mineralization in tropical lowland and montane forest soils of Peru

Climate change is affecting the amount and complexity of plant inputs to tropical forest soils. This is likely to influence the carbon (C) balance of these ecosystems by altering decomposition processes e.g., "positive priming effects" that accelerate soil organic matter mineralization. However, the mechanisms determining the magnitude of priming effects are poorly understood. We investigated potential mechanisms by adding (13)C labeled substrates, as surrogates of plant inputs, to soils from an elevation gradient of tropical lowland and montane forests. We hypothesized that priming effects would increase with elevation due to increasing microbial nitrogen limitation, and that microbial community composition would strongly influence the magnitude of priming effects. Quantifying the sources of respired C (substrate or soil organic matter) in response to substrate addition revealed no consistent patterns in priming effects with elevation. Instead we found that substrate quality (complexity and nitrogen content) was the dominant factor controlling priming effects. For example a nitrogenous substrate induced a large increase in soil organic matter mineralization whilst a complex C substrate caused negligible change. Differences in the functional capacity of specific microbial groups, rather than microbial community composition per se, were responsible for these substrate-driven differences in priming effects. Our findings suggest that the microbial pathways by which plant inputs and soil organic matter are mineralized are determined primarily by the quality of plant inputs and the functional capacity of microbial taxa, rather than the abiotic properties of the soil. Changes in the complexity and stoichiometry of plant inputs to soil in response to climate change may therefore be important in regulating soil C dynamics in tropical forest soils.This study was financed by the UK Natural Environment Research Council (NERC) grant NE/G018278/1 and is a product of the Andes Biodiversity and Ecosystem Research Group consortium (www.andesconservation.org); Patrick Meir was also supported by ARC FT110100457

Microbial carbon mineralization in tropical lowland and montane forest soils of Peru

Climate change is affecting the amount and complexity of plant inputs to tropical forest soils. This is likely to influence the carbon (C) balance of these ecosystems by altering decomposition processes e.g. ‘positive priming effects’ that accelerate soil organic matter mineralization. However, the mechanisms determining the magnitude of priming effects are poorly understood. We investigated potential mechanisms by adding 13C labelled substrates, as surrogates of plant inputs, to soils from an elevation gradient of tropical lowland and montane forests. We hypothesised that priming effects would increase with elevation due to increasing microbial nitrogen limitation, and that microbial community composition would strongly influence the magnitude of priming effects. Quantifying the sources of respired C (substrate or soil organic matter) in response to substrate addition revealed no consistent patterns in priming effects with elevation. Instead we found that substrate quality (complexity and nitrogen content) was the dominant factor controlling priming effects. For example a nitrogenous substrate induced a large increase in soil organic matter mineralization whilst a complex C substrate caused negligible change. Differences in the functional capacity of specific microbial groups, rather than microbial community composition per se, were responsible for these substrate-driven differences in priming effects. Our findings suggest that the microbial pathways by which plant inputs and soil organic matter are mineralized are determined primarily by the quality of plant inputs and the functional capacity of microbial taxa, rather than the abiotic properties of the soil. Changes in the complexity and stoichiometry of plant inputs to soil in response to climate change may therefore be important in regulating soil C dynamics in tropical forest soils

Nutrient limitations to bacterial and fungal growth during cellulose decomposition in tropical forest soils

Nutrients constrain the soil carbon cycle in tropical forests, but we lack knowledge on how these constraints vary within the soil microbial community. Here, we used in situ fertilization in a montane tropical forest and in two lowland tropical forests on contrasting soil types to test the principal hypothesis that there are different nutrient constraints to different groups of microorganisms during the decomposition of cellulose. We also tested the hypotheses that decomposers shift from nitrogen to phosphorus constraints from montane to lowland forests, respectively, and are further constrained by potassium and sodium deficiency in the western Amazon. Cellulose and nutrients (nitrogen, phosphorus, potassium, sodium, and combined) were added to soils in situ, and microbial growth on cellulose (phospholipid fatty acids and ergosterol) and respiration were measured. Microbial growth on cellulose after single nutrient additions was highest following nitrogen addition for fungi, suggesting nitrogen as the primary limiting nutrient for cellulose decomposition. This was observed at all sites, with no clear shift in nutrient constraints to decomposition between lowland and montane sites. We also observed positive respiration and fungal growth responses to sodium and potassium addition at one of the lowland sites. However, when phosphorus was added, and especially when added in combination with other nutrients, bacterial growth was highest, suggesting that bacteria out-compete fungi for nitrogen where phosphorus is abundant. In summary, nitrogen constrains fungal growth and cellulose decomposition in both lowland and montane tropical forest soils, but additional nutrients may also be of critical importance in determining the balance between fungal and bacterial decomposition of cellulose.This study is a product of the Andes Biodiversity and Ecosystem Research Group consortium (www.andesconservation.org) and was financed by the UK Natural Environment Research Council NE/G018278/1 to PM, a European Union Marie-Curie Fellowship FP7-2012-329360 to ATN and ARC award DP170104091 to PM

