Soil Microbial Community Activity Research Articles

Comprehensive evaluation of metal(loid)s pollution risk and microbial activity characteristics in non-ferrous metal smelting contaminated site

Large amounts of metal(loid)s in abandoned non-ferrous metal smelting site are released to the surrounding environment, causing serious harm to the environment. A weighted comprehensive pollution risk score (CRS), combining two typical metal(loid)s pollution and risk index evaluation methods (speciation and total content indices), and two microbial activity evaluation methods (microcalorimetry and enzyme activities), is proposed to evaluate the pollution degree and environmental risk of metal(loid)s. In the surface soil (Site SS) of contaminated site, the CRS identified seven metal(loid)s (CRSAs (20) > CRSCd (19) > CRSSb (18) > CRSZn (13) = CRSCu (13) > CRSNi (10) > CRSPb (8)) with higher risks, and six (CRSCr (7) > CRSMn (4) = CRSV (4) > CRSAl (3) = CRSMg (3) > CRSTi (2)) with lower risks. Different areas were sorted by the potential ecological risk index (RI) and CRS index from large to small: the deep soil (Site SD) > Site SS > the surrounding wasteland (Site Y), indicating that smelting site was heavily polluted by metal(loid)s. In Site SS, microbial activities were low confirming the inhibition effect of metal(loid)s on soil microbial community activities. Microbial activity characteristics were correlated to metal(loid)s concentration and mobility, indicating that microbial activity represents a potential indicator of pollution. Particularly, FDA activity and TMA are sensitive indicators to estimate soil metal(loid)s pollution level. Our study provides a comprehensive assessment of the metal(loid)s pollution risk, including microbial activity, in non-ferrous metal smelting sites, useful information for the management and remediation of metal(loid)s polluted sites.

Effects of slag and biochar amendments on microorganisms and fractions of soil organic carbon during flooding in a paddy field after two years in southeastern China

Incorporating amendments of industrial waste such as biochar and steel slag in cropland has been used to enhance the storage of soil organic carbon (SOC) while sustaining crop production. Short-term laboratory and field studies have identified important influences of biochar on active SOC fractions associated with soil microbial activity in paddy soils, but the long-term effects remain poorly understood. To address these knowledge gaps, we examined the effects of slag, biochar, and slag+biochar treatments on total SOC concentration, active SOC fractions and soil microbial communities in a paddy field two years after incorporation. Across both two seasons, the addition of slag, biochar, slag+biochar increased soil salinity by 26–80%, 1.3–37% and 42–79%, and also increased soil pH by 0.8–5.7%, 2.1–2.4% and 4.0–6.3%, respectively, relative to the control. SOC concentration was higher in the slag, biochar, and slag+biochar treatments across both rice seasons by 4.3–5%, 0.5–17% and 4.3–7%, respectively. Soil C-pool activity and C-pool management indices in the late paddy season were significantly lower in the slag+biochar treatment than the control by 26.3 and 21.3%, respectively, indicating that the amendments contributed to the stability of SOC. The C concentrations of the biochar and slag amendments affected bacterial abundance more than fungal abundance and affected C cycling. Our study suggests that combined slag and biochar amendments may increase bacterial abundance that may maintain SOC storage and reduce the abundances of potential SOC decomposers in key functional genera, indicating strong coupling relationships with changes of soil properties such as salinity, pH, and SOC concentration. These outcomes due to the amendments (e.g. slag+biochar) may increase microbial C-use efficiency and support the stability of active SOC fractions, with opportunities for long-term C sequestration.

