Soil pore characteristics and the fate of new switchgrass-derived carbon in switchgrass and prairie bioenergy cropping systems.

Monoculture switchgrass and restored prairie are promising perennial feedstock sources for bioenergy production on the lands unsuitable for conventional agriculture. Such lands often display contrasting topography that influences soil characteristics and interactions between plant growth and soil C gains. This study aimed at elucidating the influences of topography and plant systems on the fate of C originated from switchgrass plants and on its relationships with soil pore characteristics. For that, switchgrass plants were grown in intact soil cores collected from two contrasting topographies, namely steep slopes and topographical depressions, in the fields in multi-year monoculture switchgrass and restored prairie vegetation. The 13C pulse labeling allowed tracing the C of switchgrass origin, which X-ray computed micro-tomography enabled in-detail characterization of soil pore structure. In eroded slopes, the differences between the monoculture switchgrass and prairie in terms of total and microbial biomass C were greater than those in topographical depressions. While new switchgrass increased the CO2 emission in depressions, it did not significantly affect the CO2 emission in slopes. Pores of 18-90 µm Ø facilitated the accumulation of new C in soil, while > 150 µm Ø pores enhanced the mineralization of the new C. These findings suggest that polyculture prairie located in slopes can be particularly beneficial in facilitating soil C accrual and reduce C losses as CO2.

Composition and metabolism of microbial communities in soil pores.

Delineation of microbial habitats within the soil matrix and characterization of their environments and metabolic processes are crucial to understand soil functioning, yet their experimental identification remains persistently limited. We combined single- and triple-energy X-ray computed microtomography with pore specific allocation of 13C labeled glucose and subsequent stable isotope probing to demonstrate how long-term disparities in vegetation history modify spatial distribution patterns of soil pore and particulate organic matter drivers of microbial habitats, and to probe bacterial communities populating such habitats. Here we show striking differences between large (30-150 µm Ø) and small (4-10 µm Ø) soil pores in (i) microbial diversity, composition, and life-strategies, (ii) responses to added substrate, (iii) metabolic pathways, and (iv) the processing and fate of labile C. We propose a microbial habitat classification concept based on biogeochemical mechanisms and localization of soil processes and also suggests interventions to mitigate the environmental consequences of agricultural management.

U.S. cereal rye winter cover crop growth database.

Winter cover crop performance metrics (i.e., vegetative biomass quantity and quality) affect ecosystem services provisions, but they vary widely due to differences in agronomic practices, soil properties, and climate. Cereal rye (Secale cereale) is the most common winter cover crop in the United States due to its winter hardiness, low seed cost, and high biomass production. We compiled data on cereal rye winter cover crop performance metrics, agronomic practices, and soil properties across the eastern half of the United States. The dataset includes a total of 5,695 cereal rye biomass observations across 208 site-years between 2001-2022 and encompasses a wide range of agronomic, soils, and climate conditions. Cereal rye biomass values had a mean of 3,428 kg ha-1, a median of 2,458 kg ha-1, and a standard deviation of 3,163 kg ha-1. The data can be used for empirical analyses, to calibrate, validate, and evaluate process-based models, and to develop decision support tools for management and policy decisions.

The microbiome structure of decomposing plant leaves in soil depends on plant species, soil pore sizes, and soil moisture content.

Microbial communities are known as the primary decomposers of all the carbon accumulated in the soil. However, how important soil structure and its conventional or organic management, moisture content, and how different plant species impact this process are less understood. To answer these questions, we generated a soil microcosm with decomposing corn and soy leaves, as well as soil adjacent to the leaves, and compared it to control samples. We then used high-throughput amplicon sequencing of the ITS and 16S rDNA regions to characterize these microbiomes. Leaf microbiomes were the least diverse and the most even in terms of OTU richness and abundance compared to near soil and far soil, especially in their bacterial component. Microbial composition was significantly and primarily affected by niche (leaves vs. soil) but also by soil management type and plant species in the fungal microbiome, while moisture content and pore sizes were more important drivers for the bacterial communities. The pore size effect was significantly dependent on moisture content, but only in the organic management type. Overall, our results refine our understanding of the decomposition of carbon residues in the soil and the factors that influence it, which are key for environmental sustainability and for evaluating changes in ecosystem functions.

