Soil Microbial Groups Research Articles

Potential of high-throughput eDNA sequencing of soil fungi and bacteria for monitoring ecological restoration in ultramafic substrates: The case study of the New Caledonian biodiversity hotspot

Due to their central role in ecosystems functioning and their ability to rapidly respond to environmental changes, soil microorganisms could potentially be used for monitoring ecosystems recovery in the context of degraded land restoration. However, these belowground organisms have been, to date, largely neglected. Here, we investigated fungal and bacterial community diversity, composition, and structure from ultramafic soils in New Caledonia, an archipelago in the southwest Pacific recognized as a priority for conservation and restoration. The emerging approach of high-throughput amplicon sequencing of environmental DNA (eDNA) – metabarcoding of eDNA – was used to compare soil microbial communities from four different native vegetation types, representing different stages of a chronosequence and defined as reference ecosystems, to five distinct post-mining sites revegetated several years ago. Our results clearly revealed changes in soil microbial phyla and functional groups along the reference chronosequence and variable responses at the different revegetated sites, with two of the five sites showing a good trajectory of recovery. We thus propose three ratios as metrics for monitoring the restoration trajectory of soil microorganisms: the Ascomycota:Basidiomycota and Saprotrophic:Ectomycorrhizal ratios for fungi, and the Cyanobacteria:Chloroflexi ratios for bacteria. Our study, combined with recent works undertaken in other geographical areas, underpins the great promise that could represent soil microbial eDNA metabarcoding for monitoring restoration progress and success. With the emergence of these new cost-effective and scalable sequencing technologies, soil microbes could, in the near future, be included in guidelines for restoration operations in complement to more conventional approaches.

FLEXIBLE SOIL MICROBIAL CARBON METABOLISM ACROSS AN ASIAN ELEVATION GRADIENT

ABSTRACTThe function and change of global soil carbon (C) reserves in natural ecosystems are key regulators of future carbon-climate coupling. Microbes play a critical role in soil carbon cycling and yet there is poor understanding of their roles and C metabolism flexibility in many ecosystems. We wanted to determine whether vegetation type and climate zone influence soil microbial community composition (fungi and bacteria) and carbon resource preference. We used a biomarker (phospholipid fatty acids, PLFAs), natural abundance 13C and 14C probing approach to measure soil microbial composition and C resource use, along a 1900–4167-m elevation gradient on Mount Gongga (7556 m asl), China. Mount Gongga has a vertical mean annual temperature gradient of 1.2–10.1°C and a diversity of typical vegetation zones in the Tibetan Plateau. Soils were sampled at 10 locations along the gradient capturing distinct vegetation types and climate zones from lowland subtropical-forest to alpine-meadow. PLFA results showed that microbial communities were composed of 2.1–51.7% bacteria and 2.0–23.2% fungi across the elevation gradient. Microbial biomass was higher and the ratio of soil fungi to bacteria (F/B) was lower in forest soils compared to meadow soils. δ13C varied between −33‰ to −17‰ with C3 plant carbon sources dominant across the gradient. Soil organic carbon (SOC) turnover did not vary among three soils we measured from three forest types (i.e., evergreen broadleaved subtropical, mixed temperate, coniferous alpine) and dissolved organic carbon (DOC) turnover decreased with soil elevation. Forest soil microbial PLFA 14C and δ13C measurements showed that forest type and climate were related to different microbial C use. The 14C values of microbial PLFAs i15, a15, 16:1, br17 decreased with elevation while those of C16:0, cyC17, and cyC19 did not show much difference among three forest ecosystems. Bacteria and bacillus represented by C16:1 and brC17 showed considerable microbial C metabolism flexibility and tended to use ancient carbon at higher altitudes. Anaerobes represented by cyC17 and cyC19 showed stronger C metabolism selectivity. Our findings reveal specific C source differences between and within soil microbial groups along elevation gradients.

