Soil Biology and Biochemistry

Soil microbes regulate whether carbon is retained in soils or returned to the atmosphere through respiration, but the extent to which microbial community characteristics improve the prediction of heterotrophic soil CO2 production beyond predictions by environmental controls remains unclear. We tested this across a topographically structured forest-to-marsh gradient in coastal Oregon by measuring heterotrophic soil respiration, soil physicochemical properties, PLFA-based microbial biomass, metagenomic taxonomic composition, and functional gene-based trait indicators. Across the gradient, soil moisture increased from forest to marsh, while mineral soil and organic matter C:N decreased. These environmental shifts were accompanied by strong but uneven microbial responses: total microbial, fungal, and bacterial biomass declined from forest to marsh, taxonomic composition showed the strongest structuring by environmental conditions, and functional gene-based indicators showed mixed relationships with the gradient. Environmental model comparisons identified soil moisture and organic layer C as the strongest baseline predictors of respiration. Among microbial descriptors, only a small subset improved respiration prediction beyond this environmental baseline. The fungal:bacterial (F:B) biomass ratio produced the largest increase in model fit and the greatest reduction in AICc, whereas the best taxonomic and functional-gene predictors yielded more minor gains. Our results showed that the microbial descriptors most responsive to environmental gradients were not the ones most useful for predicting soil respiration; instead, a relatively simple biomass-partitioning metric captured respiration-relevant microbial variation more effectively than finer taxonomic and genomic descriptors. This suggests that F:B ratio may be especially useful for representing respiration-relevant microbial variation in local landscape-scale studies and for future carbon cycle models applied across heterogeneous ecosystem transition zones.

Reforestation is a leading natural climate solution, but bulk soil organic carbon (C) often responds slowly, obscuring early belowground change. We tested whether soil aggregates reveal early structural reorganization that affects C retention pathways at a three-year-old experimental reforestation planting established on former pasture in Oregon, USA. We sampled soils at 0-20 and 20-40 cm beneath incense cedar (Calocedrus decurrens; arbuscular mycorrhizal [AM]), black cottonwood (Populus trichocarpa; AM and ectomycorrhizal [EcM]), ponderosa pine (Pinus ponderosa; EcM), and treeless controls. We measured bulk soil C concentration and C:N, aggregate size distribution and mean weight diameter (MWD), fraction-associated C, and, in a subset of surface aggregate fractions, natural-abundance {delta}13C to evaluate soil C pools, physical structure, C distribution, and C processing. After three years, reforestation did not produce significant differences in bulk soil C between planted trees and treeless controls. In surface soil, MWD averaged 36% higher under incense cedar and 58% higher under black cottonwood than under controls, whereas ponderosa pine remained similar to controls. The clearest treatment differences in C distribution occurred in macroaggregates. Incense cedar and black cottonwood had higher large (>2000 m) macroaggregate-associated C than controls, while black cottonwood combined a greater proportion of large macroaggregates with lower C concentrations, indicating that structural development and C accumulation were partly decoupled. Species patterns were broadly consistent with stronger early aggregate responses under AM-compatible species in former-pasture legacy conditions; by contrast, the EcM-associated ponderosa pine remained closer to treeless controls across multiple aggregate measures. Treatment effects weakened with depth and were limited in microaggregates (250-53 m) and silt-and-clay (<53 m) fractions. Smaller aggregate fractions were progressively enriched in {delta}13C, consistent with greater C processing in protected fractions, but treatment-level isotope differences had not yet emerged. Soil aggregates showed species-associated belowground reorganization, revealing how tree identity and former-pasture legacy may shape early soil C organization before consistent differences emerged in bulk soil C. Aggregate measures can complement bulk soil C measurements in restoration monitoring as early indicators of belowground soil C trajectories shaped by tree species identity and land-use legacy.

Globally, contaminated soils pose serious risks to agriculture, biodiversity of ecosystems, and human health. Although a variety of monitoring and remediation methods have been developed over the years, there remains a lack of theoretical modelling to better understand the impact of contamination on soil carbon in a microbially-mediated system. In this study, we develop a model which incorporates contaminated soil organic carbon, uncontaminated soil organic carbon, dissolved organic carbon, microbes, extracellular enzymes, and CO2, to explore how different amounts of contamination and modes of contamination (pulse and press) affect microbially-mediated carbon flux within both vegetated and barren environments. The model represents contamination as a pool of contaminated soil organic carbon that is more resistant to microbial degradation than uncontaminated soil organic carbon. The results show that, in barren environments, the amount and type of contamination has no notable impact on the soil system. In contrast to this, in vegetated environments, plants mitigate the impact of large contamination inputs with differences in outcome depending on the amount and type of contamination.