The soil pore structure encountered by roots affects plant-derived carbon inputs and fate.

Plant roots are the main supplier of carbon (C) to the soil, the largest terrestrial C reservoir. Soil pore structure drives root growth, yet how it affects belowground C inputs remains a critical knowledge gap. By combining X-ray computed tomography with 14 C plant labelling, we identified root-soil contact as a previously unrecognised influence on belowground plant C allocations and on the fate of plant-derived C in the soil. Greater contact with the surrounding soil, when the growing root encounters a pore structure dominated by small (< 40 µm Ø) pores, results in strong rhizodeposition but in areas of high microbial activity. The root system of Rudbeckia hirta revealed high plasticity and thus maintained high root-soil contact. This led to greater C inputs across a wide range of soil pore structures. The root-soil contact Panicum virgatum, a promising bioenergy feedstock crop, was sensitive to the encountered structure. Pore structure built by a polyculture, for example, restored prairie, can be particularly effective in promoting lateral root growth and thus root-soil contact and associated C benefits. The findings suggest that the interaction of pore structure with roots is an important, previously unrecognised, stimulus of soil C gains.

Distribution of Mn Oxidation States in Grassland Soils and Their Relationships with Soil Pores.

Manganese (Mn) is known to be an active contributor to processing and cycling of soil organic carbon (C), yet the exact mechanisms behind its interactions with C are poorly understood. Plant diversity in terrestrial ecosystems drives feedback links between plant C inputs and soil pores, where the latter, in turn, impact the redox environment and Mn. This study examined associations between soil pores (>36 µm Ø) and Mn within intact soils from two grassland ecosystems, after their >6-year implementation in a replicated field experiment. We used µ-XRF imaging and XANES spectroscopy to explore spatial distribution patterns of Mn oxidation states, combined with X-ray computed microtomography and 2D zymography. A high plant diversity system (restored prairie) increased soil C and modified spatial distribution patterns of soil pores as compared to a single species system (monoculture switchgrass). In switchgrass, the abundance of oxidized and reduced Mn oxidation states varied with distance from pores consistently with anticipated O2 diffusion, while in the soil from restored prairie, the spatial patterns suggested that biological activity played a greater role in influencing Mn distributions. Based on the findings, we propose a hypothesis that Mn transformations promote C gains in soils of high plant diversity grasslands.

Cover crop influence on pore size distribution and biopore dynamics: Enumerating root and soil faunal effects.

Pore structure is a key determinant of soil functioning, and both root growth and activity of soil fauna are modified by and interact with pore structure in multiple ways. Cover cropping is a rapidly growing popular strategy for improving agricultural sustainability, including improvements in pore structure. However, since cover crop species encompass a variety of contrasting root architectures, they can have disparate effects on formation of soil pores and their characteristics, thus on the pore structure formation. Moreover, utilization of the existing pore systems and its modification by new root growth, in conjunction with soil fauna activity, can also vary by cover crop species, affecting the dynamics of biopores (creation and demolition). The objectives of this study were (i) to quantify the influence of 5 cover crop species on formation and size distribution of soil macropores (>36 µm Ø); (ii) to explore the changes in the originally developed pore architecture after an additional season of cover crop growth; and (iii) to assess the relative contributions of plant roots and soil fauna to fate and modifications of biopores. Intact soil cores were taken from 5 to 10 cm depth after one season of cover crop growth, followed by X-ray computed micro-tomography (CT) characterization, and then, the cores were reburied for a second root growing period of cover crops to explore subsequent changes in pore characteristics with the second CT scanning. Our data suggest that interactions of soil fauna and roots with pore structure changed over time. While in the first season, large biopores were created at the expense of small pores, in the second year these biopores were reused or destroyed by the creation of new ones through earthworm activities and large root growth. In addition, the creation of large biopores (>0.5 mm) increased total macroporosity. During the second root growing period, these large sized macropores, however, are reduced in size again through the action of soil fauna smaller than earthworms, suggesting a highly dynamic equilibrium. Different effects of cover crops on pore structure mainly arise from their differences in root volume, mean diameter as well as their reuse of existing macropores.