Roots alter soil microbial diversity and interkingdom interactions in diversified agricultural landscapes

The complex interactions between plant roots and soil microorganisms are, broadly, well described. Yet the patterns of microbe–microbe interaction and their association with the root functional traits are less known especially in plant communities at the edges of agricultural landscapes. To address this gap, we measured the active soil microbial communities with and without the presence of plant roots, using in situ root exclusions, in four plant communities at the edges of agricultural fields: undisturbed natural deciduous forests (FOREST1), coniferous forests (FOREST2), rehabilitated agroforests (AGROFOREST) and perennial herbaceous grass buffers (GRASS). Amplicon‐based analysis of 16S rRNA and ITS transcripts was used to evaluate soil bacterial, archaeal and fungal communities, and their interactions, with ‘roots' and with ‘no roots'. Plants roots were measured for a suite of functional traits and explored in association with microbial community composition. Significant differences in bacterial and archaeal but not fungal diversity were observed between soil plots with ‘roots' and with ‘no roots'. Network analysis illustrated intra and inter kingdoms co‐occurrence patterns respond to the presence of plant roots, with GRASS exhibiting distinct patterns in comparison to tree‐dominated soils. A shift in microbial hub from bacterial to fungal was observed with the exclusion of roots; Planctomycetes (OM190)_10 was replaced by Archaeorhizomyces in AGROFOREST site. Microbial taxa strongly correlate with root traits especially specific root length, root diameter and root tissue density indicating root traits are predictors of microbial community composition. This study validates the vital role of root traits in predicting plant–microbe interactions and highlights the key role of fungi in microbial interkingdom interactions when roots are absent. These findings have significant ecosystem level implications, with the rising interest in associated biodiversity in and at the edges of agricultural landscapes, this work suggests that plant community selection for specific root traits may drive microbial community structure and ecosystem services.

Changes in soil microbial community activity and composition following substrate amendment within the MicroResp™ system

Changes in soil microbial community activity and composition following substrate amendment within the MicroResp™ system

Fertilization and Soil Microbial Community: A Review

The present paper reviews the most recent advances regarding the effects of chemical and organic fertilizers on soil microbial communities. Based on the results from the articles considered, some details are presented on how the use of various types of fertilizers affects the composition and activity of soil microbial communities. Soil microbes have different responses to fertilization based on differences in the total carbon (C), nitrogen (N) and phosphorus (P) contents in the soil, along with soil moisture and the presence of plant species. These articles show that the use of chemical fertilizers changes the abundance of microbial populations and stimulates their growth thanks to the nutrient supply added. Overall, however, the data revealed that chemical fertilizers have no significant influence on the richness and diversity of the bacteria and fungi. Instead, the abundance of individual bacterial or fungal species was sensitive to fertilization and was mainly attributed to the changes in the soil chemical properties induced by chemical or organic fertilization. Among the negative effects of chemical fertilization, the decrease in enzymatic activity has been highlighted by several papers, especially in soils that have received the largest amounts of fertilizers together with losses in organic matter.

Depth dependence of climatic controls on soil microbial community activity and composition

Subsoil microbiomes play important roles in soil carbon and nutrient cycling, yet our understanding of the controls on subsoil microbial communities is limited. Here, we investigated the direct (mean annual temperature and precipitation) and indirect (soil chemistry) effects of climate on microbiome composition and extracellular enzyme activity throughout the soil profile across two elevation-bioclimatic gradients in central California, USA. We found that microbiome composition changes and activity decreases with depth. Across these sites, the direct influence of climate on microbiome composition and activity was relatively lower at depth. Furthermore, we found that certain microbial taxa change in relative abundance over large temperature and precipitation gradients only in specific soil horizons, highlighting the depth dependence of the climatic controls on microbiome composition. Our finding that the direct impacts of climate are muted at depth suggests that deep soil microbiomes may lag in their acclimation to new temperatures with a changing climate.

