FEMS Microbiology Ecology

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.

Background: Cyanobacteria are the major phototrophs in many endolithic ecosystems, yet their genomic diversity and metabolic adaptations remain poorly characterized. Here, we investigated cyanobacterial diversity in endolithic dolomite rocks from the Piora Valley in the southern Swiss Alps using genome-resolved metagenomics. Results: We reconstructed 138 medium-quality metagenome-assembled genomes (MAGs) from four neighboring endolithic rock communities, including 15 cyanobacterial MAGs distributed across six order-level lineages. The cyanobacterial communities showed limited taxonomic overlap among rocks, and most recovered MAGs represented potentially novel species. Only one Gloeobacter lineage occurred in all sampled rocks, which we propose as Gloeobacter dolomitensis sp. nov., representing the first Gloeobacter genome recovered from an endolithic environment. Comparative genomic analyses identified a cynS gene encoding cyanase unique to G. dolomitensis among the Gloeobacter. Phylogenetic analyses support its horizontal acquisition from Pseudomonadota. Interestingly, the genome of G. dolomitensis lacks a canonical CynABD cyanate transporter and instead contains a distinct ATP-synthase binding cassette (ABC) transporter adjacent to cynS. Although the available genomic and structural evidence does not establish cyanate transport, its genomic association with cynS suggests a potentially non-canonical mechanism. We further show that horizontal gene transfer was unevenly distributed among cyanobacterial lineages, with Acaryochloridales acting predominantly as donors, Chroococcidiopsidales as recipients, and Gloeobacterales showing a comparatively high frequency of interphylum gene exchange. Conclusions: The Piora Valley dolomite environment represents an underexplored reservoir of cyanobacterial diversity, including basal and previously undescribed lineages. The discovery of G. dolomitensis and its unusual cyanate-associated genomic architecture expands our understanding of Gloeobacterales diversity and highlights the potential importance of horizontal gene acquisition and metabolic innovation in endolithic microbial communities.

Anaerobic gut fungi (AGF) are an integral part of the herbivore gut microbiome, primary decomposers of lignocellulose, and play a crucial role in establishing foundational links of syntrophic associations. The syntrophy with methanogens appears beneficial for mitigating feedback inhibition and results in the augmentation of AGF activity. However, the thermodynamic advantages of the presence of methanogens to AGF remain poorly understood. This study explores the preferred pathways adopted by Cyllamyces sp. and Methanobrevibacter olleyae, using 13C-glucose as a substrate and spiked with malate and pyruvate in different experimental set-ups. The results indicated reduced biomass formation by Cyllamyces sp. in monoxenic culture with Methanobrevibacter olleyae compared to axenic AGF culture supplemented with glucose. Additionally, metabolic analyses revealed the pyruvate:ferredoxin oxidoreductase (PFO) as a key contributor to pyruvate metabolism. Malate supplementation notably enhanced the growth of Cyllamyces sp. and M. olleyae, whereas pyruvate supplementation enhanced the growth of Cyllamyces sp. only in axenic culture. This investigation provides insights into the preferred metabolic pathways operating in the hydrogenosomes of axenic anaerobic gut fungi (AGF) cultures and monoxenic AGF-methanogen co-cultures.

The high stability of enteric viruses in freshwater increases their risk of waterborne transmission. In aquatic environments, bacteria are known to enhance viral removal and inactivation. However, the differences in viral inactivation across freshwater ecosystems and the influence of community diversity on this process remains poorly understood. Here, we used dilution-to-extinction to generate 64 distinct freshwater communities from three lakes and three aquifers. After establishing freshwater communities in chemostat cultures, each community was challenged with two viruses, coxsackievirus B5 and human adenovirus 2. Both viruses were inactivated more rapidly in lake-derived than in groundwater-derived communities, and adenovirus was inactivated faster than coxsackievirus in both freshwater types. Community-level parameters (cell numbers, richness, evenness) were not significant predictors of viral inactivation. In contrast, differential abundance analyses identified bacterial OTUs associated with inactivation: Acidovorax sp. were associated across sources and Brevundimonas sp., Sphingopyxis sp., and Hydrogenophaga sp. showed source-specific associations. Together, these findings provide new insights into the ecological drivers of viral stability and suggest that viral inactivation may depend more strongly on specific microbial taxa and their ecological context than on overall community diversity. Identifying these associations improves our understanding of the factors governing viral persistence in freshwater environments.

