Microbial Functional Groups Research Articles

Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function.

Microbial communities play key roles across diverse environments. Predicting their function and dynamics is a key goal of microbial ecology, but detailed microscopic descriptions of these systems can be prohibitively complex. One approach to deal with this complexity is to resort to coarser representations. Several approaches have sought to identify useful groupings of microbial species in a data-driven way. Of these, recent work has claimed some empirical success at de novo discovery of coarse representations predictive of a given function using methods as simple as a linear regression, against multiple groups of species or even a single such group (the ensemble quotient optimization (EQO) approach). Modeling community function as a linear combination of individual species' contributions appears simplistic. However, the task of identifying a predictive coarsening of an ecosystem is distinct from the task of predicting the function well, and it is conceivable that the former could be accomplished by a simpler methodology than the latter. Here, we use the resource competition framework to design a model where the "correct" grouping to be discovered is well-defined, and use synthetic data to evaluate and compare three regression-based methods, namely, two proposed previously and one we introduce. We find that regression-based methods can recover the groupings even when the function is manifestly nonlinear; that multi-group methods offer an advantage over a single-group EQO; and crucially, that simpler (linear) methods can outperform more complex ones.

Livestock grazing strengthens the effect of vole activity on the soil microbial community

Livestock grazing may affect small mammalian herbivore-soil microbe interactions and their association with the structure and functions of the ecosystem. However, the role of factors such as vegetation and soil nutrients in regulating these impacts is not clear. Here we conducted a 9-year experiment in temperate steppe to study how Brandt’s vole (Lasiopodomys brandtii) affects the soil microbial community under different livestock grazing intensities. This experiment contained 12 field enclosures with three livestock grazing intensities: control (CK), light grazing (LG), and moderate grazing (MG). We found that vole activity does not significantly change soil microbial diversity under non-grazing conditions. However, under livestock grazing conditions, vole activity led to a significant reduction in soil bacterial diversity and an increase in fungal diversity, demonstrating the impacts of livestock grazing on rodents-soil microbe interactions. The activity of voles significantly altered soil bacterial community composition, with changes primarily attributed to variations in the relative abundance of the phyla Actinobacteria, Bacteroidetes, Firmicutes, Gemmatimonadetes, and Proteobacteria. The soil fungal community remained relatively stable despite vole activity, which can be attributed to the richness of fungal colonies in mycelium and their low sensitivity to changes in external conditions. Vole activity also influenced soil microbial functional groups, and the variations in these groups were further amplified by livestock grazing. Furthermore, the shift in the microbial community composition and diversity induced by vole activity were mainly associated with the reduction of plant aboveground biomass. Overall, our study suggested that livestock grazing enhanced the changes in the soil microbial community induced by rodents, underscoring the importance of managing livestock grazing regimes for grassland conservation.

Community structure, diversity and function of endophytic and soil microorganisms in boreal forest.

Despite extensive studies on soil microbial community structure and functions, the significance of plant-associated microorganisms, especially endophytes, has been overlooked. To comprehensively anticipate future changes in forest ecosystem function under future climate change scenarios, it is imperative to gain a thorough understanding of the community structure, diversity, and function of both plant-associated microorganisms and soil microorganisms. In our study, we aimed to elucidate the structure, diversity, and function of leaf endophytes, root endophytes, rhizosphere, and soil microbial communities in boreal forest. The microbial structure and composition were determined by high-throughput sequencing. FAPROTAX and FUNGuild were used to analyze the microbial functional groups. Our findings revealed significant differences in the community structure and diversity of fungi and bacteria across leaves, roots, rhizosphere, and soil. Notably, we observed that the endophytic fungal or bacterial communities associated with plants comprised many species distinct from those found in the soil microbial communities, challenging the assumption that most of endophytic fungal or bacterial species in plants originate from the soil. Furthermore, our results indicated noteworthy differences in the composition functional groups of bacteria or fungi in leaf endophytes, root endophytes, rhizosphere, and soil, suggesting distinct roles played by microbial communities in plants and soil. These findings underscore the importance of recognizing the diverse functions performed by microbial communities in both plant and soil environments. In conclusion, our study emphasizes the necessity of a comprehensive understanding of the structure and function microbial communities in both plants and soil for assessing the functions of boreal forest ecosystems.