Anthropogenic climate change is driving increased temperature and altered precipitation patterns in tropical rainforests, yet the impact of severe drought on soil viral communities and their recovery capacity remains poorly understood. Soil viruses can exert strong controls on bacterial populations impacting microbially-mediated soil processes such as carbon cycling. At the same time, viruses are very sensitive to changes in the soil environment. We leverage meta-omics data from soils collected during a two-month drought and one-month recovery experiment carried in the Biosphere 2 Tropical Rainforest artificial biome. Our results indicate that soil viral community structure responds to small scale soil habitat heterogeneity more strongly than on overall changes in moisture. Additionally, the abundance of soil viruses was associated with a higher diversity of metabolites in the soil, suggesting viruses play a key role in soil biogeochemical processes. Altogether, our study suggests that soil viruses are an active part of tropical rainforest soil microbial communities and that is necessary to understand their response to drought.

Secondary forests are increasingly important for biodiversity recovery and ecosystem functioning after disturbance. As vegetation regenerates, accompanying shifts in soil conditions and microbial communities regulate climate-relevant processes such as atmospheric methane (CH$_4$) uptake. Whether these belowground dimensions recover synchronously, however, remains unclear. Here we show that belowground recovery followed asynchronous trajectories across a forest chronosequence in Metok, Eastern Himalayas. Soil inorganic properties and microbial community composition converged progressively on the primary-forest state as soils acidified. By contrast, soil organic carbon, microbial diversity and abundance appeared to recover by 25 years but diverged again at 40 years. Co-occurrence network topology resembled the primary forest by 40 years, yet the keystone taxa underlying it were entirely stage specific. Atmospheric CH$_4$ uptake fluctuated: uptake recovered to primary-forest levels in 25-year stands but weakened in 40-year stands to rates comparable with the recently disturbed 5-year forest. Rather than canonical methane-cycling taxa, four amplicon sequence variants---three assigned to \textit{Mycobacterium}---tracked CH$_4$ flux closely while acting as hubs or connectors in the co-occurrence networks, warranting genomic and experimental work to resolve their function. Apparent recovery within the first 25 years therefore did not persist, cautioning against inferring restoration success from early succession alone and highlighting the need for longer chronosequences and repeated observation to resolve the dynamics of secondary-forest recovery.

As circular agricultural inputs are increasingly sought, feather hydrolysate (FH), derived from keratin-rich poultry waste, has emerged as a promising fertilizer and biostimulant. However, how FH shapes soil microbiome succession over time, and what functional potential this restructuring carries, remains poorly understood. Here, we used multi-marker high-throughput sequencing of 16S, 18S, and ITS rDNA to track soil microbial communities over 30 days following FH amendment, with sampling at days 0, 1, 4, 14, and 30. FH induced a rapid and reproducible microbial succession characterized by an early decline in alpha diversity and a pronounced day-1 bloom of copiotrophic taxa, as inferred from predicted rrn operon copy-number profiles. This initial response was accompanied by enrichment of bacterial genera previously associated with plant growth-promoting traits, including pathogen suppression, nutrient solubilization, siderophore production, phytohormone synthesis, and ACC deaminase activity. Although these groups gradually declined after the initial peak, several remained at significantly elevated abundances throughout the 30-day experimental period. In parallel, FH-treated soils showed a sustained reduction in the cumulative relative abundance of genera annotated as putative phytopathogens. By integrating temporal community profiling, rrn-based life-strategy inference, and literature-derived functional annotation, we show that FH acts as a strong ecological filter, shifting the soil microbiome toward copiotrophic and putatively plant-beneficial taxa. These findings provide a temporal framework for understanding FH-mediated microbiome restructuring and highlight the need for future studies linking inferred microbial functional potential to measured disease incidence, nutrient fluxes, and plant performance across diverse soil contexts.