Pore architecture and particulate organic matter in soils under monoculture switchgrass and restored prairie in contrasting topography.

Bioenergy cropping systems can substantially contribute to climate change mitigation. However, limited information is available on how they affect soil characteristics, including pores and particulate organic matter (POM), both essential components of the soil C cycle. The objective of this study was to determine effects of bioenergy systems and field topography on soil pore characteristics, POM, and POM decomposition under new plant growth. We collected intact soil cores from two systems: monoculture switchgrass (Panicum virgatum L.) and native prairie, at two contrasting topographical positions (depressions and slopes), planting half of the cores with switchgrass. Pore and POM characteristics were obtained using X-ray computed micro-tomography (µCT) (18.2 µm resolution) before and after new switchgrass growth. Diverse prairie vegetation led to higher soil C than switchgrass, with concomitantly higher volumes of 30-90 µm radius pores and greater solid-pore interface. Yet, that effect was present only in the coarse-textured soils on slopes and coincided with higher root biomass of prairie vegetation. Surprisingly, new switchgrass growth did not intensify decomposition of POM, but even somewhat decreased it in monoculture switchgrass as compared to non-planted controls. Our results suggest that topography can play a substantial role in regulating factors driving C sequestration in bioenergy systems.

Crops for Carbon Farming.

Agricultural cropping systems and pasture comprise one third of the world's arable land and have the potential to draw down a considerable amount of atmospheric CO2 for storage as soil organic carbon (SOC) and improving the soil carbon budget. An improved soil carbon budget serves the dual purpose of promoting soil health, which supports crop productivity, and constituting a pool from which carbon can be converted to recalcitrant forms for long-term storage as a mitigation measure for global warming. In this perspective, we propose the design of crop ideotypes with the dual functionality of being highly productive for the purposes of food, feed, and fuel, while at the same time being able to facilitate higher contribution to soil carbon and improve the below ground ecology. We advocate a holistic approach of the integrated plant-microbe-soil system and suggest that significant improvements in soil carbon storage can be achieved by a three-pronged approach: (1) design plants with an increased root strength to further allocation of carbon belowground; (2) balance the increase in belowground carbon allocation with increased source strength for enhanced photosynthesis and biomass accumulation; and (3) design soil microbial consortia for increased rhizosphere sink strength and plant growth-promoting (PGP) properties.

Effectivity of homecare and professional biofilm removal procedures on initial supragingival biofilm on laser-microtextured implant surfaces in an ex vivo model.

