Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil.

Phosphorus is a scarce nutrient in many tropical ecosystems, yet how soil microbial communities cope with growth-limiting phosphorus deficiency at the gene and protein levels remains unknown. Here, we report a metagenomic and metaproteomic comparison of microbial communities in phosphorus-deficient and phosphorus-rich soils in a 17-year fertilization experiment in a tropical forest. The large-scale proteogenomics analyses provided extensive coverage of many microbial functions and taxa in the complex soil communities. A greater than fourfold increase in the gene abundance of 3-phytase was the strongest response of soil communities to phosphorus deficiency. Phytase catalyses the release of phosphate from phytate, the most recalcitrant phosphorus-containing compound in soil organic matter. Genes and proteins for the degradation of phosphorus-containing nucleic acids and phospholipids, as well as the decomposition of labile carbon and nitrogen, were also enhanced in the phosphorus-deficient soils. In contrast, microbial communities in the phosphorus-rich soils showed increased gene abundances for the degradation of recalcitrant aromatic compounds, transformation of nitrogenous compounds and assimilation of sulfur. Overall, these results demonstrate the adaptive allocation of genes and proteins in soil microbial communities in response to shifting nutrient constraints

Radiocarbon Analyses Quantify Peat Carbon Losses With Increasing Temperature in a Whole Ecosystem Warming Experiment

Climate warming is expected to accelerate peatland degradation and release rates of carbon dioxide (CO2) and methane (CH4). Spruce and Peatlands Responses Under Changing Environments is an ecosystem-scale climate manipulation experiment, designed to examine peatland ecosystem response to climate forcings. We examined whether heating up to +9 °C to 3 m-deep in a peat bog over a 7-year period led to higher C turnover and CO2 and CH4 emissions, by measuring 14C of solid peat, dissolved organic carbon (DOC), CH4, and dissolved CO2 (DIC). DOC, a major substrate for heterotrophic respiration, increased significantly with warming. There was no 7-year trend in the DI14 C of the ambient plots which remained similar to their DO14 C. At +6.75 °C and +9 °C, the 14C of DIC, a product of microbial respiration, initially resembled ambient plots but became more depleted over 7 years of warming. We attributed the shifts in DI14 C to the increasing importance of solid phase peat as a substrate for microbial respiration and quantified this shift via the radiocarbon mass balance. The mass-balance model revealed increases in peat-supported respiration of the catotelm depths in heated plots over time and relative to ambient enclosures, from a baseline of 20%–25% in ambient enclosures, to 35%–40% in the heated plots. We find that warming stimulates microorganisms to respire ancient peat C, deposited under prior climate (cooler) conditions. This apparent destabilization of the large peat C reservoir has implications for peatland-climate feedbacks especially if the balance of the peatland is tipped from net C sink to C source. Plain Language Summary Since the end of the last glacial period, about 20 thousand years ago, peatlands have taken up carbon and now store an amount nearly equivalent to the quantity in the atmosphere. Microorganisms consume and respire that peat C releasing it back to the atmosphere as CO2 and CH4. Until now, many studies have shown that microorganisms prefer to consume the most recently fixed carbon and that the deeply buried ancient peat carbon reservoir is relatively stable. However, climate warming is expected to upset that balance. The Spruce and Peatlands Responses Under Changing Environments is large-scale experimental warming of a Minnesota peatland designed to study these effects. We conducted radiocarbon analysis of the peat and the microbially produced CO2 and dissolved organic carbon in ambient and heated areas of the peatland and show that at warmer temperatures more of the ancient peat carbon is being mobilized and respired to CO2. This is troubling as it signifies a positive feedback loop wherein warming stimulates peat to produce more CO2 which further exacerbates climate change

Soil Metabolome Response to Whole-Ecosystem Warming at the Spruce and Peatland Responses Under Changing Environments Experiment

While peatlands have historically stored massive amounts of soil carbon, warming is expected to enhance decomposition, leading to a positive feedback with climate change. In this study, a unique whole-ecosystem warming experiment was conducted in northern Minnesota to warm peat profiles to 2 m deep while keeping water flow intact. After nearly 2 y, warming enhanced the degradation of soil organic matter and increased greenhouse gas production. Changes in organic matter quality with warming were accompanied by a stimulation of methane production relative to carbon dioxide. Our results revealed increased decomposition to be fueled by the availability of reactive carbon substrates produced by surface vegetation. The elevated rates of methanogenesis are likely to persist and exacerbate climate warming