Integrated above and below-ground responses of the gypsum specialist Helianthemum squamatum (L.). to drought

Gypsum endemics (i.e. gypsophiles) have adapted to live in gypsum-rich soils where nutrient unbalance and drought can be extreme. Despite their relevance as plants adapted to extreme conditions, a complete analysis of the physiological responses of gypsophiles to drought is still lacking. Helianthemum squamatum (L.) Dum. Cours. is a conspicuous Iberian gypsophile that has been reported to use gypsum crystallization water during the driest period, but the mechanisms behind this process are unknown. To characterize gypsophile responses to drought and unravel the mechanisms underlying gypsum crystalline water use, H. squamatum plants were grown in pots with natural gypsum soil and gypsum soil with deuterium-labelled crystalline water. After three years, a drought experiment was carried out and whole-plant responses were investigated. Unexpectedly, the labelling treatment affected soil physicochemical characteristics and reduced microbial biomass and organic matter content, decreasing plant aerial biomass. H. squamatum plants did not use gypsum crystallization water during simulated drought neither in the labelled soil, nor in the natural one. Drought reduced plant transpiration, stomatal conductance, water use, photosynthetic rate and the foliar concentration of most elements except P and N, which were higher in the drought stressed plants. We detected increased root exudation of choline, an osmoprotector, by drought stressed plants. The drought treatment also affected the structure of microbial communities but did not reduce the relative abundance of functional microbial groups, highly adapted to the natural drought pulses. Our results highlight an integrated water-saving strategy of H. squamatum plants in the short-term, where responses at the leaf level are combined with belowground processes, like altered root exudation. Our findings also underline the remarkable resistance to drought of microbial communities present in gypsum soils.

Spatial patterns and effects of invasive plants on soil microbial activity and diversity along river corridors

Abstract Background and aims Invasive species represent a threat to the conservation of biological systems. Riparian ecosystems are vulnerable to plant invasions, as waterflow facilitates the dispersal of plant propagules, while invasive species may subsequently impact soil, including soil microbial communities. Downstream connectivity among disparate riverine segments is expected to cause spatial continuity of abiotic and biotic components of riparian ecosystems. Methods We studied diversity of microbial communities in three headwater streams in Central Europe. Plant diversity, soil properties and soil microbiota were assessed on 20 sample plots per river. Soil microbial activity and community-level physiological profiling were used to study the soil microbial community. Results While the α-diversity of plants and soil microbiota was similar among rivers, plant communities were substantially more differentiated than microbial communities. Richness in alien and invasive plants significantly differed among rivers, which was reflected in different spatial patterns of microbial activity and diversity. A high level of spatial continuity was observed in the Kysuca river with straightened riverbed and artificial surfaces in the adjacent areas. The cover of invasive plants affects the composition of microbial functional groups of riverbed soils. Conclusion The expectation of spatial continuity of riverbed soil properties including those of soil microbiota caused by connectivity between different river segments was only partially fulfilled. Spatial continuity strongly depends on the environmental setting and stream characteristics of a particular river. The presence of invasive herbs affected the functional composition of soil microbiota but had no effect on microbial activity and diversity.

Discovering the role of fairy ring fungi in accelerating nitrogen cycling to promote plant productivity in grasslands