Variations in soil microbial communities in the sedge-dominated peatlands along an altitude gradient on the northern slope of Changbai Mountain, China

The mechanisms that shape soil microbes in peatlands along the altitude gradient remain unresolved due to limited data and inconsistent findings along different vertical vegetation belts from investigations. In this study, we present results of soil phospholipid fatty acids (PLFAs) profiles from an altitude gradient survey (300–1500 m) in Changbai Mountain aimed at determining the elevational patterns of soil microbial communities and their driving forces in the sedge-dominated peatlands. The results showed that the total microbial lipid biomass in the sedge-dominated peatlands increased with altitude. However, there were no obvious trends with altitude in ratios of the fungi to bacteria (F/B), the Gram positive bacteria to Gram negative bacteria (G+/G-), and the bacteria to actinomycetes (B/ACT). Redundancy analysis indicated that the dissolved organic carbon (DOC) explained most variation in soil microbial groups, while mean annual temperature (MAT) explained most variation in microbial community structure. Variation partitioning analysis revealed that climatic factors had greater influences on soil microbial community structure than soil physical and chemical properties, and 53% of the total variance was explained by MAT, mean annual precipitation (MAP) and their combined effects. This finding challenges the prevailing view that local soil properties, but not climate, control soil microbial community structure along the altitude gradient, and enhances our understanding of the role of soil microbes as carbon pumps in sedge-dominated peatlands in the process of global warming.

MICROBIOTA OF URBAN SOILS OF GREEN PLANTATIONS OF KYIV WITH THE ADDITION OF SILICON-CONTAINING COMPOUNDS

Problem. Intensive human pressure on urban ecosystems in big cities, such as Kyiv, leads to cenotic and trophic relations disbalance, agronomically useful microbiota and microfauna inhibition, plant resistance to any stressors decrease and disruption of normal soil formation. Therefore, it is important to find new effective, economically viable and environmentally safe methods to overcome soil sickness in city plantations. Aim. To study the structural and functional peculiarities of organization of soil microbial groups in anthropogenically disturbed zones of Kyiv green plantations in order to overcome soil fatigue with the use of natural substances - silicon-containing mineral analcime. Methods. Investigations were carried out on the basis of the National Botanical Garden M.M. Gryshko NAS of Ukraine, Department of Allelopathy. Six research regions in the most сontaminated and anthropogenically disturbed green areas of the Kyiv Obolonsky district were selected as objects. Twice a year, samples of root soil were taken at 0-20 cm depth before application (May) and 3.5 months after application of silicon-containing mixture (analcime) (September). The selection of soil samples, preparation and saving for the study of aerobic microbiota were carried out in accordance with ISO 10381-6-2001. The quantity of microorganisms of main ecological and trophic groups, direction of microbiological processes, identification of soil micromycetes were determined by conventional microbiological methods. Results. The results of this work showed that 3.5 months after the addition of the silicon-containing mixture, there were significant changes in the structure of the soil microbiocenosis. The increase in the number of microorganisms involved in the transformation of nitrogen compounds and the reduction of phytotoxic forms of soil fungi were detected, which indicates favorable conditions for the synthesis of humic compounds. The biggest changes were observed on the side of the highway with active emissions from automobiles and in the park, where higher content of iron ions was determined in the water for irrigation. Conclusions. The conducted research made it possible to estimate the structural and functional organization of microbial groups of the soils in a separate Kyiv district under different anthropogenic influence before and after the addition of silicon-containing mixture.

Restoration Efficacy of Picea likiangensis var. rubescens Rehder & E. H. Wilson Plantations on the Soil Microbial Community Structure and Function in a Subalpine Area.

The knowledge concerning the relationship between vegetation restoration and soil microorganisms is limited, especially at high altitudes. In order to evaluate the restoration efficacy of the reforestation on the soil microbial community, we have examined vegetation composition, edaphic properties and structure and function of different soil microbial groups in two different aged (25- and 40-year-old) Picea likiangensis var. rubescens Rehder & E. H. Wilson (P. rubescens) plantations and the primeval coniferous forest (PCF) dominated by Abies squamata Masters by plot-level inventories and sampling in western Sichuan Province, China. Our results suggested that only the fungal samples in 25-year-old P. rubescens plantation could be distinguished from those in the PCF in both structure and function. The structure and function of the fungal community recovered relatively slowly compared with bacterial and archaeal communities. In addition to the soil chemical properties and tree species composition, the shrub composition was also a key factor influencing the soil microbial community. The P. rubescens plantations were conducive to restoring the soil microbial community in both structure and function. However, there were uncertainties in the variations of the bacterial and archaeal communities with increasing the P. rubescens plantation age.