Microbial respiration and functional diversity of soil microbial community under treeline shifts in the Northwestern Caucasus

In mountain areas, one of the noticeable results of modern climate change is rapid shift of treelines to subalpine and alpine meadows. Such vegetation shifts is associated with a change in quality of the plant residues entering the soils, which in turn can affect the mineralization activity (basal respiration) and functional diversity of the soil microbial community. Therefore, the study was aimed at assessing the soil microbial (basal respiration and functional diversity) and chemical (C, N, C/N, pH) properties (0-10 cm) along the reserved and grazed forest-meadow transects of the Northwestern Caucasus (Karachay-Cherkess Republic), as well as evaluating an effect of vegetation type and land use on variation of these soil properties. It was found that the C and N contents (for both land usees), pH and basal respiration (reserved slope) significantly increase from forest to meadow soils. In contrary, the microbial functional diversity decreased from forest to meadow soils, which might be due to less diverse organic compounds entering the soil only with grass residues than their combination with forest litter. Two-way ANOVA showed that soil microbial functional diversity, pH, C and N along the studied forest-meadow transects was mostly associated with vegetation type (1439 % of the explained variation), and C/N and basal respiration - with land use (3336 % of the explained variation). Thus, a land use change will have a more significant effect on the mineralization activity of soil microbial community than a treeline shifts.

Forest plantations reduce soil functioning in terrestrial ecosystems from South Africa

The role of forest plantations in regulating soil ecosystem functions remains poorly understood in terrestrial ecosystems from Africa. Here, we evaluated the importance of forest plantations in regulating soil microbial functional profiles, community-level physiological profiles (CLPPs) and activities of soil microbial communities compared with native forests in two contrasting seasons. We found that forest plantations consistently reduced the rates of multiple soil functions associated with soil nutrient and carbon (C) cycling and shifted the activity and functional profile of microbial communities in two contrasting seasons and two independent regions from South Africa. Our results suggest land use changes from natural forests to plantations to maintain a continuously growing human population will have important negative consequences for soil functions in forest ecosystems from Africa with implications for ecosystem functioning under changing environments.

Differences in Precipitation Regime Shape Microbial Community Composition and Functional Potential in Namib Desert Soils.

Precipitation is one of the major constraints influencing the diversity, structure, and activity of soil microbial communities in desert ecosystems. However, the effect of changes in precipitation on soil microbial communities in arid soil microbiomes remains unresolved. In this study, using 16S rRNA gene high-throughput sequencing and shotgun metagenome sequencing, we explored changes in taxonomic composition and functional potential across two zones in the Namib Desert with contrasting precipitation regime. We found that precipitation regime had no effect on taxonomic and functional alpha-diversity, but that microbial community composition and functional potential (beta-diversity) changed with increased precipitation. For instance, Acidobacteriota and 'resistance to antibiotics and toxic compounds' related genes were relatively more abundant in the high-rainfall zone. These changes were largely due to a small set of microbial taxa, some of which were present in low abundance (i.e. members of the rare biosphere). Overall, these results indicate that key climatic factors (i.e. precipitation) shape the taxonomic and functional attributes of the arid soil microbiome. This research provides insight into how changes in precipitation patterns associated with global climate change may impact microbial community structure and function in desert soils.

Divergent effects of snow exclusion on microbial variables across aggregate size classes

Projected changes in winter climate can have large implications for the functioning of terrestrial ecosystems. In particular, increased soil frost associated with reduced insulating snow cover can affect the structure and activity of soil microbial communities in cold ecosystems, but little known about the variability of these effects among the fractions of soil aggregates. We used a snow-exclusion experiment to examine the influence of increased soil frost on microbial biomass and activity in aggregate fractions in a Tibetan alpine spruce forest. We measured the concentrations of phospholipid fatty acids (PLFAs) and the activities of extracellular enzymes involved in carbon and nutrient cycling in soil aggregate fractions (<0.25 mm, 0.25–2 mm and >2 mm) during early thawing years of 2016 and 2017. We found that snow exclusion reduced the concentrations of PLFAs (total, bacterial and fungal) and the activities of enzymes (β-glucosidase, β-N-acetyl-glucosaminidase and acid phosphatase) in three aggregate fractions due to severe abiotic environments, but did not affect the microbial community or enzymatic stoichiometry. Although they varied across the aggregate fractions, soil microbial variables responded to snow exclusion significantly only in the small macroaggregates (0.25–2 mm), which indicated that aggregate size may have a stronger effect than did snow exclusion on microbial variables. Notably, A significant decrease of PLFAs and enzymatic activities in the small macroaggregates under snow exclusion revealed that soil microbes in this fraction were more sensitive to changes in snow cover than in the other aggregate fractions. These findings highlight the ecological importance of microbial processes in aggregates in Tibetan forests experiencing large decreases in snowfall.