The mechanisms by which coarse woody debris (CWD) affects soil microbial diversity across different spatial scales and forest disturbance regimes remain poorly understood. This study investigated the impact of CWD from multiple tree species on forest floor bacterial and fungal communities under varying landscape-scale conditions, specifically comparing old-growth forests situated on Phaozems and Retisols with mass-windthrow areas located on loamy Retisols and sandy Podzols. We analyzed both chemical compound and metagenomic profiles of 63 CWD-associated soil samples collected from the Kaluzhskie Zaseki Nature Reserve (European part of Russia). High-throughput Illumina sequencing of the 16S rRNA gene and the ITS region was used to profile both bacterial and fungal communities, respectively. Scale-dependent diversity patterns and taxonomic accumulation were assessed using GLM, NMDS, dbRDA, and iNEXT frameworks. Our findings revealed a profound spatial decoupling in forest floor microbial communities, where a localized reduction in alpha-diversity under CWD drove a sharp increase in landscape-scale gamma-diversity. While standard soil physicochemical properties rigidly dictated baseline matrix richness, CWD operated as a powerful micro-environmental hotspot overriding these constraints. Deadwood inputs filtered out dominant matrix-associated taxa, creating highly specialized micro-refugia characterized by high compositional dispersion. This niche selection was particularly pronounced beneath Quercus logs on Phaozems and Retisols. Furthermore, post-windthrow microbial responses were heavily filtered by wood traits and baseline soil textures. On loamy Retisols within the windthrow mosaic, this breakaway dynamic was highly taxon-specific: while Acer and Fraxinus CWD triggered partitioned, site-specific hotspot dynamics yielding an exceptionally large pool of unique ASVs for bacteria, the distinct enrichment for fungal communities was primarily driven by Ulmus CWD and log-free windthrow areas. Ultimately, iNEXT accumulation profiles confirmed that deadwood does not merely multiply common soil taxa, but enriches the forest landscape by injecting critical beta-level heterogeneity into the soil matrix. These insights emphasize the role of diverse CWD retention in buffering forest microbiomes against large-scale environmental disturbances across heterogeneous soil landscapes.

Microbial community assembly on leaves (the phyllosphere) is influenced by deterministic, stochastic, and historical processes. However, the importance of historical processes such as priority effects, where the timing and order of colonization influence community assembly, has not been extensively investigated in field-based phyllosphere studies. We designed a field experiment in a temperate forest in Quebec where we inoculated five strains of Methylobacterium onto the leaves of red maple and American beech trees, either early or late during the growing season. We quantified microbial community structure throughout the season using metabarcoding of a Methylobacterium-targeting rpoB primer as well as a 16S rRNA primer targeting the entire bacterial community. We show that the effects of inoculation on bacterial communities depend on inoculation timing: early-season inoculation led to strain-specific shifts in community composition, while late-season inoculation had no significant effect. Although the effect of early-season inoculation weakened over time, early- and late-season inoculation still led to different community compositions at the end of the growing season. Our study demonstrates that priority effects contribute to the assembly of phyllosphere bacterial communities under field conditions, with arrival timing and strain identity shaping community trajectories. Considering historical processes will thus be crucial for successful microbiome management.

Abstract: Background Despite the ecological importance of viral anti-defense systems (ADS), yet how viral ADS repertoires vary across microbial ecosystems remains poorly understood. Here, we integrated global virus datasets with metagenomes from heavy metal-contaminated soils and chromium-stress microcosms to investigate ecological determinants of viral ADS. Results We found that ADS repertoires were constrained by viral genome capacity, with most ADS-carrying viruses encoded a single system, whereas multi-ADS occurred mainly in larger genomes. Viral lifestyle partitioned ADS, with temperate viruses enriched in ADS targeting early-stage defenses and virulent viruses preferentially encoding ADS against mid- and late-stage defense. ADS composition also varied by host lineage and across habitats, linking viral ADS repertoires to host immune landscapes and ecosystem-specific viral strategies. Moreover, along the heavy metal contamination gradient, changes in the prevalence of ADS-carrying viruses occurred alongside shifts in prokaryotic defense profiles. In addition, expanded ADS repertoires may further increase dissemination potential of MGE-borne adaptive genes, highlighting viral ADS as a potential contributor to the adaptive evolution of microbial community. Conclusions These findings reveal that viral ADS are shaped by genomic traits, host immunity and environmental stress, with implications for virus-host interaction and microbial adaptive evolution. More broadly, this study extends anti-defense research beyond individual virus-host systems, offering an integrative, community-level perspective to guide future studies testing whether and how virus-prokaryote immune interactions contribute to microbial community dynamics and evolution in changing environments.