Eutrophication-driven hypoxia and harmful algal blooms are an expanding threat to water quality in estuaries. Engineered aeration is a technology used in freshwater and, to a lesser extent, estuarine systems to mitigate both hypoxia and algal blooms. However, the efficacy of engineered aeration has not been well studied within estuarine ecosystems and very little is known about the impact of aeration on microbial communities in either estuarine or freshwater environments. Here we present a time series investigation of microbial community response to aeration and cessation of aeration in a eutrophic estuary. Samples for 16S rRNA gene analysis were collected over about a month-long period during which time the aerators transitioned from being "on" to "off" to "on" again. Cessation of aeration selected for the dominance of a eukaryotic algae similar to Heterosigma akashiwo. After the resumption of aeration, H. akashiwo dominance decreased rapidly. Cessation of aeration also shifted the structure of the entire microbial community, where diversity decreased and the structure of microbial communities at the surface diverged from those from the bottom of the water column. These changes did not occur at non-aerated control sites. Distinct groups of taxa responded to the disruption in a successional pattern through time, with most taxa never returning to their pre-aeration-cessation abundance during the observational period. These findings demonstrate the complex community response to anthropogenic interventions and provide support for bloom suppression through aeration.

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.

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.

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.

Background Symbiosis with microbes is a key strategy that has enabled plants to colonize extreme environments. Since the benefits conferred by root-associated microbes depend on both environmental conditions and host-microbe combinations, plant adaptation to harsh environments is closely linked to the assembly of root microbial communities. Understanding how environmental and host filtering jointly shape these communities is therefore fundamental to elucidating the mechanisms underlying plant adaptation to extreme environments. Results In this study, we investigated the differentiation of root-associated prokaryotic and fungal communities and individual operational taxonomic units (OTUs) across two contrasting habitats surrounding fumaroles, solfatara-field and forest-edge habitats, and six dominant Ericaceae and ectomycorrhizal plant taxa. Prokaryotic and fungal OTUs rarely exhibited strong preferences for both habitat and host identity. Instead, many of prokaryotic and fungal OTUs specialized to one of these niches, collectively generating root microbial communities differentiated by both factors. Nonetheless, striking specializations in habitat and host niches were observed in the fungal family Hyaloscyphaceae (Helotiales). To gain insight into the evolutionary basis of microbial specialization, we examined phylogenetic signals in preference phenotypes. The resulting weak phylogenetic signals in these preference phenotypes further suggest that this fungal clade has undergone substantial ecological divergence. Conclusion Overall, our findings indicate that root-associated microbial communities in extreme environments are assembled through the accumulation of microbial taxa specialized to either habitat or host, and that strong ecological specialization in fungi can arise with little phylogenetic constraint.

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.

Accelerated retreat of the Greenland Ice Sheets is increasing freshwater discharge to coastal fjords and promoting transitions from marine-terminating glacier (MTG) regimes to land-terminating (LTG) ones. These changes strongly affect the physical and chemical features of the water column, which in turn impact the structure and functioning of fjord ecosystems. We used high-throughput imaging and DNA metabarcoding approaches to investigate seasonal (spring vs summer) differences in the structure of pelagic microbial communities in two contrasting fjord systems (MTG vs LTG) in southwest Greenland, with focus on the bacterial and heterotrophic protist components, which to date remain understudied in Greenland fjords. Our analyses revealed a marked seasonal restructuring in the microbial communities, especially in the surface layers. In spring, heterotrophic community composition in both fjords manifested a strong link with the diatom spring bloom, being dominated by typical phytoplankton-associated and copiotroph bacterial groups that can utilize algal-derived organic matter, and protists grazing on phytoplankton. In summer, heterotroph communities strongly diverged between the two fjords, most likely caused by the differential impact of MTG vs LTG glaciers on water column structure and chemistry. There was a marked increase in pico- and nano-sized heterotrophs, parasitic protists (dinoflagellate Syndiniales), and bacterial groups indicative of low-nutrient environments. In addition, bacterial, phytoplankton and heterotrophic protist communities become more strongly coupled, either through stronger interactions and/or stronger environmental filtering acting on all groups simultaneously. These observations are indicative of a shift from resource-replete systems in spring to more resourced-depleted systems in summer. However, this shift was less pronounced in the MTG fjord, where subglacial upwelling enabled the persistence of diatom bloom related communities into summer. Finally, we uncovered the presence of a unique, ice melange associated inner fjord microbial community, which shows similarities with both supraglacial and sea-ice associated communities, in the inner part of the MTG impacted fjord.