Impact of diesel and biodiesel contamination on soil microbial community activity and structure

Soil contamination as a result of oil spills is a serious issue due to the global demand for diesel fuel. As an alternative to diesel, biodiesel has been introduced based on its high degradability rates and potential for reducing of greenhouse gases emissions. This study assessed the impacts diesel and biodiesel contamination on soil microbial community activity and structure. Our results suggest higher microbial activity in biodiesel contaminated soils and analysis of PLFA profiles confirmed shifts in microbial community structure in response to contamination. High-throughput 16S rRNA amplicon sequencing also revealed a lower bacterial richness and diversity in contaminated soils when compared to control samples, supporting evidence of the detrimental effects of hydrocarbons on soil microbiota. Control samples comprised mostly of Actinobacteria, whereas Proteobacteria were predominantly observed in diesel and biodiesel contaminated soils. At genus level, diesel and biodiesel amendments highly selected for Rhodococcus and Pseudomonas spp., respectively. Moreover, predicted functional profiles based on hydrocarbon-degrading enzymes revealed significant differences between contaminated soils mostly due to the chemical composition of diesel and biodiesel fuel. Here, we also identified that Burkholderiaceae, Novosphingobium, Anaeromyxobacter, Pseudomonas and Rhodococcus were the main bacterial taxa contributing to these enzymes. Together, this study supports the evidence of diesel/biodiesel adverse effects in soil microbial community structure and highlights microbial taxa that could be further investigated for their biodegradation potential.

Soil microbial structure and activity in a semiarid rangeland of Patagonia, Argentina: Plant species and defoliation effects

Natural grasslands are an important renewable resource for livestock production. Grazing in these areas alters the plant community composition, litter quality, and soil microbial structure and activity. Three cool-season species were studied in a semiarid rangeland area of Argentina: Poa ligularis and Nassella tenuis (desirable/preferred for livestock) and Amelichloa ambigua (undesirable/non preferred). The objective was to analyze the effect of moderate defoliation and plant species on the structure and activity of soil microbial communities associated with their roots. In winter 2012, soil samples (0–10 cm) were taken underneath marked plant canopies of the three species (n = 8). Immediately thereafter, half of the plants (n = 4) were defoliated (5 cm stubble height) and the other half remained undefoliated (controls). The defoliation treatment was conducted again in the spring. Soil samples were taken 30 days after each defoliation event. The study was repeated in 2013, using a different plant set. Bacterial community structure and soil microbial activity were analyzed using PCR-DGGE analysis and basal soil respiration, respectively. Moderate and early defoliations allowed compensatory growth in the defoliated plants. Variations in the soil genetic profiles of A. ambigua suggest a higher dependence on its rhizospheric bacterial communities. Defoliation treatments did not substantially affect basal soil respiration but showed strong links between desirable species and soil microbial activity. Sustainable management practices that promote the persistence of these species are important for the development of microbial communities that respond quickly to stress conditions, favoring decomposition processes that maintain soil fertility in semiarid grasslands.

Corn-Soybean Intercropping Improved the Nutritional Quality of Forage Cultivated on Podzols in Boreal Climate.