Soil microorganisms play a key role in the provision of plant-bioavailable nutrients, which is crucial for ecosystem functioning and plant productivity. Fairy rings are widespread features in grasslands accompanied by lush dark-green vegetation bands. This enigmatic feature is caused by increased soil bioavailable nitrogen (N) due to the expansion of fairy ring fungi (FRF). However, little is known about how FRF enhance soil bioavailable N concentrations. Here, we conducted a survey of 35 fairy rings in temperate grasslands to reveal the role of FRF in regulating soil microorganisms and N cycling using amplicon and metagenomic sequencing. The presence of FRF accelerated organic N mineralization via promoting extracellular enzyme (β-1,4-N-acetylglucosaminidase) activity, leading to a 455% increase in ammonium-N. This further stimulated nitrification to enhance nitrate-N concentration by favoring ammonia-oxidizing archaea. Concomitantly, the increased nitrate-N did not promote denitrification or affect the potential risk of N loss. Furthermore, the relative abundance of other saprotrophic and symbiotrophic fungi was significantly reduced by FRF but the changes in these fungi did not affect the activity of extracellular enzymes involved in N mineralization. Our results suggest that FRF can act as ecosystem engineer species shaping fairy rings by driving soil N cycling without the involvement of other microbial functional groups of saprotroph and symbiotroph to boost plant productivity. Thus, due to the stronger N mobilizing ability, FRF show great potential to be exploited as beneficial microorganisms in plant production and sustainable agricultural development.

Soil health is associated with higher primary productivity across Europe.

Soil health is expected to be of key importance for plant growth and ecosystem functioning. However, whether soil health is linked to primary productivity across environmental gradients and land-use types remains poorly understood. To address this gap, we conducted a pan-European field study including 588 sites from 27 countries to investigate the link between soil health and primary productivity across three major land-use types: woodlands, grasslands and croplands. We found that mean soil health (a composite index based on soil properties, biodiversity and plant disease control) in woodlands was 31.4% higher than in grasslands and 76.1% higher than in croplands. Soil health was positively linked to cropland and grassland productivity at the continental scale, whereas climate best explained woodland productivity. Among microbial diversity indicators, we observed a positive association between the richness of Acidobacteria, Firmicutes and Proteobacteria and primary productivity. Among microbial functional groups, we found that primary productivity in croplands and grasslands was positively related to nitrogen-fixing bacteria and mycorrhizal fungi and negatively related to plant pathogens. Together, our results point to the importance of soil biodiversity and soil health for maintaining primary productivity across contrasting land-use types.

Climate determines diversity but not abundance of nitrogen-cycling microorganisms in rivers across a latitudinal gradient

ABSTRACT A central goal in microecology is to understand the ecological factors shaping spatial patterns of microbial communities and the underlying mechanisms. However, the biogeographical patterns of microbial functional groups involved in nitrogen cycling (e.g., nitrifiers and denitrifiers) and their drivers at a large scale remain poorly understood. In this study, we evaluated the geographical distributions of nitrifiers and denitrifiers in riparian rhizosphere soils, riparian bulk soils, and channel sediments of 30 river regions along a latitudinal gradient from 21.8°N to 45.1°N across eastern China. We found that the diversity of nitrifiers and denitrifiers exhibited a gradual latitudinal gradient, in direct contrast to no significant changes observed for their abundance along the same latitudinal gradient. Statistical analyses suggested that climatic factors (mean annual temperature and mean annual precipitation) were the major drivers for the diversity of nitrifiers and denitrifiers, whereas soil properties were the key environmental factors shaping the abundance of nitrifiers and denitrifiers. These results provide new insights into the biogeographical distributions and ecological drivers for nitrogen-cycling microorganisms in river ecosystems at a large scale and can help us to improve simulation models of the nitrogen cycle for accurately predicting the diversity of nitrogen-cycling microbes under ongoing climate changes.

Climate regulates the effect of land‐use change on the diversity of soil microbial functional groups and soil multifunctionality