Effect of dark septate endophytes on plant performance of Artemisia ordosica and associated soil microbial functional group abundance under salt stress

Fungal endophytes can improve plant tolerance to abiotic stress, however, the role of these plant–fungal interactions in desert species ecology and their management implications remain unclear. This study aimed to assess the effects of dark septate endophytes (DSE) on the performance of Artemisia ordosica and associated soil factors and microbial functional group abundance under salt stress. We investigated the effects of three DSE (Alternaria chlamydosporigena [AC], Paraphoma chrysanthemicola [PC] and Bipolaris sorokiniana [BS]) isolated from desert habitats on plant morphology, physiology and rhizosphere soil microhabitat of A. ordosica seedlings under different NaCl concentrations (0, 1, 2, 3 g NaCl/kg soil) in a growth chamber. The three DSE strains could colonize the roots of A. ordosica, and the symbiotic response with host plants depended on DSE species and NaCl concentration. The greatest benefits associated with DSE occurred under 1 g NaCl/kg soil. Specifically, AC promoted the accumulation of total biomass and enhanced superoxide dismutase (SOD) activity; PC promoted the accumulation of root biomass and increased indoleacetic acid (IAA) contents; and BS enhanced SOD activity and glutathione (GSH) and IAA contents. DSE reduced the root Na+ content. Interestingly, BS promoted gram-positive (G +) under 1 g NaCl/kg soil and the abundance of arbuscular mycorrhizal (AM) fungi under 3 g NaCl/kg soil. PC positively affected fungi, AM fungi, gram-negative (G −) bacteria and actinomycetes under 2 g NaCl/kg soil, and increased AM fungi and G – bacteria under 3 g NaCl/kg soil, while AC increased the abundance of all examined microbes under 3 g NaCl/kg soil. Structural equation modeling (SEM) demonstrated that DSE inoculation significantly influenced the relationship between the growth of A. ordosica, soil factors and rhizospheric microbial functional groups under NaCl stress treatments. DSE enhanced the root development of host plants and altered the soil nutrient content and microbiota under different NaCl concentrations, possibly contributing to plant growth and ecological adaptability under saline environment. These results contribute to the understanding of ecological function of DSE inoculation in improving the adaptability of plants to salt stress and may be used to promote vegetation restoration in salinized desert areas.

Structure of rhizospheric microbial community and N cycling functional gene shifts with reduced N input in sugarcane-soybean intercropping in South China

A six-year (2010–2015) study of sugarcane (Saccharum officinarum) and soybean (Glycine max) intercropping combined with reduced nitrogen (N) fertilizer input was conducted to investigate sustainable agriculture via the functional soil microbial community in Southern China. The Illumina MiSeq platform and the microarray GeoChip 5.0 were applied in this study to detect the abundance, diversity and structure of bacterial and fungal communities, and to link specific functional genes with soil microbial-mediated N-cycling processes under experimental practice. The results revealed the α-diversity of bacterial communities to be relatively stable while the fungal α-diversity increased over the years. Intercropped sugarcane on rhizosphere soils under reduced and conventional N input harbor different bacterial and fungal community structures. Specifically, fungal α-diversity (e.g. Ascomycota and Basidiomycota) was found to be more sensitive to field practices while bacterial community (e.g. Bacteroidetes and Acidobacteria) changed moderately in abundance. Besides that, soil TN, AP, pH, and C/N ratio could explain the major variations in structure of soil microbial groups and in key functional genes. This study revealed the effect of N reduction and cropping patterns on functional traits based on both taxa and gene categories of microbial community, thereby improving understanding of structure-function relationships of microbial N-cycling processes in the different N input levels combined with cropping systems.

Dynamics of Fungal and Bacterial Biomass Carbon in Natural Ecosystems: Site‐Level Applications of the CLM‐Microbe Model