Intercropping systems could be a potential source of nutrient-rich forage production in cool climates on podzolic soils common in boreal ecosystems. In this study, we evaluated the effects of corn–soybean intercropping (IC) on the nutritional quality of forage. Two silage corn varieties were cultivated as monocropping (MC) or were intercropped with three forage soybean varieties using a randomized complete block design. IC significantly increased the crude protein (22%) and decreased the acid detergent (14%) and neutral detergent (6%) fibers. Forage net energy, total digestible nutrients, ash, dry matter intake, digestible dry matter and relative feed value were also significantly increased (p ≤ 0.05) in the IC treatments compared to corn MC. The macro and micro nutrients were higher in IC than corn MC. Intercropping increased the omega 3 fatty acid (FA) contents (67%) compared to corn MC. IC also increased the active microbial community in the plant root zone, which may contribute to the improvement in forage nutritional quality because the active soil microbial community composition showed significant correlations with soluble sugars, soluble proteins and potassium contents of the forage. These results demonstrate that corn–soybean IC could be a suitable cropping system to increase the nutritional quality of forage cultivated on podzols in boreal climates. The resultant forage has the potential to be a source of high-value animal feed for livestock production in cool climate regions of the world.

Invasive plant Reynoutria japonica produces large amounts of phenolic compounds and reduces the biomass but not activity of soil microbial communities

Reynoutria japonica is one of the most invasive plant species. Its success in new habitats may be associated with the release of secondary metabolites. The aim of this study was to compare phenolic concentrations in plant biomass and soils between plots with R. japonica and resident plants (control), and determine the effects of these compounds on soil microbial communities. Samples of plant shoots and rhizomes/roots, and soil were collected from 25 paired plots in fallow and riparian habitats in Poland. We measured concentrations of total phenolics, condensed tannins, catechin, chlorogenic acid, emodin, epicatechin, hyperoside, physcion, piceatannol, polydatin, procyanidin B3, quercetin, resveratrol, and resveratroloside. Soil microbial parameters were represented by acid and alkaline phosphomonoesterases, β-glucosidase, phenoloxidase, and peroxidase activity, culturable bacteria activity and functional diversity measured with Biolog Ecoplates, and microbial biomass and community structure measured with phospholipid fatty acid (PLFA) analysis. We found that concentrations of total phenolics and condensed tannins were very high in R. japonica leaves and rhizomes/roots, and concentrations of most phenolic compounds were very high in R. japonica rhizomes/roots when compared to resident plant species. Concentrations of most phenolics in mineral soil did not differ between R. japonica and control plots; the only exceptions were catechin and resveratrol which were higher and lower, respectively, under the invader. Total microbial and bacterial (G+, G–) biomass was decreased by approx. 30% and fungal biomass by approx. 25% in invaded soils in comparison to control. Among soil functional microbial parameters, only peroxidase activity and functional diversity differed between R. japonica and resident plant plots; peroxidase activity was higher, while functional diversity was lower in soil under R. japonica. The negative effects of R. japonica on microbial biomass may be related to catechin or its polymers (proanthocyanidins) or to other phenolics contained in high concentrations in R. japonica rhizomes.

Application of Erythromycin and/or Raoultella sp. Strain MC3 Alters the Metabolic Activity of Soil Microbial Communities as Revealed by the Community Level Physiological Profiling Approach.

Erythromycin (EM), a macrolide antibiotic, by influencing the biodiversity of microorganisms, might change the catabolic activity of the entire soil microbial community. Hence, the goal of this study was to determine the metabolic biodiversity in soil treated with EM (1 and 10 mg/kg soil) using the community-level physiological profiling (CLPP) method during a 90-day experiment. In addition, the effect of soil inoculation with antibiotic-resistant Raoultella sp. strain MC3 on CLPP was evaluated. The resistance and resilience concept as well as multifactorial analysis of data was exploited to interpret the outcomes obtained. EM negatively affected the metabolic microbial activity, as indicated by the values of the CLPP indices, i.e., microbial activity expressed as the average well-color development (AWCD), substrate richness (R), the Shannon–Wiener (H) and evenness (E) indices and the AWCD values for the six groups of carbon substrate present in EcoPlates until 15 days. The introduction of strain MC3 into soil increased the degradative activity of soil microorganisms in comparison with non-inoculated control. In contrast, at the consecutive sampling days, an increase in the values of the CLPP parameters was observed, especially for EM-10 + MC3-treated soil. Considering the average values of the resistance index for all of the measurement days, the resistance of the CLPP indices and the AWCD values for carbon substrate groups were categorized as follows: E > H > R > AWCD and polymers > amino acids > carbohydrates > miscellaneous > amines > carboxylic acids. The obtained results suggest a low level of resistance of soil microorganisms to EM and/or strain MC3 at the beginning of the exposure time, but the microbial community exhibited the ability to recover its initial decrease in catabolic activity over the experimental period. Despite the short-term effects, the balance of the soil ecosystem may be disturbed.