Abstract Although studies have explored how soil microbial diversity and soil multifunctionality respond to land‐use change at local scales, they have rarely been explored at larger scales and across different climatic and soil environmental conditions. By sampling 40 paired sites of land‐use change from natural forests to agricultural lands (including croplands and orchards) along the middle and lower Yangtze River, combined with a global meta‐analysis, we investigated the effects of land‐use change and climate on the alpha and beta diversity of soil bacterial and fungal functional groups (FGs) and their associated soil multifunctionality at a regional scale. Our results showed that land‐use change strongly changed the diversity of soil bacterial and fungal FGs and decreased multifunctionality, which was supported by our meta‐analysis at a global scale. Direct effects of land‐use change and climate and their interaction, together with changes in soil environmental variables, were the main determinants of the land‐use change‐induced changes in the diversity of soil bacterial or fungal FGs. The land‐use change‐induced decrease in multifunctionality was mainly associated with the direct effect of forest conversion, soil fertility and diversity of fungal FGs. Furthermore, climate also regulated the effects of land‐use change on multifunctionality by affecting soil fertility and fungal FGs diversity along the Yangtze River. Synthesis and applications. Taken together, our findings highlight the important effects of land‐use change, climate and their interactions on microbial diversity and multifunctionality and suggest that effective land‐use management and climate change mitigation strategies should be adopted to protect biodiversity and ecosystem function in the Yangtze River Basin.

Low-dose natural clay Kaolin promotes the growth of submerged macrophytes and alters the rhizosphere microorganism community: Implications for lake restoration

Sediment properties have a crucial effect on the growth and recovery of aquatic plants in lakes. Addition of various chemical substances has been proposed to reinforce the recovery of plants after a nutrient loading reduction. However, the effects of such sediment amendments on plant growth, especially those from rhizosphere microorganisms, is limited. We added Kaolin clay to sediments in different concentrations to explore its impact on the growth of Vallisneria natans and Ottelia acuminate and the concurrent shift in rhizosphere microorganisms using high-throughput sequencing technology. We found that the addition of low doses (10 % and 20 % in mass ratio) of Kaolin significantly modified sediment conditions (oxidation reduction potential and pH), with implications also for the composition, diversity, and stability of rhizosphere microorganisms. LEfSe analysis revealed that low-dose addition of Kaolin increased the abundances of functional microbial groups that benefit plant nutrient absorption and enhance plant stress resistance, such as Spirillaceae, Rhodocyclaceae, and Burkholderiales. Moreover, low doses of Kaolin significantly promoted the photosynthesis and nutrient absorption of submerged macrophytes, thereby facilitating plant growth. A structural equation model (SEM) indicated that the direct impact of Kaolin on the growth of submerged plants was relatively minor, while the indirect effect through modulation of rhizosphere microorganisms was important. Our study suggests that low doses of Kaolin may be used to promote the growth of submerged macrophytes when lakes with a high organic content in the sediment are recovering after nutrient loading reduction.

Metabolic Plasticity Shapes Microbial Communities across a Temperature Gradient.

AbstractA central challenge in community ecology is understanding and predicting the effects of abiotic factors on community assembly. In particular, microbial communities play a central role in the ecosystem, but we do not understand how changing factors like temperature are going to affect community composition or function. In this article, we studied the self-assembly of multiple communities in synthetic environments to understand changes in microbial community composition based on metabolic responses of different functional groups along a temperature gradient. In many microbial communities, different microbial functional groups coexist through the partitioning of carbon sources in an emergent trophic structure (cross-feeding). In this system, respirofermentative bacteria display a preference for the sugars supplied as the only carbon source but secrete secondary carbon sources (organic acids) that are more efficiently consumed by obligate respirators. As a consequence of this trophic structure, the metabolic plasticity of the respirofermenters has downstream consequences for the relative abundance of respirators across temperatures. We found that the effects of different temperatures on microbial composition can largely be described by an increase in fermentation by-products with increasing temperatures from the respirofermentative bacteria. This research highlights the importance of metabolic plasticity and metabolic trade-offs in predicting species interactions and community dynamics across abiotic gradients.

Shifts in the nitrogen cycle under different fertilizer management practices

Human population is dependent on agricultural production, but these activities pose multiple threats to soil health and indirectly to ecological sustainability. Synthesis of fertilizers proved to be a miraculous solution to enhance soil productivity, but this advancement came with many unseen risks. Long-term research stations that have decades long experiments with fertilizers additions are paramount in better understanding long-term impact of fertilizer use. Our study focused on ammonium and nitrate levels found in soils in an experiment of inorganic nitrogen addition than began in 1975. We further directed our attention to soil mineralization potential, nitrate reductase activities and densities of two major microbial functional groups: ammonifiers and denitrifiers. Our data suggests that ammonium has a stronger tendency of soil buildup than nitrate and that increased levels of inorganic nitrogen species also impacted molecular compartments and processes such as mineralization potential, soil microbiota and enzymatic activities. Another result indicates that analysed soils reached a storage limit for phosphorus which threatens to overburden other ecosystems.