Pyrroloquinoline quinone (PQQ) is known to promote plant growth, yet how the rhizosphere microbiome varies with PQQ concentration remains poorly understood. We applied metagenomic sequencing to characterize the taxonomic composition and functional potential of the tobacco rhizosphere microbiome across PQQ treatments at 0.5, 1 and 2 mol/L plus an untreated control. The rhizosphere microbiome was dominated by Pseudomonadota and Actinomycetota and differed among treatments in a concentration-associated, non-monotonic manner. The most pronounced differences were observed at 1 mol/L, where alpha diversity showed dimension-specific variation and beta-diversity analysis resolved the most distinct community profile. Taxonomic and functional profiles varied concurrently, with Streptomyces, Sphingomonas, Rhodanobacter and Lysobacter, together with functions related to biosynthesis, energy metabolism, colonization and environmental sensing, showing higher relative abundance at this concentration. No broad-spectrum antimicrobial effect was detected at the community level, and antibiotic resistance gene abundance showed no significant differences among treatments after correction for multiple testing. These findings provide a basis for further evaluation of PQQ in modulating the rhizosphere microbiome in continuous cropping systems.

Coinfections are common in a nature and often involve competition among coinfecting parasites to extract resources from the host. As a consequence of this competition, parasites can face trade-offs between investing in competition with other parasites and exploiting the host for their own growth and transmission. Such within-host interactions among parasites can either increase or decrease virulence depending on how they alter parasite density, resource use, and host damage. We tested the inhibitory effect of different species of the entomopathogenic fungus Metarhizium on one another in vitro and the impact of coinfection on virulence towards Tribolium castaneum. We found that Metarhizium pemphigi is able to inhibit all other isolates of Metarhizium tested, whereas Metarhizium pingshaense was relatively resistant to inhibition by other Metarhizium strains. Virulence towards the host, Tribolium castaneum, differed very little among isolates tested. We did, however, observe differences between virulence in single and coinfections in two cases. Where there were virulence differences, these were both consistent with in vitro inhibition patterns and interestingly resulted in reduced virulence in coinfection. This is inconsistent with broader patterns of virulence in coinfection, where virulence seems to be driven by the more virulent parasite. It is, however, consistent with data from other systems where there is evidence of interference competition. Our data thus support the idea that, in contrast to other forms of between parasite interaction, interference competition results in reduced virulence in coinfection.

Marine microbial communities vary seasonally and spatially, shaped by physiochemical gradients and biotic interactions. Spatiotemporal variability of seawater microbiomes in tropical coastal regions is comparatively understudied, especially in Southeast Asia with high pressures from development and anthropogenic activities. Here, we examined the microspatial and temporal variability of bacterioplankton in the Singapore Strait, which is a tropical system in Southeast Asia influenced by monsoons. By applying total community amplicon sequencing to three particle size fractions reflecting microspatial habitats of seawater (0.22-1 {micro}m ''free-living'', 1-10 {micro}m ''large cells and small aggregates'' and 10-150 {micro}m ''particle-associated''), we show that the seawater microbial community was structured by their microspatial habitats, monsoon seasons and physiochemical variables. Monsoon-driven alternation of water masses originating from the South China Sea to the East and from off the Sumatran coast to the West resulted in a distinct community during the Southwest monsoon across all three size fractions. Total DNA (biomass) was lowest in the 10-150 {micro}m fraction, but these particle-associated sequences had the highest diversity and were surprisingly enriched with picocyanobacterial and some pathogenic taxa, potentially reflecting aggregate formation and/or host-derived particle association. This fraction also exhibited greater temporal variability than the two smaller fractions, which could be related to a more heterogenous environment in particle microhabitats. Overall, this study demonstrated compositional variability in the bacterioplankton across space and time in an equatorial region influenced by monsoons.