Soil nematodes play key roles in regulating organic matter decomposition, nutrient cycling and trophic interactions in the soil ecosystem, and are very useful bioindicators of soil condition and soil health. But to characterise them, we need reliable measurements of nematode biodiversity in soils. DNA-based techniques such as metabarcoding have recently explored their biodiversity, with successful results. However, there are many methodological steps that can modify the outcome considerably and require informed decisions. In this study, we tested the effect on nematode alpha and beta diversity metrics of three methodological steps, namely i) type of extraction of genetic material from the matrix, either from soil directly with different starting amount of material or extracting nematodes first via the Baermann or Oostenbrink methods, ii) the choice of taxonomically-relevant DNA segment for amplification, with a nematode specific primer (NemF/18Sr2b) and a universal eukaryotic primer (3NDf/1132rmod), both within 18S rDNA, and iii) the selection of appropriate reference library for taxonomic assignment (comparing three nematode specialised databases and three broad taxonomic databases). Observed differences in alpha diversity were more pronounced when comparing the nematode extraction vs soil extractions. In particular, direct soil extractions co-extracted many non-nematode taxa, especially if amplified with a universal primer, which can significantly reduce the number of nematode reads obtained and therefore the accuracy of nematode community indexes and other nematode-based metrics. The choice of the reference database strongly affected the taxonomic identification, which calls for extreme caution when making this selection. Notably, specialised databases tended to over assign reads to nematodes that were detected as non-nematodes by broad taxonomic databases. However, beta diversity metrics were consistent across methods, highlighting these metrics as robust against methodological choices. Our study clearly demonstrates that the choices of methods for nematode biodiversity studies using molecular tools can have a big impact on the results, and decisions should be made consciously and carefully.

Abstract Background: Soil microbiomes play critical roles in plant health and resilience, yet it is still poorly understood how disruptions in local microbial communities, such as during soil management, impact these ecological functions. In this study, we investigated how compost addition, a widely used soil management practice, and microbiome origin influence microbiome-mediated plant resistance to insects. We combined surveys of working organic farms across New York with controlled laboratory experiments, amplicon sequencing, plant-insect bioassays, and mass spectrometry. Results: Compost use was associated with shifts in the relative abundance of 20 fungal and 2 bacterial genera across ten working farms. However, no consistent changes in bacterial or fungal diversity or community structure in fields with compost were observed across the farms. Under controlled conditions using a common compost source, compost increased rhizosphere microbial diversity and significantly altered rhizosphere community structure, including the relative abundance of 6 fungal and 41 bacterial genera. Despite these substantial community-level changes, compost did not affect populations of green peach aphids (Myzus persicae) on kale (Brassica oleracea). Instead, aphid populations and plant salicylic acid concentrations were more strongly associated with microbiome origin, demonstrating that compost can substantially restructure soil and rhizosphere microbial communities without corresponding changes in microbiome-mediated plant resistance to insects. Conclusions: Our findings demonstrate that microbial diversity and compositional responses to management are not necessarily reliable indicators of all microbiome functions. More broadly, this work highlights the importance of local soil microbiome variation in shaping plant-insect interactions and emphasizes the need to link community-level responses to direct functional measurements when evaluating microbiome responses to agricultural management.

Carbon farming practices are increasingly adopted as part of regenerative agriculture to enhance soil carbon sequestration and improve agricultural sustainability. However, their effects on the phyllosphere microbiome, and how these interact with field biodiversity, remain poorly understood. We investigated how field biodiversity and carbon farming practices (cover crops, all-in mixes, adaptive grazing and ley mixture) influence leaf microbial communities across 19 Finnish farms using ITS and 16S amplicon sequencing. Foliar fungal - but not bacterial - diversity increased with plant species richness. Carbon farming altered both fungal and bacterial community composition, but only fungal community was positively associated with disease load. Network analysis identified three candidate keystone taxa: Alternaria sp. (FASV 34) and Sporobolomyces roseus (FASV 2070), which were mutually exclusive, and Methylobacterium sp. (BASV 75), which co-occurred with FASV 2070. Together, these findings demonstrate that different carbon farming practices shape distinct leaf microbiomes cover crop systems tending to favor potential fungal pathogens, whereas ley mixture and adaptive grazing strategies promote microbial taxa associated with healthier phyllosphere communities. Our study underscores the importance of understanding the complex microbial interactions within leaf ecosystems to inform sustainable agricultural practices.