BACKGROUND: The aim of the current study was the evaluation of initial biofilm adhesion and development on laser-microtextured implant collar surfaces and the examination of effectivity of different biofilm management methods. METHODS: Initial biofilm formation was investigated on hydrophobic machined and laser-microtextured (Laser-Lok) titanium surfaces and hydrophobic machined and laser-microtextured (Laser-Lok) titanium aluminium vanadium surfaces and compared to hydrophobic smooth pickled titanium surfaces, hydrophilic smooth and acid etched titanium surfaces, hydrophobic sandblasted large grid and acid etched titanium surfaces (titanium Promote) via erythrosine staining and subsequent histomorphometrical analysis and scanning electron microscopic investigations. After decontamination procedures, performed via tooth brushing and glycine powder blasting, clean implant surface was detected via histomorphometrical analysis. RESULTS: After 24 h mean initial plaque area was detected in the following descending order: smooth pickled titanium > titanium Promote > hydrophilic smooth and acid etched titanium > Laser-Lok titanium > Laser-Lok titanium aluminium vanadium. The same order was determined after 48 h of biofilm formation. After glycine powder blasting all samples depicted almost 100% clean implant surface. After tooth brushing, Laser-Lok titanium (67.19%) and Laser-Lok titanium aluminium vanadium (69.80%) showed significantly more clean implant surface than the other structured surfaces, hydrophilic smooth and acid etched titanium (50.34%) and titanium Promote (33.89%). Smooth pickled titanium showed almost complete clean implant surface (98.84%) after tooth brushing. CONCLUSIONS: Both Laser-Lok surfaces showed less initial biofilm formation after 24 and 48 h than the other implant surfaces. In combination with the significant higher clean implant surfaces after domestic decontamination procedure via tooth brushing, both Laser-Lok surfaces could be a candidate for modified implant and abutment designs, especially in transmucosal areas.

Genetic Evidence for a Mixed Composition of the Genus Myoxocephalus (Cottoidei: Cottidae) Necessitates Generic Realignment.

Sculpin fishes belonging to the family Cottidae represent a large and complex group, inhabiting a wide range of freshwater, brackish-water, and marine environments. Numerous studies based on analysis of their morphology and genetic makeup frequently provided controversial results. In the present work, we sequenced complete mitochondrial (mt) genomes and fragments of nuclear ribosomal DNA (rDNA) of the fourhorn sculpin Myoxocephalus quadricornis and some related cottids to increase the power of phylogenetic and taxonomic analyses of this complex fish group. A comparison of the My. quadricornis mt genomes obtained by us with other complete mt genomes available in GenBank has revealed a surprisingly low divergence (3.06 ± 0.12%) with Megalocottus platycephalus and, at the same time, a significantly higher divergence (7.89 ± 0.16%) with the species of the genus Myoxocephalus. Correspondingly, phylogenetic analyses have shown that My. quadricornis is clustered with Me. platycephalus but not with the Myoxocephalus species. Completely consistent patterns of divergence and tree topologies have been obtained based on nuclear rDNA. Thus, the multi-gene data in the present work indicates obvious contradictions in the relationships between the Myoxocephalus and Megalocottus species studied. An extensive phylogenetic analysis has provided evidence for a closer affinity of My. quadricornis with the species of the genus Megalocottus than with the species of the genus Myoxocephalus. A recombination analysis, along with the additional GenBank data, excludes introgression and/or incorrect taxonomic identification as the possible causative factors responsible for the observed closer affinity between the two species from different genera. The above facts necessitate realignment of the genera Myoxocephalus and Megalocottus. The genetic data supports the two recognized genera, Myoxocephalus and Megalocottus, but suggests changing their compositions through transferring My. quadricornis to the genus Megalocottus. The results of the present study resolve the relationships within a complex group of sculpin fishes and show a promising approach to phylogenetic systematics (as a key organizing principle in biodiversity research) for a better understanding of the taxonomy and evolution of fishes and for supplying relevant information to address various fish biodiversity conservation and management issues.

Testing Os Staining Approach for Visualizing Soil Organic Matter Patterns in Intact Samples via X-ray Dual-Energy Tomography Scanning.