AbstractExplicitly representing microbial processes has been recognized as a key improvement to Earth system models for the realistic projections of soil carbon (C) and climate dynamics. The CLM‐Microbe model builds upon the CLM4.5 and explicitly represents two major soil microbial groups, fungi and bacteria. Based on the compiled time‐series data of fungal (FBC) and bacterial (BBC) biomass C from nine biomes, we parameterized and validated the CLM‐Microbe model, and further conducted sensitivity and uncertainty analysis for simulating C cycling. The model performance was evaluated with mean absolute error (MAE), root mean square error (RMSE), and coefficient of determination (R2) for relative change in FBC and BBC. The CLM‐Microbe model is able to reasonably capture the seasonal dynamics of FBC and BBC across biomes, particularly for tropical/subtropical forest, temperate broadleaf forest, and grassland, with MAE <0.49 for FBC and <0.36 for BBC and RMSE <0.52 FBC and <0.39 for BBC, while R2 values are relatively smaller in some biomes (e.g., shrub) due to small sample sizes. We found good consistencies between simulated and observed FBC (R2 = 0.70, P < 0.001) and BBC (R2 = 0.26, P < 0.05) on average across biomes, but the model is not able to fully capture the large variation in observed FBC and BBC. Sensitivity analysis shows that the most critical parameters are turnover rate and carbon‐to‐nitrogen ratio of fungi and bacteria and microbial assimilation efficiency. This study confirms that the explicit representation of soil microbial mechanisms enhances model performance in simulating C variables such as heterotrophic respiration and soil organic C density. The further application of the CLM‐Microbe model would deepen our understanding of microbial contributions to global C cycle.

Disentangling Responses of the Subsurface Microbiome to Wetland Status and Implications for Indicating Ecosystem Functions.

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China—the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.

Determination of soil heterogeneity by precision farming methods

The paper presents the results of optimization of crop management in specific areas of the field while taking into account spatial and temporal changes in soil conditions. The aim of the study was to identify soil microbial groups that affect the production cycle with different tillage and the use of different techniques for measuring the biological activity of soil and yield. Main results of Experiment 1: Dilution of 1/100000 of nitrogen fertilizers applied to post-harvest residues provided the highest reproducibility of measurements for the largest number of microorganisms of different ecological and trophic groups. Differences in the mean values of the six repeated measurements on the two repeated samples can be considered significant. Main results of Experiment 2: The addition of CAS-32 in early October did not lead to significant changes in microbiological activity in early November. However, there was a significant difference in microbiological activity for different samples depending on their location and time of the study.

Resistance of the soil microbial community to land-surface disturbances of high-intensity winter grazing and wildfire

Common land-surface disturbances in rangelands with potential to influence the resistance and resilience of the ecosystem include livestock grazing and fire. The impact of these land-use disturbances on the soil microbial community is important to understand because the soil microbial community provides and supports many ecosystem services. Conventional management of land-surface disturbances have led to a decrease in the ecosystem services provided by rangelands. To combat this decrease, alternative land-surface disturbance regimes are being investigated. Therefore, this study assessed the impact of alternative land-surface disturbances (high-intensity winter-grazing and a wildfire, compared to a widely used conventional summer-long continuous grazing on the soil microbial community measured by changes in total soil microbial biomass, soil microbial functional groups, and soil microbial diversity. The soil microbial community was evaluated at beginning of the growing season and peak growing season for two years following the treatments. Prior to the treatments, the pastures had a long history of summer-long continuous grazing. Our results indicate that the soil microbial community is resistant to land-surface disturbance treatments (high-intensity winter-grazing and wildfire) although the response of soil microbial community was influenced by the composition of aboveground vegetation. Overall, neither wildfire nor high-intensity winter-grazing caused significant impacts on the soil microbial community.

Soil extracellular enzyme activities and the abundance of nitrogen-cycling functional genes responded more to N addition than P addition in an Inner Mongolian meadow steppe

Nitrogen (N) and phosphorus (P) availability in soils commonly limit belowground biological processes in terrestrial ecosystems. Soil extracellular enzyme activities (EEAs) and microbial functional groups play critical roles in soil biological processes and nutrient cycling, yet their response to nutrient addition are poorly understood. To address this issue, we applied six fertilization treatments composed of combinations of N (0, 1.55, 13.95 g N m−2 yr−1) and P (0, 5.24 g P m−2 yr−1) for two years in a meadow steppe of Inner Mongolia. Soils were collected from each plot in July and August and analyzed for abundances of N-cycling genes and EEAs, and their relationships with treatments. The addition of N significantly increased C-acquisition enzyme activity and enzyme C:N and C:P ratios. Enzymatic stoichiometry indicated that N addition alleviated microbial demand for N, while it increased microbial C limitation. Microbial C and N limitation were significantly correlated with NH4+–N in July, yet they were correlated with soil water content (SWC) in August. The abundance of amoA significantly increased with N addition and was positively related to mineral-N accumulation. The abundance of denitrifier genes and gaseous N loss potential were accelerated by N addition in July, while a neutral effect was observed in August. Nitrate leaching potential was significantly increased by N addition, yet it declined with P addition in July. P addition also suppressed amoA abundance of ammonia oxidizing bacteria. Partial least squares path modelling indicated that N addition positively affected microbial-C limitation, soil N-loss potential and negatively affected microbial-N limitation. P addition negatively affected soil N-loss potential. Ultimately, this study highlights the importance of soil N availability in regulating microbial metabolism and soil N-loss potential, and enhances our understanding of the mechanisms responsible for variation in microbial nutrient cycling in meadow steppe soils.