DNA-Stable Isotope Probing Shotgun Metagenomics Reveals the Resilience of Active Microbial Communities to Biochar Amendment in Oxisol Soil.

The functions and interactions of individual microbial populations and their genes in agricultural soils amended with biochar remain elusive but are crucial for a deeper understanding of nutrient cycling and carbon (C) sequestration. In this study, we coupled DNA stable isotope probing (SIP) with shotgun metagenomics in order to target the active community in microcosms which contained soil collected from biochar-amended and control plots under napiergrass cultivation. Our analyses revealed that the active community was composed of high-abundant and low-abundant populations, including Actinobacteria, Proteobacteria, Gemmatimonadetes, and Acidobacteria. Although biochar did not significantly shift the active taxonomic and functional communities, we found that the narG (nitrate reductase) gene was significantly more abundant in the control metagenomes. Interestingly, putative denitrifier genomes generally encoded one gene or a partial denitrification pathway, suggesting denitrification is typically carried out by an assembly of different populations within this Oxisol soil. Altogether, these findings indicate that the impact of biochar on the active soil microbial community are transient in nature. As such, the addition of biochar to soils appears to be a promising strategy for the long-term C sequestration in agricultural soils, does not impart lasting effects on the microbial functional community, and thus mitigates un-intended microbial community shifts that may lead to fertilizer loss through increased N cycling.

Soil microbial communities respond to an environmental gradient of grazing intensity in south Patagonia Argentina

Soil microorganisms communities regulate key functions in terrestrial ecosystems and contributes to the formation of stable organic matter and hence climate change mitigation. The structure, diversity and activity of soil microbial communities are influenced by the quantity and quality of organic compounds entering soils through the contribution of their root exudates and plant litter, which the microorganisms use as a substrate for biosynthesis and energy source. However, grazing effect on the soil microorganisms showed variable results dependent on the ecosystem under study. One of the main challenges of this millennium is the sustainability of agricultural production, especially in fragile soils such as those present in Patagonia. Therefore, our objective was to evaluate the responses of microbial biomass carbon (MBC), soil basal respiration (SBR), the derived coefficients and the abundance of fungi and bacteria under contrasting long-term grazing intensities in an environmental gradient. The study was established in three ecological areas Mata Negra Thicket (MNT), Dry Magellanic Steppe (DMS) and Humid Magellanic Steppe (HMS) with two grazing intensities. Soil samples were taken over two years in different seasons (autumn, winter, spring and summer). Results showed that biotic and abiotic factors (temperature and precipitation), plant communities and soil characteristics modulated the microbial structure and function in ecological area. On the other hand, high grazing intensity decreased the MBC and microbial coefficient (qM). There was a seasonal and interannual dynamic in the MBC and the bacteria and fungal communities, attributed mainly to temperature and precipitation. The results indicated that the effect of grazing intensity in soil microbial communities depends largely on intrinsic characteristics of each ecological area defined by the environmental gradient.