Source to sink: Evolution of lignin composition in the Madre de Dios River system with connection to the Amazon basin and offshore:Lignin evolution in Amazon

While lignin geochemistry has been extensively investigated in the Amazon River, little is known about lignin distribution and dynamics within deep, stratified river channels or its transformations within soils prior to delivery to rivers. We characterized lignin phenols in soils, river particulate organic matter (POM), and dissolved organic matter (DOM) across a 4 km elevation gradient in the Madre de Dios River system, Peru, as well as in marine sediments to investigate the source-to-sink evolution of lignin. In soils, we found more oxidized lignin in organic horizons relative to mineral horizons. The oxidized lignin signature was maintained during transfer into rivers, and lignin was a relatively constant fraction of bulk organic carbon in soils and riverine POM. Lignin in DOM became increasingly oxidized downstream, indicating active transformation of dissolved lignin during transport, especially in the dry season. In contrast, POM accumulated undegraded lignin downstream during the wet season, suggesting that terrestrial input exceeded in-river degradation. We discovered high concentrations of relatively undegraded lignin in POM at depth in the lower Madre de Dios River in both seasons, revealing a woody undercurrent for its transfer within these deep rivers. Our study of lignin evolution in the soil-river-ocean continuum highlights important seasonal and depth variations of river carbon components and their connection to soil carbon pools, providing new insights into fluvial carbon dynamics associated with the transfer of lignin biomarkers from source to sink

Microbial responses to warming enhance soil carbon loss following translocation across a tropical forest elevation gradient

Tropical soils contain huge carbon stocks, which climate warming is projected to reduce by stimulating organic matter decomposition, creating a positive feedback that will promote further warming. Models predict that the loss of carbon from warming soils will be mediated by microbial physiology, but no empirical data are available on the response of soil carbon and microbial physiology to warming in tropical forests, which dominate the terrestrial carbon cycle. Here we show that warming caused a considerable loss of soil carbon that was enhanced by associated changes in microbial physiology. By translocating soils across a 3000 m elevation gradient in tropical forest, equivalent to a temperature change of ± 15 °C, we found that soil carbon declined over 5 years by 4% in response to each 1 °C increase in temperature. The total loss of carbon was related to its original quantity and lability, and was enhanced by changes in microbial physiology including increased microbial carbon‐use‐efficiency, shifts in community composition towards microbial taxa associated with warmer temperatures, and increased activity of hydrolytic enzymes. These findings suggest that microbial feedbacks will cause considerable loss of carbon from tropical forest soils in response to predicted climatic warming this century

Soil carbon loss by experimental warming in a tropical forest

Tropical soils contain one-third of the carbon stored in soils globally1, so destabilization of soil organic matter caused by the warming predicted for tropical regions this century2 could accelerate climate change by releasing additional carbon dioxide (CO2) to the atmosphere3,4,5,6. Theory predicts that warming should cause only modest carbon loss from tropical soils relative to those at higher latitudes5,7, but there have been no warming experiments in tropical forests to test this8. Here we show that in situ experimental warming of a lowland tropical forest soil on Barro Colorado Island, Panama, caused an unexpectedly large increase in soil CO2 emissions. Two years of warming of the whole soil profile by four degrees Celsius increased CO2 emissions by 55 per cent compared to soils at ambient temperature. The additional CO2 originated from heterotrophic rather than autotrophic sources, and equated to a loss of 8.2 ± 4.2 (one standard error) tonnes of carbon per hectare per year from the breakdown of soil organic matter. During this time, we detected no acclimation of respiration rates, no thermal compensation or change in the temperature sensitivity of enzyme activities, and no change in microbial carbon-use efficiency. These results demonstrate that soil carbon in tropical forests is highly sensitive to warming, creating a potentially substantial positive feedback to climate chang

Climate Warming and Soil Carbon in Tropical Forests: Insights from an Elevation Gradient in the Peruvian Andes