Effects of Soil Microorganisms on Carbon Sequestration under Different Mixed Modification Models in Pinus massoniana L. Plantation

In forests, microbial populations in the soil can directly influence the decomposition of carbon from surface plants, promoting carbon storage and stability. However, in sustainable forest management, it is still unclear how soil microorganisms under different plantation types affect organic carbon sequestration and whether the mechanisms of influence are the same. In this research, we focused on four mixed forests and pure Pinus massoniana-planted forest in the state-owned forest farm of Dushan County. Three replicated plots were set up for each model, and soil samples were collected from different layers (0–20 cm, 20–40 cm, and 40–60 cm), totaling 45 samples. We elucidated the effects of soil microorganisms on carbon sequestration under five mixed modification models of P. massoniana and further explored the mechanisms by which microbial functional communities regulate soil carbon sequestration under different mixed models through molecular sequencing and collinear network analysis. Variance analysis indicated that the soil organic carbon (SOC) of the same soil layer varied significantly, and there were also significant differences in the composition of soil bacterial and fungal microbial communities. Moreover, the bacterial community was more sensitive to changes in the vegetation environment, while the fungal community structure was more resistant to changes in the soil environment. Correlation analysis indicated that the diversity and composition of the bacterial community had more positive effects on soil organic carbon than those of the fungal community. Linear fitting and redundancy analysis (RDA) showed that particulate organic carbon (POC) in soil had the strongest correlation with SOC content. Soil microorganisms affected the storage and stability of soil carbon mainly by regulating the conversion of litter (carbon sources) into POC. The soil environment of different mixed models had different effects on soil carbon accumulation. Both correlation and collinearity network analyses indicated that soil microbial functional groups could enhance carbon storage by regulating readily oxidizable carbon (EOC) and POC content in mixed forest plantations. The results of our study provide a sound basis for replanting a reasonable forest model structure to improve forest carbon storage.

Analysis of effects and factors linked to soil microbial populations and nitrogen cycling under long-term biosolids application

Information about impacts of long-term biosolids application on soil microbial populations and functional groups and N cycling is important for evaluating soil health and agroecosystem sustainability under long-term biosolids application. Mine spoil plots received annual biosolids application from 1973 to 2010 at low (16.8 Mg ha−1 yr−1), medium (33.6 Mg ha−1 yr−1), and high rates (67.2 Mg ha−1 yr−1). A no-biosolids control received chemical fertilizer at the agronomic rate. Soil samples were collected in three seasons per year spanning 2003–2005 for measuring soil moisture, pH, soil organic C (SOC), total and extractable heavy metals (Cd, Cu, Ni, Zn), NO3−, N mineralization potential (NMP), microbial biomass C (MBC), and populations of three N-cycling bacteria (NCB) groups: ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), and denitrifying bacteria (DNB). Soil samples were collected again in 2008 and 2010 for quantifying total and extractable heavy metals, and in 2018 (eight years after biosolids applications ended) for measuring SOC, MBC, NMP, and microbial respiration. During 2003–2005, mean MBC was 315, 554, 794, and 1001 mg kg−1 in the control, low, medium, and high biosolids treatments, respectively. Populations of NCB did not differ among treatments. Biosolids application increased total and extractable metal concentrations but the effect of biosolids rates were much lower on extractable than total concentrations. Soil extractable Cd and Cu concentrations decreased from medium to high applications, likely due to complexing with biosolids organic matter. Partial least squares regression analysis identified a strong positive effect on MBC of SOC and a weak negative effect of Cu, explaining the strong net positive effect of biosolids on MBC. In 2018, the medium and high biosolids treatments maintained higher SOC, MBC, NMP, and microbial respiration than the control. This study provided further evidence that long-term biosolids application has positive effects on soil microbes that persist for years after ending application.

