Increasing the potential of soil to store carbon (C) is an acknowledged and emphasized strategy for capturing atmospheric CO 2 . Well-recognized approaches for soil C accretion include reducing soil disturbance, increasing plant biomass inputs, and enhancing plant diversity. Yet experimental evidence often fails to support anticipated C gains, suggesting that our integrated understanding of soil C accretion remains insufficient. Here we use a unique combination of X-ray micro-tomography and micro-scale enzyme mapping to demonstrate for the first time that plant-stimulated soil pore formation appears to be a major, hitherto unrecognized, determinant of whether new C inputs are stored or lost to the atmosphere. Unlike monocultures, diverse plant communities favor the development of 30–150 µm pores. Such pores are the micro-environments associated with higher enzyme activities, and greater abundance of such pores translates into a greater spatial footprint that microorganisms make on the soil and consequently soil C storage capacity.

While renewable biofuels can reduce negative effects of fossil fuel energy consumption, the magnitude of their benefits depends on the magnitude of N2O emissions. High variability of N2O emissions overpowers efforts to curb uncertainties in estimating N2O fluxes from biofuel systems. In this study, we explored (a) N2O production via bacterial denitrification and (b) N2O emissions from soils under several contrasting bioenergy cropping systems, with specific focus on explaining N2O variations by accounting for soil pore characteristics. Intact soil samples were collected after 9 years of implementing five biofuel systems: continuous corn with and without winter cover crop, monoculture switchgrass, poplars, and early‐successional vegetation. After incubation, N2O emissions were measured and bacterial denitrification was determined based on the site‐preference method. Soil pore characteristics were quantified using X‐ray computed microtomography. Three bioenergy systems with low plant diversity, that is, corn and switchgrass systems, had low porosities, low organic carbon contents, and large volumes of poorly aerated soil. In these systems, greater volumes of poorly aerated soil were associated with greater bacterial denitrification, which in turn was associated with greater N2O emissions (R2 = 0.52, p < 0.05). However, the two systems with high plant diversity, that is, poplars and early‐successional vegetation, over the 9 years of implementation had developed higher porosities and organic carbon contents. In these systems, volumes of poorly aerated soil were positively associated with N2O emissions without a concomitant increase in bacterial denitrification. Our results suggest that changes in soil pore architecture generated by long‐term implementation of contrasting bioenergy systems may affect the pathways of N2O production, thus, change associations between N2O emissions and other soil properties. Plant diversity appears as one of the factors determining which microscale soil characteristics will influence the amounts of N2O emitted into the atmosphere and, thus, which can be used as effective empirical predictors.

Shape is data and data is shape. Biologists are accustomed to thinking about how the shape of biomolecules, cells, tissues, and organisms arise from the effects of genetics, development, and the environment. Less often do we consider that data itself has shape and structure, or that it is possible to measure the shape of data and analyze it. Here, we review applications of topological data analysis (TDA) to biology in a way accessible to biologists and applied mathematicians alike. TDA uses principles from algebraic topology to comprehensively measure shape in data sets. Using a function that relates the similarity of data points to each other, we can monitor the evolution of topological features—connected components, loops, and voids. This evolution, a topological signature, concisely summarizes large, complex data sets. We first provide a TDA primer for biologists before exploring the use of TDA across biological sub‐disciplines, spanning structural biology, molecular biology, evolution, and development. We end by comparing and contrasting different TDA approaches and the potential for their use in biology. The vision of TDA, that data are shape and shape is data, will be relevant as biology transitions into a data‐driven era where the meaningful interpretation of large data sets is a limiting factor.

Macroaggregates are of interest because of their fast response to land management and their role in the loss or restoration of soil organic carbon (SOC). The study included two experiments. In Experiment I, we investigated the effect of long‐term (27 years) land management on the chemical composition of organic matter (OM) of macroaggregates. Macroaggregates were sampled from topsoil under conventional cropping, cover cropping and natural succession systems. The OM of macroaggregates from conventional cropping was more decomposed than that of cover cropping and especially natural succession, based on larger δ15N values and decomposition indices determined by multiple magic‐angle spinning nuclear magnetic resonance (13C CP/MAS NMR) and Fourier transform infrared (FTIR) spectroscopy. Previous research at the sites studied suggested that this was mainly because of reduced diversity and activity of the decomposer community, change in nutrient stoichiometry from fertilization and contrasting formation pathways of macroaggregates in conventional cropping compared with cover cropping and, specifically, natural succession. In Experiment II, we investigated the relation between OM composition and pore characteristics of macroaggregates. Macroaggregates from the natural succession system only were studied. We determined 3‐D pore‐size distribution of macroaggregates with X‐ray microtomography, for which we cut the macroaggregates into sections that had contrasting dominant pore sizes. Then, we characterized the OM of macroaggregate sections with FTIR and δ15N methods. The results showed that within a macroaggregate, the OM was less decomposed in areas where the small (13–32 µm) or large (136–260 µm) pores were abundant. This was attributed to the role of large pores in supplying fresh OM and small pores in the effective protection of OM in macroaggregates. Previous research at the site studied had shown increased abundance of large and small intra‐aggregate pores following adoption of less intensive management systems. It appears that land management can alter the OM composition of macroaggregates, partly by the regulation of OM turnover at the intra‐aggregate scale. Highlights OM and pore characteristics were studied in soil macroaggregates under different land management. Long‐term intensive land management increased degree of OM decomposition in macroaggregates. Abundance of < 32 and > 136 µm pores was positively related to less decomposed OM. Land management may affect rate of SOM turnover by changing intra‐aggregate pore‐size distribution.

Pores create a transportation network within a soil matrix, which controls the flow of air, water, and movement of microorganisms. The flow of air, water, and movement of microbes, in turn, control soil carbon dynamics. Computed microtomography (µCT) allows for the visualization of pore structure at micron scale, but quantitative information on contribution of pores to the fate and protection of soil carbon, essential for modeling, is still lacking. This study uses the natural difference between carbon isotopes of C3 and C4 plants to determine how the presence of pores of different sizes affects spatial distribution patterns of newly added carbon immediately after plant termination and then after 1-month incubation. We considered two contrasting soil structure scenarios: soil with the structure kept intact and soil for which the structure was destroyed via sieving. For the experiment, soil was collected from 0-15 cm depth at a 20-year continuous maize (Zea mays L., C4 plant) experiment into which cereal rye (Secale cereale L., C3 plant) was planted. Intact soil fragments (5-6 mm) were procured after 3 months rye growth in a greenhouse. Pore characteristics of the fragments were determined through µCT imaging. Each fragment was sectioned and total carbon, total nitrogen, δ 13 C, and δ 15 N were measured. The results indicate that, prior to incubation, greater presence of 40-90 µm pores was associated with higher levels of C3 carbon, pointing to the positive role of these pores in transport of new C inputs. Nevertheless, after incubation, the association became negative, indicating greater losses of newly added C in such pores. These trends were statistically significant in destroyed-structure soil and numerical in intact-structure soil. In soils of intact-structures, after incubation, higher levels of total carbon were associated with greater abundance of 6.5-15 and 15-40 µm pores, indicating a lower carbon loss associated with these pores. The results indicate that, in the studied soil, pores of 40-90 µm size range are associated with the fast influx of new C followed by its quick decomposition, while pores <40 µm tend to be associated with C protection.