1. Grassland ecosystems are pivotal for global biodiversity, carbon (C) storage and food security. This biome, however, together with the ecosystem services it provides, is threatened by global change perturbations. These perturbations rarely occur in isolation and most often affect environments simultaneously, which is a pressing issue in ecology. Nevertheless, most of the research conducted so far has focussed on single simultaneous perturbations or pairs thereof. The few examples considering the effect of more than two simultaneous perturbations focussed only on plants or soil separately, which ignores the potential buffering or feedback effects on ecosystem functioning induced by plant-soils interactions. 2. To tackle this knowledge gap, we used an experimental setup involving mesocosms (soil and plants intact) collected in an extensively managed permanent grassland. Mesocosms were arranged in a greenhouse experiment where we applied individual and combined global change perturbations (up to ten in total) including application of fertilisers, pesticides and antibiotics, simulated trampling and grazing, heat stress and drought. Measured ecosystem functions and properties included a large set of biological, physical and chemical soil and plant associated variables. 3. Results showed that multiple perturbations in most cases had negative effects irrespective of the direction found for individual perturbations. However, in contrast to previous bare soil experiments, we only found scarce evidence for substantial synergistic effects of simultaneous perturbations in our experiment conducted with mesocosms that contained vegetation. This suggests a mitigating impact of plants on soil responses to global change. Moreover, we found a strong dominative effect of drought on ecosystem functioning, driving most of the effects observed. 4. Synthesis: Our results highlight the importance of evaluating global change impacts under more realistic settings, i.e., applying multiple perturbations simultaneously and including plant-soil interactions. Mitigation of global change in terrestrial ecosystems will only be possible once we holistically understand how ecosystems respond to altered conditions.

Mangrove reforestation is expanding across the Caribbean, but restoration success is still judged almost exclusively by tree survival and canopy cover. Whether the sediment microbiome, which governs carbon burial and nutrient cycling, follows the recovery of the vegetation remains largely unknown. We combined 16S rRNA gene metabarcoding (V4, Illumina MiSeq) with CHNS elemental analysis, pH and salinity measurements to compare sediment prokaryotic communities along 0-100 cm profiles in a reference, a reforested (Rhizophora mangle plantings since 2019) and an altered mangrove within the Las Dunas de Las Calderas Natural Monument, Dominican Republic (39 cores pooled into 28 depth-resolved composite samples). Reference sediments contained 2.5-5.5-fold more organic carbon (median 7.5% vs 3.0% in altered and 1.3% in reforested sediments), had higher C/N ratios and were less alkaline (pH 8.2 vs 8.8). Reference communities were more diverse and even, and differed in composition from both disturbed stands (pairwise PERMANOVA, R^2 ~ 0.09, adjusted P = 0.0015), whereas reforested and altered communities were statistically indistinguishable (R^2 = 0.04, P = 0.25). Disturbed sediments were dominated by Cyanobacteriota (~41-45% of reads), which tracked high pH, whereas reference sediments were enriched in Chloroflexota, Thermodesulfobacteriota and Thermoproteota, lineages linked to anaerobic degradation of complex organic matter and sulfate reduction. Depth structured communities by separating surface from subsurface layers, and sediment organic carbon and nitrogen were the only significant constraints in distance-based redundancy analysis. These results indicate that, within a few years of the first plantings (2019), reforestation had not restored the carbon-rich, anaerobic sediment habitat of the reference forest. We propose sediment organic carbon and microbial community structure as complementary indicators for mangrove restoration monitoring in the Caribbean.