Effect of organic acids on fermentation quality and microbiota of horseshoe residue and corn protein powder

This experiment aimed to investigate the impact of malic acid (MA) and citric acid (CA) on the nutritional composition, fermentation quality, rumen degradation rate, and microbial diversity of a mixture of apple pomace and corn protein powder during ensiling. The experiment used apple pomace and corn protein powder as raw materials, with four groups: control group (CON), malic acid treatment group (MA, 10 g/kg), citric acid treatment group (CA, 10 g/kg), and citric acid + malic acid treatment group (MA, 10 g/kg + CA, 10 g/kg). Each group has 3 replicates, with 2 repetitions in parallel, subjected to mixed ensiling for 60 days. The results indicated: (1) Compared to the CON group, the crude protein content significantly increased in the MA, CA, and MA + CA groups (p < 0.05), with the highest content observed in the MA + CA group. The addition of MA and CA effectively reduced the water-soluble carbohydrate (WSC) content (p < 0.05). Simultaneously, the CA group showed a decreasing trend in NDFom and hemicellulose content (p = 0.08; p = 0.09). (2) Compared to the CON group, the pH significantly decreased in the MA, CA, and MA + CA groups (p < 0.01), and the three treatment groups exhibited a significant increase in lactic acid and acetic acid content (p < 0.01). The quantity of lactic acid bacteria increased significantly (p < 0.01), with the MA + CA group showing a more significant increase than the MA and CA groups (p < 0.05). (3) Compared to the CON group, the in situ dry matter disappearance (ISDMD) significantly increased in the MA, CA, and MA + CA groups (p < 0.05). All three treatment groups showed highly significant differences in in situ crude protein disappearance (ISCPD) compared to the CON group (p < 0.01). (4) Good’s Coverage for all experimental groups was greater than 0.99, meeting the conditions for subsequent sequencing. Compared to the CON group, the Shannon index significantly increased in the CA group (p < 0.01), and the Simpson index increased significantly in the MA group (p < 0.05). However, there was no significant difference in the Chao index among the three treatment groups and the CON group (p > 0.05). At the genus level, the abundance of Lentilactobacillus in the MA, CA, and MA + CA groups was significantly higher than in the control group (p < 0.05). PICRUSt prediction results indicated that the metabolic functional microbial groups in the CA and MA treatment groups were significantly higher than in the CON group (p < 0.05), suggesting that the addition of MA or CA could reduce the loss of nutritional components such as protein and carbohydrates in mixed ensilage. In conclusion, the addition of malic acid and citric acid to a mixture of apple pomace and corn protein powder during ensiling reduces nutritional losses, improves fermentation quality and rumen degradation rate, enhances the diversity of the microbial community in ensiled feed, and improves microbial structure. The combined addition of malic acid and citric acid demonstrates a superior effect.

Prairie restoration promotes the abundance and diversity of mutualistic arbuscular mycorrhizal fungi.

Predicting how biological communities assemble in restored ecosystems can assist in conservation efforts, but most research has focused on plants, with relatively little attention paid to soil microbial organisms that plants interact with. Arbuscular mycorrhizal (AM) fungi are an ecologically significant functional group of soil microbes that form mutualistic symbioses with plants and could therefore respond positively to plant community restoration. To evaluate the effects of plant community restoration on AM fungi, we compared AM fungal abundance, species richness, and community composition of five annually cultivated, conventionally managed agricultural fields with paired adjacent retired agricultural fields that had undergone prairie restoration 5-9 years prior to sampling. We hypothesized that restoration stimulates AM fungal abundance and species richness, particularly for disturbance-sensitive taxa, and that gains of new taxa would not displace AM fungal species present prior to restoration due to legacy effects. AM fungal abundance was quantified by measuring soil spore density and root colonization. AM fungal species richness and community composition were determined in soils and plant roots using DNA high-throughput sequencing. Soil spore density was 2.3 times higher in restored prairies compared to agricultural fields, but AM fungal root colonization did not differ between land use types. AM fungal species richness was 2.7 and 1.4 times higher in restored prairies versus agricultural fields for soil and roots, respectively. The abundance of Glomeraceae, a disturbance-tolerant family, decreased by 25% from agricultural to restored prairie soils but did not differ in plant roots. The abundance of Claroideoglomeraceae and Diversisporaceae, both disturbance-sensitive families, was 4.6 and 3.2 times higher in restored prairie versus agricultural soils, respectively. Species turnover was higher than expected relative to a null model, indicating that AM fungal species were gained by replacement. Our findings demonstrate that restoration can promote a relatively rapid increase in the abundance and diversity of soil microbial communities that had been degraded by decades of intensive land use, and community compositional change can be predicted by the disturbance tolerance of soil microbial taxonomic and functional groups.