The temperature sensitivity of soil organic matter (SOM) decomposition in tropical forests will influence future climate. Studies of a 3.5-kilometer elevation gradient in the Peruvian Andes, including short-term translocation experiments and the examination of the long-term adaptation of biota to local thermal and edaphic conditions, have revealed several factors that may regulate this sensitivity. Collectively this work suggests that, in the absence of a moisture constraint, the temperature sensitivity of decomposition is regulated by the chemical composition of plant debris (litter) and both the physical and chemical composition of preexisting SOM: higher temperature sensitivities are found in litter or SOM that is more chemically complex and in SOM that is less occluded within aggregates. In addition, the temperature sensitivity of SOM in tropical montane forests may be larger than previously recognized because of the presence of “cold-adapted” and nitrogen-limited microbial decomposers and the possible future alterations in plant and microbial communities associated with warming. Studies along elevation transects, such as those reviewed here, can reveal factors that will regulate the temperature sensitivity of SOM. They can also complement and guide in situ soil-warming experiments, which will be needed to understand how this vulnerability to temperature may be mediated by altered plant productivity under future climatic change

Source to sink: Evolution of lignin composition in the Madre de Dios River system with connection to the Amazon basin and offshore

While lignin geochemistry has been extensively investigated in the Amazon River, little is known about lignin distribution and dynamics within deep, stratified river channels or its transformations within soils prior to delivery to rivers. We characterized lignin phenols in soils, river particulate organic matter (POM), and dissolved organic matter (DOM) across a 4 km elevation gradient in the Madre de Dios River system, Peru, as well as in marine sediments to investigate the source-to-sink evolution of lignin. In soils, we found more oxidized lignin in organic horizons relative to mineral horizons. The oxidized lignin signature was maintained during transfer into rivers, and lignin was a relatively constant fraction of bulk organic carbon in soils and riverine POM. Lignin in DOM became increasingly oxidized downstream, indicating active transformation of dissolved lignin during transport, especially in the dry season. In contrast, POM accumulated undegraded lignin downstream during the wet season, suggesting that terrestrial input exceeded in-river degradation. We discovered high concentrations of relatively undegraded lignin in POM at depth in the lower Madre de Dios River in both seasons, revealing a woody undercurrent for its transfer within these deep rivers. Our study of lignin evolution in the soil-river-ocean continuum highlights important seasonal and depth variations of river carbon components and their connection to soil carbon pools, providing new insights into fluvial carbon dynamics associated with the transfer of lignin biomarkers from source to sink

Microbes follow Humboldt: temperature drives plant and soil microbial diversity patterns from the Amazon to the Andes

Soil microbial diversity, by high-throughput sequencing data to characterise the variation in marker gene sequences, for 14 sites along a 3000 m elevation gradient in tropical forest in Peru. For bacterial community composition, the 16S rRNA gene was amplified in triplicate PCR reactions using the 515f and 806r primers. For fungal community composition, the first internal transcribed spacer region (ITS1) of the rRNA gene was amplified using the ITS1-F and ITS2 primer pair

Targeting transcription regulation in cancer with a covalent CDK7 inhibitor

Tumour oncogenes include transcription factors that co-opt the general transcriptional machinery to sustain the oncogenic state, but direct pharmacological inhibition of transcription factors has so far proven difficult. However, the transcriptional machinery contains various enzymatic cofactors that can be targeted for the development of new therapeutic candidates, including cyclin-dependent kinases (CDKs). Here we present the discovery and characterization of a covalent CDK7 inhibitor, THZ1, which has the unprecedented ability to target a remote cysteine residue located outside of the canonical kinase domain, providing an unanticipated means of achieving selectivity for CDK7. Cancer cell-line profiling indicates that a subset of cancer cell lines, including human T-cell acute lymphoblastic leukaemia (T-ALL), have exceptional sensitivity to THZ1. Genome-wide analysis in Jurkat T-ALL cells shows that THZ1 disproportionally affects transcription of RUNX1 and suggests that sensitivity to THZ1 may be due to vulnerability conferred by the RUNX1 super-enhancer and the key role of RUNX1 in the core transcriptional regulatory circuitry of these tumour cells. Pharmacological modulation of CDK7 kinase activity may thus provide an approach to identify and treat tumour types that are dependent on transcription for maintenance of the oncogenic state.National Institutes of Health (U.S.) (Grant HG002668)National Institutes of Health (U.S.) (Grant CA109901