1. Soil invertebrate biomass is closely linked to ecosystem processes, yet its routine quantification remains constrained by the effort required to weigh large numbers of small individuals. Length-mass relationships provide an indirect alternative, but body length can be difficult to standardise and extract automatically from images of curved, coiled or contracted organisms. Projected body area may provide a more tractable image-derived predictor, but its performance across diverse soil-faunal taxa and at the community scale remains insufficiently evaluated. 2. Here, we developed a framework using projected body area and contour length to estimate fresh and dry mass from measurements of 1,792 soil invertebrates representing 15 higher-level taxa. We fitted taxon-specific models for six well-represented groups and general models across taxa, and evaluated predictive performance using leave-one-out cross-validation. We then assessed cross-dataset transferability by comparing our data with those of Lemoine et al. (2026) and pooled the two datasets to derive combined models. Finally, we tested whether individual predictions could be scaled to independently measured community biomass. 3. Taxon-specific models generally reduced prediction error relative to general models, with mean absolute percentage error (MAPE) values of 6.9-37.3% for fresh mass and 7.6-30.2% for dry mass. General models retained MAPEs of 27.2% and 22.4%, respectively. Comparisons of our dataset with that of Lemoine et al. (2026) showed no detectable differences in six of eight taxon-by-mass slopes. Although intercepts frequently differed, no overall dataset effect was detected after accounting for taxa. Pooling both datasets broadened model development, while taxon-specific models generally retained lower error than the combined general model. Finally, community-level predictions tracked measured biomass across all model sets (R2 = 0.87-0.99), but absolute error varied among models and faunal groups (MAPE = 9.6-52.5%). 4. Body area and contour length extracted from images therefore provide a practical basis for scaling soil invertebrate biomass estimation from individuals to communities. Integration with automated imaging and segmentation tools such as flatbug, BIODISCOVER and CollembolAI could extend soil invertebrate monitoring at larger scales beyond abundance and taxonomic composition to biomass, while providing scalable inputs for analyses of food webs and general ecosystem ecology.

Stemflow transports water and biological material from forest canopies to the stem base, yet fungal studies of this flux have largely relied on microscopy of conidia. We used ITS2 metabarcoding to characterize fungal environmental DNA (eDNA) in stemflow from 15 trees - five each of American beech (Fagus grandifolia), sugar maple (Acer saccharum), and tulip poplar (Liriodendron tulipifera) in a closed-canopy forest in northeastern Ohio, USA. Stemflow was sampled during eight rain events in the leafless season (November 2024-May 2025), along with simulated bark and gutter washes to assess near-collar and collector signals. Natural stemflow communities were compositionally distinct from both controls and occupied greater ordination space. Ascomycota dominated across all samples, with Parafenestella, Cytospora, Microcera, Nectria, and Aureobasidium among the most abundant resolved genera and 13 of the 25 most abundant taxa differed significantly among host species. Woody-plant-associated endophytes, canker fungi, and saprobes dominated ecological guild composition. Storm event explained 28.6% of taxonomic variation, host tree species 24.1%, and their interaction 10.0%. Guild composition was more strongly structured by host species (35.4%) than storm event (20.4%). Lichenized fungi and lichen-associated fungi were detected. Thus, leafless-season stemflow integrates broad bark-associated fungal eDNA, including recurrent lichen-derived material, beyond the morphologically distinctive conidia captured by traditional methods. Stemflow eDNA therefore offers a minimally invasive means of monitoring canopy fungal diversity and the strong host and temporal filtering of DNA exported from woody surfaces.

Boreal forested streams receive substantial inputs of terrestrial carbon (C) from riparian vegetation in the form of leaf litter, which is processed by litter-associated microorganisms. In addition to these leaf-litter C inputs, boreal streams also receive significant concentrations of dissolved organic carbon (DOC), which may represent an alternative major resource pool for litter-associated microorganisms. As leaf litter quality decreases over the process of decomposition, DOC may increasingly become a more suitable C source for the microbial communities. We investigated how DOC availability, litter type, and microbial succession influenced respiration and decomposition. Alder, birch, and spruce litter were incubated for 65 days in 12 outdoor experimental channels supplied with natural boreal stream water. Higher time-adjusted DOC concentrations were associated with higher respiration and lower relative mass remaining, whereas DOC flux received less support. Respiration and mass loss followed litter-specific trajectories, with birch showing a respiration peak that was not matched by proportional mass loss. Prokaryotic and eukaryotic communities differed among litter types and changed through time but explained process variation only for specific litter types and responses. Our results suggest that DOC can sustain litter-associated microbial activity and partly decouple respiration from litter decomposition, thereby affecting boreal stream C processing.