The Impact of Aboveground Epichloë Endophytic Fungi on the Rhizosphere Microbial Functions of the Host Melica transsilvanica.

In nature, the symbiotic relationship between plants and microorganisms is crucial for ecosystem balance and plant growth. This study investigates the impact of Epichloë endophytic fungi, which are exclusively present aboveground, on the rhizosphere microbial functions of the host Melica transsilvanica. Using metagenomic methods, we analyzed the differences in microbial functional groups and functional genes in the rhizosphere soil between symbiotic (EI) and non-symbiotic (EF) plants. The results reveal that the presence of Epichloë altered the community structure of carbon and nitrogen cycling-related microbial populations in the host's rhizosphere, significantly increasing the abundance of the genes (porA, porG, IDH1) involved in the rTCA cycle of the carbon fixation pathway, as well as the abundance of nxrAB genes related to nitrification in the nitrogen-cycling pathway. Furthermore, the presence of Epichloë reduces the enrichment of virulence factors in the host rhizosphere microbiome, while significantly increasing the accumulation of resistance genes against heavy metals such as Zn, Sb, and Pb. This study provides new insights into the interactions among endophytic fungi, host plants, and rhizosphere microorganisms, and offers potential applications for utilizing endophytic fungi resources to improve plant growth and soil health.

Early changes in carbon uptake and partitioning moderate belowground carbon storage in a perennial grain

There is increasing interest in perennial crops to build soil carbon (C), but the mechanisms underlying soil C accrual in perennial croplands remain unclear, especially over time in the first years of perennial crop growth. To address this gap, research is needed that directly tracks intra-annual C fluxes through crop-microbial-soil pools, evaluating the capacity of perennial crops to build soil C over intra-decadal time periods. We conducted a 13C isotope-tracer study to compare within-season C uptake and crop-microbial-soil C partitioning patterns between 1-year-old (IWG-1) and 2-year-old (IWG-2) stands of a novel perennial grain crop, intermediate wheatgrass (IWG; Thinopyrum intermedium (Host) Barkworth and Dewey). We compared these to a common annual grain crop, spring wheat (Triticum aestivum L.). Crop shoots, roots, soil, and soil respired-C were sampled ten times over a 90-day chase period. We also measured the incorporation of recently assimilated 13C into soil microbial biomass (13C PLFA) and functional groups over the first 7 days post-label application. Overall, IWG-1 assimilated almost 1670 mg 13C m−2 during the study period, nearly twice that of IWG-2 or wheat, but neither IWG system retained significant amounts of new C in soil. Rather, a higher proportion of assimilated new C was retained in IWG-1 in root tissues (14%) and arbuscular mycorrhizal fungi when compared to other cropping systems, while IWG-2 retained almost 50% of total assimilated C in aboveground crop tissues. We expect the shift from new C retention in belowground root-mycorrhizal networks to aboveground tissues is associated with a shift from an acquisitive to conservative growth strategy that occurs between the first and second IWG production years. The observed shift in C partitioning patterns and potential change in growth strategy limited the allocation and retention of new C in soil as IWG aged, adding valuable context to our understanding of why perennial grain crop establishment seldom leads to significant carbon gains in the first several years following establishment.