Challenges with in situ visualization of nonparticulate organics in porous materials limit understanding and modeling processes of transport, decomposition, and storage of organic compounds. In particular, it impedes deciphering the mechanisms driving accumulation and protection of soil organic matter (SOM), processes crucial for sustaining soil fertility and mitigating effects of global climate change. A recently proposed method of staining soil organics by OsO4 vapors with subsequent dual-energy X-ray computed microtomography scanning (µCT) offers new opportunities to visualize SOM within intact soil matrix. Our objective was to test the method's performance in staining different organic materials located in media with contrasting pore characteristics: (1) roots of switchgrass (Panicum virgatum L.), either placed within fine and coarse sands or grown within soil microcores, (2) biochar fragments, and (3) soils with relatively low and high C contents. We found that the method was effective in staining organic materials of root origin and the organics associated with fine soil particles, but not the biochar. The estimated percent of total C that reacted with OsO4 vapors ranged from 0.7% in plant roots to 3.2% in sand-free fraction of the high C soil and was only 0.2% in the studied biochar. Total soil C and Os concentrations were strongly linearly related, suggesting a potential for future method development. However, we would recommend caution when interpreting the results in cases when gas diffusion through the soil matrix is limited.

Empirical Evidence for the Potential Climate Benefits of Decarbonizing Light Vehicle Transport in the U.S. with Bioenergy from Purpose-Grown Biomass with and without BECCS.

Climate mitigation scenarios limiting global temperature increases to 1.5 °C rely on decarbonizing vehicle transport with bioenergy production plus carbon capture and storage (BECCS), but climate impacts for producing different bioenergy feedstocks have not been directly compared experimentally or for ethanol vs electric light-duty vehicles. A field experiment at two Midwest U.S. sites on contrasting soils revealed that feedstock yields of seven potential bioenergy cropping systems varied substantially within sites but little between. Bioenergy produced per hectare reflected yields: miscanthus > poplar > switchgrass > native grasses ≈ maize stover (residue) > restored prairie ≈ early successional. Greenhouse gas emission intensities for ethanol vehicles ranged from 20 to -179 g CO2e MJ-1: maize stover ≫ miscanthus ≈ switchgrass ≈ native grasses ≈ poplar > early successional ≥ restored prairie; direct climate benefits ranged from ∼80% (stover) to 290% (restored prairie) reductions in CO2e compared to petroleum and were similar for electric vehicles. With carbon capture and storage (CCS), reductions in emission intensities ranged from 204% (stover) to 416% (restored prairie) for ethanol vehicles and from 329 to 558% for electric vehicles, declining 27 and 15%, respectively, once soil carbon equilibrates within several decades of establishment. Extrapolation based on expected U.S. transportation energy use suggests that, once CCS potential is maximized with CO2 pipeline infrastructure, negative emissions from bioenergy with CCS for light-duty electric vehicles could capture >900 Tg CO2e year-1 in the U.S. In the future, as other renewable electricity sources become more important, electricity production from biomass would offset less fossil fuel electricity, and the advantage of electric over ethanol vehicles would decrease proportionately.

A phylogenomic perspective on diversity, hybridization and evolutionary affinities in the stickleback genus Pungitius.

Hybridization and convergent evolution are phenomena of broad interest in evolutionary biology, but their occurrence poses challenges for reconstructing evolutionary affinities among affected taxa. Sticklebacks in the genus Pungitius are a case in point: evolutionary relationships and taxonomic validity of different species and populations in this circumpolarly distributed species complex remain contentious due to convergent evolution of traits regarded as diagnostic in their taxonomy, and possibly also due to frequent hybridization among taxa. To clarify the evolutionary relationships among different Pungitius species and populations globally, as well as to study the prevalence and extent of introgression among recognized species, genomic data sets of both reference genome-anchored single nucleotide polymorphisms and de novo assembled RAD-tag loci were constructed with RAD-seq data. Both data sets yielded topologically identical and well-supported species trees. Incongruence between nuclear and mitochondrial DNA-based trees was found and suggested possibly frequent hybridization and mitogenome capture during the evolution of Pungitius sticklebacks. Further analyses revealed evidence for frequent nuclear genetic introgression among Pungitius species, although the estimated proportions of autosomal introgression were low. Apart from providing evidence for frequent hybridization, the results challenge earlier mitochondrial and morphology-based hypotheses regarding the number of species and their affinities in this genus: at least seven extant species can be recognized on the basis of genetic data. The results also shed new light on the biogeographical history of the Pungitius-complex, including suggestion of several trans-Arctic invasions of Europe from the Northern Pacific. The well-resolved phylogeny should facilitate the utility of this genus as a model system for future comparative evolutionary studies.