Responses of active soil microorganisms facing to a soil biostimulant input compared to plant legacy effects

Agriculture is changing to rely on agroecological practices that take into account biodiversity, and the ecological processes occurring in soils. The use of agricultural biostimulants has emerged as a valid alternative to chemicals to indirectly sustain plant growth and productivity. Certain BS have been shown to select and stimulate plant beneficial soil microorganisms. However, there is a lack of knowledge on the effects and way of action of the biostimulants operating on soil functioning as well as on the extent and dynamic of these effects. In this study we aimed to decipher the way of action of a seaweed and amino-acids based biostimulant intended to be applied on soil crop residues to increase their microbial mineralization and the further release of nutrients. By setting-up a two-phase experiment (soil plant-growing and soil incubation), our objectives were to (1) determine the effects of the soil biostimulant over time on the active soil bacteria and fungi and the consequences on the organic carbon mineralization in bare soils, and (2) assess the biostimulant effects on soil microorganisms relatively to plant legacy effects in planted soils. We demonstrated that the soil biostimulant had a delayed effect on the active soil microorganisms and activated both plant growth promoting bacteria and saprophytes microorganisms at the medium-term of 49 days. However, the changes in the abundances of active microbial decomposers were not associated to a higher mineralization rate of organic carbon derived from soil and/or litter. The present study assessed the biostimulant beneficial effect on active soil microbial communities as similar as or even higher than the legacy effects of either A. thaliana or T. aestivum plants. We specifically showed that the biostimulant increased the active fungal richness to a higher extent than observed in soils that previously grew the two plants tested.

Increased litter input significantly changed the total and active microbial communities in degraded grassland soils

Increasing organic matter input and phosphorus fertilization are employed extensively to restore degraded grasslands. Nevertheless, little is known about their effects on microbes, especially on active microbial populations. Therefore, this study is aimed at examining the short-term influences of litter and phosphorus addition on microbes in degraded grassland soils. A microcosm experiment was established using soils sampled from a heavily degraded Tibetan alpine meadow. The experiment used a two-way factorial design with grass litter and phosphorus addition as the main factors. Microbial abundance and rDNA transcriptional activity were assessed through quantitative PCR. Total and active microbial community profiles were measured using DNA- and RNA-based MiSeq sequencing, respectively. As shown in this study, litter addition significantly increased microbial rDNA transcriptional activity and fungal abundance, but it decreased microbial α-diversity. However, prokaryote abundance was unaffected by the litter addition. Total and active soil microbial community profiles and interaction patterns were also significantly altered by litter addition. The relative abundance of copiotrophic and oligotrophic microbial lineages significantly increased and decreased, respectively, in the soils with litter addition. Functional predictions suggested that litter addition might significantly increase the abundance of pathogens, as well as microbes related to nitrogen fixation, denitrification, and chitinolysis, while decreasing nitrifier abundance. In contrast, no significant effects of the phosphorus addition on soil microbes were observed. These findings highlight the significant effects of increasing litter input on total and active soil microbial communities and suggest that microbial responses should be considered when restoring degraded grasslands by increasing organic matter input.

Dormancy dynamics and dispersal contribute to soil microbiome resilience.

In disturbance ecology, stability is composed of resistance to change and resilience towards recovery after the disturbance subsides. Two key microbial mechanisms that can support microbiome stability include dormancy and dispersal. Specifically, microbial populations that are sensitive to disturbance can be re-seeded by local dormant pools of viable and reactivated cells, or by immigrants dispersed from regional metacommunities. However, it is difficult to quantify the contributions of these mechanisms to stability without, first, distinguishing the active from inactive membership, and, second, distinguishing the populations recovered by local resuscitation from those recovered by dispersed immigrants. Here, we investigate the contributions of dormancy dynamics (activation and inactivation), and dispersal to soil microbial community resistance and resilience. We designed a replicated, 45-week time-series experiment to quantify the responses of the active soil microbial community to a thermal press disturbance, including unwarmed control mesocosms, disturbed mesocosms without dispersal, and disturbed mesocosms with dispersal after the release of the stressor. Communities changed in structure within one week of warming. Though the disturbed mesocosms did not fully recover within 29 weeks, resuscitation of thermotolerant taxa was key for community transition during the press, and both resuscitation of opportunistic taxa and immigration contributed to community resilience. Also, mesocosms with dispersal were more resilient than mesocosms without. This work advances the mechanistic understanding of how microbiomes respond to disturbances in their environment.This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.