Wheat straw and microbial inoculants have an additive effect on N2O emissions by changing microbial functional groups

AbstractStraw‐decomposing microbial inoculants (MIs) have been increasingly applied to straw‐amended soils. However, the interactive effects and underlying microbial mechanisms of straw and decomposing MIs on nitrous oxide (N2O) emissions remain unclear. Here, a pot experiment with an Aquic Inceptisol was conducted to determine soil N2O emissions and the abundance and composition of microbial functional genes under six amendments: wheat straw (W), Bacillus subtilis MI (B), Streptomyces rochei MI (S), a combination of straw and B. subtilis MI (WB), a combination of straw and S. rochei MI (WS), and a control without wheat straw or MI (C). Compared with the control, the amendments of straw, decomposing MIs, and their combinations decreased soil N2O emissions by 43%, 22–30%, and 46–60%, respectively. Mechanistically, the positive relationship between ammonia‐oxidizing bacteria (AOB) and soil potential nitrification rate (PNR), along with decreased AOB abundance (−36%) following straw and decomposing MI amendments, further suggested that AOB predominated soil nitrification and was responsible for the suppressed nitrification. In addition, straw amendment increased nirK gene abundance (by 48%) and potential denitrification rate (by 11%), while the increase in nosZI gene abundance (+25%) involved in N2O consumption contributed to the decrease in N2O emissions. Overall, the additive effect of straw and decomposing MIs on soil N2O emissions was associated with two amendment‐induced changes in the abundance and composition of AOB and straw‐stimulated the abundance of the nosZI gene. Our results revealed the potential for mitigating N2O emissions following the amendments of straw and MI by influencing soil N2O‐related microbial groups.

Innovative approaches for Microcystin removal: Bacterioplankton biodegradation and multi-soil-layering system performance assessment

Microcystins (MCs) pose a significant threat to human health and the environment due to their persistence and toxicity as potent cyanobacterial toxins. Effective biodegradation strategies are required for their removal and detoxification. In this study, bacterioplankton were isolated from eutrophic reservoir water used for crop irrigation and tested for their ability to degrade MCs. These bacteria are hydrologically transported from the contaminated reservoir to downstream farms where they are able to grow under the favorable conditions provided by a multi-soil-layering (MSL) system, a low-cost and locally applicable ecotechnology for the removal and detoxification of MCs. These bacteria enhance the ability of the MSL to remove MCs by forming biofilms within the MSL system. The bacterial strains were then sequenced and their partial 16S rRNA was compared to the reference strains in the NCBI database. The effectiveness of the MSL system in the removal of MCs from water was evaluated. The MSL utilizes a layered soil matrix that promotes microbial growth and physicochemical interactions that enable the removal of various contaminants. The mechanisms of MC removal in the MSL were evaluated by studying the physicochemical properties of the system substrate before and after treatment using X-ray fluorescence, zeta potential, and scanning electron microscopy (SEM) analyses. The microbial functional groups, including ammonifying and denitrifying bacteria, were also investigated in the MSL soil matrices before and after treatment. The results showed that seven bacterial strains exhibited high MC degradation capabilities, with MC degradation performance exceeding 97%. These isolated bacterial strains had a nucleotide identity score of 100% and an E value of 0.0 compared to reference strains. The MSL showed a 99% removal rate for MC-LR and MC-YR, as well as significant reductions in other pollutants, including COD (60%), BOD5 (60%), chlorophyll-a (96%), pheophytin (70%), organic nitrogen (80%), and nitrites (90%). After treatment, there was a statistically significant increase in the total bacterial count, as well as ammonifying and denitrifying bacteria, in the MSL soil matrices compared to their state before treatment. SEM analyses revealed the formation of dense biofilm microbiota, indicating additional biological processes besides adsorption for MC reduction. Overall, the MSL provides a low-cost alternative for the removal of MCs and cyanobacteria with minimal resource requirements and maintenance. It offers a promising solution for mitigating toxic cyanobacterial blooms, ensuring safe agricultural water reuse.