Soil aggregates as biogeochemical reactors: Not a way forward in the research on soil-atmosphere exchange of greenhouse gases.

The goal of this comment is to show that the "aggregate reactor" framework recently proposed in an article published in this journal is severely limited by two kinds of indeterminacy. The first is related to the size of aggregates, which is not defined precisely. The second issue is with the impossibility to replicate boundary conditions that are identical to what chunks of soils would have experienced in their natural state. We suggest that the study of GHG release in undisturbed soil samples is a better way to proceed forward.

Complete mitochondrial genome of the great sculpin Myoxocephalus polyacanthocephalus (Cottoidei: Cottidae).

The complete mitochondrial genome was sequenced in two specimens of the great sculpin Myoxocephalus polyacanthocephalus by high-throughput sequencing technology (Ion S5 platform). The genome sequences are 16,651 and 16,652 bp in size, and the gene arrangement, composition, and size are similar to the other sculpin mitochondrial genomes published previously. Overall base composition of the complete mitochondrial DNA is A (26.9%), G (17.0%), C (29.5%), and T (26.6.0%), the percentage of A and T (53.5%) is higher than G and C (46.5%). The difference between the two genomes studied is low, 0.15%. A relatively low level of divergence (3.48%) is detected between M. polyacanthocephalus and M. scorpius, which however is high enough to consider them as separate biological species.

Complete mitochondrial genome of the Belligerent sculpin Megalocottus platycephalus (Cottoidei: Cottidae).

The complete mitochondrial (mt) genome was sequenced in two specimens of the Belligerent sculpin Megalocottus platycephalus by high-throughput sequencing technology (Ion S5 platform). The sequences are 16,673 bp in size, and the gene arrangement, composition, and size are very similar to the other sculpin mt genomes published previously. Comparison of the two M. platycephalus mt genomes now obtained with other complete mt genomes available in GenBank reveals an affinity to the sculpin fishes from the genus Myoxocephalus. The intergeneric difference between the Megalocottus and Myoxocephalus is 0.0757 ± 0.0019, which is significantly less than the corresponding value, 0.1240 ± 0.0120, obtained previously for the sculpin fishes based on the COI barcoding marker.

Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain.

Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the bulk, macroscopic parameters (e.g., granulometry, pH, soil organic matter, and biomass contents) commonly used to characterize soils provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gasses. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale) that is commensurate with the habitat of many microorganisms. For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. With regard to the microbial aspects, although a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because of the scarcity of relevant experimental data. For significant progress to be made, it is crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead. Fortunately, a number of these challenges may be resolved by brand new measuring equipment that will become commercially available in the very near future.

Complete mitochondrial genome of the European smelt Osmerus eperlanus (Osmeriformes, Osmeridae).

The complete mitochondrial (mt) genome was sequenced in two individuals of the European smelt Osmerus eperlanus. The genome sequences are 16,608 and 16,609 bp in size, and the gene arrangement, composition, and size are very similar to the other smelt mt genomes previously published. The difference between the two genomes studied is low, 0.05%. The difference is significantly higher (6.95%) between the O. eperlanus genomes studied here and the genome of the congeneric species, O. mordax (HM106493.1) available in GenBank. The distribution of divergence is non-uniform along the genomes. There is a continuous segment (≈2.5 kb) encompassing tRNA-Phe, complete 12S rRNA gene, tRNA-Val, and partial 16S rRNA gene, which demonstrates significantly lower levels of divergence than on average for the whole genome. The 12S rRNA and 16S rRNA genes are frequently used for phylogenetic and molecular taxonomy analyses and could underestimate the level of divergence between osmerid fishes.