Spontaneous vegetable fermentation is driven by the indigenous microbiota associated with the raw ingredients. The process often involves an initial heterofermentative phase followed by a predominantly homofermentative phase, both ensured by lactic acid bacteria (LAB). While microbial dynamics during fermentation are well characterized, phage communities remain poorly understood, despite evidence linking phage activity to LAB succession. We monitored viral and bacterial succession during sauerkraut and carrot fermentations using a metagenomics approach to characterize community dynamics. To further assess the impact of phage PLE001 on bacterial community dynamics, we developed a simplified carrot fermentation model comprising representative strains of Rahnella aquatilis, Leuconostoc mesenteroides and Lactiplantibacillus plantarum. Two consortia were assembled: one containing the PLE001-susceptible strain L. mesenteroides CIM3004, and the other containing also its phage-resistant derivative, CIM3004 BIM. We observed major shifts in the viral community during the first week of fermentation, coinciding with changes in bacterial structure during hetero- and homofermentative phases transition. In the simplified model, phage PLE001 reduced the population of the host during the heterofermentative phase but did not affect overall fermentation dynamics nor metabolite production. These results suggest that bacteriophages contribute to bacterial succession during fermentation, while communities remain resilient to phage infection, preserving fermentation stability.

Schistosoma mansoni infection is associated with alterations of the host gut microbial community structure, yet its impact on microbial genome dynamics and horizontal gene transfer remains poorly understood. In this study, we investigated the activity of Mobile Genetic Elements (MGEs), and of Insertion Sequences (IS) in particular, in the gut microbiome of wild-type (WT) and human-microbiota-associated (HMA) mice. Taxonomic profiling revealed significant differences in bacterial diversity between WT and HMA mice, with reduced richness and alpha diversity observed in HMA gut microbiomes regardless of the infection status. Principal Coordinates Analysis demonstrated clear separation between microbial communities, reflecting differences in host background and bacterial composition. In contrast, differences were observed between plasmid and viral community profiles and between these and bacterial diversity, suggesting that different MGEs may follow distinct ecological dynamics within the gut microbiome. IS elements within bacterial genomes were widespread across all microbiome communities analysed in this study, with higher insertion counts observed not only in HMA compared to WT mice, but also in infected compared to uninfected mice. IS elements were predominantly associated with dominant gut bacterial taxa, particularly members of Bacteroidia and Clostridia. At the genomic level, insertion events occurred more frequently in intergenic regions than in coding sequences, suggesting a preferential selective pressure towards alteration of gene expression rather than gene disruption. Furthermore, IS activity was dominated by a subset of IS families, with consistent patterns observed across experimental groups. Notably, infection was associated with increased insertion frequencies across multiple taxa and IS families, suggesting enhanced mobilisation under conditions of host-associated stress (the physiological and molecular pressure experienced by microorganisms, pathogens, or the host itself during their interactions within a symbiotic or infected environment) and microbiome perturbation. Together, these findings demonstrate that S. mansoni infection may promote IS mobilisation in the mouse gut microbiome, potentially contributing to microbial genome plasticity and facilitating horizontal gene transfer within host-associated microbial communities.

Cyclosporiasis is a foodborne illness caused by the parasite Cyclospora cayetanensis. Clinical surveillance often lags infection by weeks because diagnosis depends on a clinician ordering a test that is not part of routine parasite panels. Wastewater metagenomic sequencing does not depend on care seeking, which may be useful for early detection and community monitoring. We designed 1,670 31-mers from C. cayetanensis mature ribosomal RNA and retained 1,464 without an exact non-target match in the 28 July 2025 NCBI core_nt release. By analyzing 293 public wastewater metagenomes, we selected a threshold of 24 distinct diagnostic 31-mers on one read. Applying that threshold to 2,333 public runs from BioProject PRJNA1247874 yielded putative C. cayetanensis reads in 81 runs, or 3.5%, and in 24 of the 30 longitudinally sampled sewersheds. Detections rose through the summer in two consecutive years, matching the known seasonality of cyclosporiasis. The most parsimonious explanation is that these reads come from parasites shed into wastewater, although undescribed Cyclospora species absent from reference databases cannot be excluded. The same approach can be applied to other pathogens in existing wastewater sequencing data.

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.

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.

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.