Microbially-mediated mineral precipitation is important in the natural world and to a number of emerging climate, energy, and water technologies. Central to many microbial mineralization processes is the preferential accumulation of precipitates on microbial surfaces. In some systems, including ureolytic microbially-induced carbonate precipitation (MICP), precipitates may entomb cells in a process termed "encapsulation." Encapsulation is known to greatly affect microbial systems, but understanding these relationships quantitatively has proven difficult, largely because nucleic acid extraction from encapsulated cells yields inconsistent results. Here, a demineralization protocol adapted from studies of natural microbialites is shown to recover genomic DNA from carbonate-encapsulated Sporosarcina pasteurii at yields indistinguishable from unmineralized cells and of sufficient quality for quantitative PCR. This method allows the degree of encapsulation to be expressed quantitatively as the amount of precipitate formed normalized to the estimated number of cells present, and allows growing populations to be tracked with increased precision. Simultaneous growth and mineralization experiments in mixed batch reactors suggest encapsulation-induced growth suppression at calcium concentrations of 250 mM, which are commonly employed in MICP under different physicochemical conditions. Variable rates of precipitate accumulation on cells, possibly stemming from local mass transport constraints, are proposed as a mechanism of calcium concentration-dependent growth suppression. Accordingly, mass transport principles are used to derive a reaction rate scaling function, allowing the observed growth and precipitation behavior to be replicated by a numerical model. These findings lay the groundwork for a more fundamental understanding of how encapsulation shapes microbial mineralization processes.

Forests are threatened by a multitude of stressors, including anthropogenic disturbances and climate change. Assessing how forests will respond to these stressors requires a comprehensive understanding of net primary productivity (Npp), environmental constraints on growth, and adaptive capacity. A parameter of significant uncertainty is belowground Npp (bNpp), which can account for up to 80% of total Npp but is poorly estimated and rarely measured directly. We used a cross-biome dataset of direct, field-based measurements of aboveground and belowground primary productivity and 21 climatic and soil variables to identify potential constraints on bNpp and belowground carbon allocation in boreal and cold temperate forests. Soil variables, rather than climate variables, were the main drivers of bNpp and belowground allocation across biomes. The importance of soil variables suggests that soil nutrient dynamics, especially soil nutrient pool and flux variables, must be explicitly modeled to more accurately predict feedbacks between climate, productivity, and within-tree carbon allocation. Within biomes, environmental drivers of belowground allocation varied between low versus high allocation forests, indicating that environmental drivers are site-specific and the development of within-biome, site-scale classifications for forest ecosystems could be useful. Changes in soil variables, such as increasing soil nitrogen pools, caused abrupt and large decreases in bNpp for boreal, but not cold temperate forests. Threshold-like shifts indicate that boreal forests might have lower adaptive capacity and higher sensitivity to disturbances than cold temperate forests. With 70% of boreal forests characterized by low bNpp, disturbances such as anthropogenic nitrogen deposition could cause large-scale decreases in bNpp that could push these forests beyond their adaptive capacity.

Soil is one of the most biodiverse habitats on the planet, yet the extent of soil biodiversity knowledge in Canada is unknown. To better understand our knowledge, we systematically mapped soil invertebrate biodiversity knowledge from peer-reviewed literature to identify spatial and taxonomic gaps and to assess whether areas projected to experience different magnitudes of climate change are adequately sampled. A total of 1,176 Canadian sampling locations were identified from 427 articles. We found biases in sampling coverage spatially and in relation to current and projected climatic conditions. The geographic region above 60 degrees North is sparsely sampled. Colder regions (< -0.12 C) and regions receiving the least (< 646.47 mm), moderately high (2268.67 to 2809.40 mm), and high (2809.40 to 3350.14 mm) amounts of precipitation were under sampled. Regions projected to have the smallest (< 0.86 C) and greatest (> 1.59 C) magnitudes in temperature change and regions projected to have moderate (-2.06 to +2.69 mm) to large changes (+2.69 to +7.44 mm) in precipitation were underrepresented. The sampled locations also suffer from taxonomic biases which were skewed toward Nematoda (19%), Annelida (18%), Acari (15%), and Collembola (14%). Our results suggest that methods such as stratified sampling is essential to capture underrepresented regions, taxonomic groups, and an array of current and projected climatic conditions. Additionally, shifting to a multispecies sampling approach is essential for broader soil ecosystem knowledge. Importantly, data from well-sampled areas should be examined to determine how it can be leveraged to advance conservation management of soil invertebrates.