Root Metabolic Responses to Drought Drive Plant-Microbe Interactions in the Rhizosphere

t the interface of plant-soil-microbe interactions lies the rhizosphere, a narrow zone surrounding roots rich in metabolic activity and nutrient cycling. As climate warming and its accompanying water scarcity increases in both frequency and duration, it is unknown how plant-mediated processes such as root exudation will alter and influence soil organic matter composition in the rhizosphere. Here we integrated 16S rRNA gene amplicon sequencing for microbial community analysis, high-resolution organic matter measurements for meta-metabolome characterization, and position-specific 13C-pyruvate labeling to track carbon allocation pathways to fully characterize how microbes and species-specific plant roots influence rhizosphere soil organic carbon turnover. In situ metabolic and microbial rhizosphere profiles of three plant species, Piper auritum, Hibiscus rosa sinensis, and Clitoria fairchildiana revealed drastically different drought-response mechanisms, enhancing our understanding of niche rhizosphere dynamics. Overall, drought conditions intensified the exclusion of phylogenetically distant microbes, sufficiently conserved microbial functional traits, and decreased microbial heterogeneity across roots of all plant species. Yet, individual host rhizosphere profiles responded differently; P. auritum decreased root exudation into the rhizosphere indicating a decreased dependence on surrounding microbes. Meanwhile, H. rosa sinensis and C. fairchildiana responded aptly to water stress through modulating their exudate metabolic composition and, therefore, rhizosphere microbial communities. Our results revealed how plant species-specific microbial interactions systematically progressed with the root metabolome; as roots responded to drought, their associated microbial communities adapted, potentially supplementing drought tolerance strategies for plant roots. These findings have significant implications for maintaining plant health during drought stress and improving plant performance for climate change mitigation in both natural systems and agriculture

Shifts In Pore Connectivity From Precipitation Versus Groundwater Rewetting Increases Soil Carbon Loss After Drought

Droughts and other extreme precipitation events are predicted to increase in intensity, duration, and extent, with uncertain implications for terrestrial carbon (C) sequestration. Soil wetting from above (precipitation) results in a characteristically different pattern of pore-filling than wetting from below (groundwater), with larger, well-connected pores filling before finer pore spaces, unlike groundwater rise in which capillary forces saturate the finest pores first. Here we demonstrate that pore-scale wetting patterns interact with antecedent soil moisture conditions to alter pore-scale, core-scale, and field-scale C dynamics. Drought legacy and wetting direction are perhaps more important determinants of short-term C mineralization than current soil moisture content in these soils. Our results highlight that microbial access to C is not solely limited by physical protection, but also by drought or wetting-induced shifts in hydrologic connectivity. We argue that models should treat soil moisture within a three-dimensional framework emphasizing hydrologic conduits for C and resource diffusion

Using Macro- and Microscale Preservation in Vertebrate Fossils as Predictors for Molecular Preservation in Fluvial Environments

Exceptionally preserved fossils retain soft tissues and often the biomolecules that were present in an animal during its life. The majority of terrestrial vertebrate fossils are not traditionally considered exceptionally preserved, with fossils falling on a spectrum ranging from very well-preserved to poorly preserved when considering completeness, morphology and the presence of microstructures. Within this variability of anatomical preservation, high-quality macro-scale preservation (e.g., articulated skeletons) may not be reflected in molecular-scale preservation (i.e., biomolecules). Excavation of the Hayden Quarry (HQ; Chinle Formation, Ghost Ranch, NM, USA) has resulted in the recovery of thousands of fossilized vertebrate specimens. This has contributed greatly to our knowledge of early dinosaur evolution and paleoenvironmental conditions during the Late Triassic Period (~212 Ma). The number of specimens, completeness of skeletons and fidelity of osteohistological microstructures preserved in the bone all demonstrate the remarkable quality of the fossils preserved at this locality. Because the Hayden Quarry is an excellent example of good preservation in a fluvial environment, we have tested different fossil types (i.e., bone, tooth, coprolite) to examine the molecular preservation and overall taphonomy of the HQ to determine how different scales of preservation vary within a single locality. We used multiple high-resolution mass spectrometry techniques (TOF-SIMS, GC-MS, FT-ICR MS) to compare the fossils to unaltered bone from extant vertebrates, experimentally matured bone, and younger dinosaurian skeletal material from other fluvial environments. FT-ICR MS provides detailed molecular information about complex mixtures, and TOF-SIMS has high elemental spatial sensitivity. Using these techniques, we did not find convincing evidence of a molecular signal that can be confidently interpreted as endogenous, indicating that very good macro- and microscale preservation are not necessarily good predictors of molecular preservation. © 2022 by the authors.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]