Heavy metal pollution increases CH4 and decreases CO2 emissions due to soil microbial changes in a mangrove wetland: Microcosm experiment and field examination

Mangrove plays an important role in modulating global warming through substantial blue carbon storage relative to their greenhouse gas emission potential. The presence of heavy metals in mangrove wetlands can influence soil microbial communities with implications for decomposition of soil organic matter and emission of greenhouse gases. In this study, field monitoring and a microcosm experiment were conducted to examine the impacts of heavy metal pollution on soil microbial communities and greenhouse gas fluxes. The results show that heavy metal pollution decreased the richness and diversity of the overall soil microbial functional groups (heterotrophs and lithotrophs); however, it did not inhibit the activities of the methanogenic communities, possibly due to their stronger tolerance to heavy metal toxicity compared to the broader soil microbial communities. Consequently, the presence of heavy metals in the mangrove soils significantly increased the emission of CH4 while the emission of CO2 as a proxy of soil microbial respiration was decreased. The soil organic carbon content could also buffer the effect of heavy metal pollution and influence CO2 emissions due to reduced toxicity to microbes. The findings have implications for understanding the complication of greenhouse gas emissions by heavy metal pollution in mangrove wetlands.

Effects of Plants on Metacommunities and Correlation Networks of Soil Microbial Groups in an Ecologically Restored Wetland.

Plants may influence different aspects of the belowground microorganisms, including abundance, distribution, and interaction, in wetlands. Microbial communities were scrutinized in a 4-year-old restored wetland ecosystem with 5 distinct sites: a bare-soil site (10 local patches) and sites dominated by Miscanthus, Phragmites, Typha, and Zizania (20 patches per site). Ordination analysis revealed that plant-induced attributes (e.g., organic matter and total carbon and nitrogen) could explain the total environmental variance. Community comparisons showed that all groups (Bacteria, Fungi, Protista, and Metazoa) differed in community structure among the 5 sites (P < 0.05). Comparisons between the community and environmental ordination plots revealed that community structural variation among the sites correlated with the environmental change across all groups (R2 ≥ 0.61). This indicates that all groups were primarily influenced by plant detritus. In addition, correlation networks markedly varied in topology and composition among the sites across all groups. There was a strong coupling between the metacommunity and correlation network for both Bacteria and Fungi (R2 ≥ 0.58), indicating that the plants determined the spatial covariation patterns of microbial populations. Multi-group networks and group synchrony results revealed that Bacteria, Fungi, and Protista were synchronized with each other (R2 ≥ 0.52) as the key founders of the microbial systems, while Metazoa participated in the system only under Miscanthus. Our findings concluded that the plants shaped the communities by controlling the abundance and interaction of their populations.

Allocation and turnover of rhizodeposited carbon in different soil microbial groups

Recent advances in soil organic carbon (SOC) formation indicate that labile plant C is disproportionately important for stable SOC pool because it is utilized more efficiently by soil microbes. Rhizodeposited C, accounting for 5–20% of photosynthates, are highly bioavailable and readily metabolized substrates for soil microbes. However, it remains poorly understood how different microbial functional groups contribute to transforming rhizodeposited C to SOC. Here, we synthesized 23 studies performing 13CO2 pulse labelling of plants in conjunction with stable isotope probing of microbial phospholipid fatty acids, and explored the fate of rhizodeposited C in different soil microbial functional groups. Among microbial groups, fungi (25.3%) and gram-negative bacteria (GN; 23.5%) took up most of the rhizodeposition-derived C, while the relative abundance of fungi (13.7%) was less than a half of GN (32.7%). These results suggest that fungi have a higher capability of acquiring rhizodeposition-derived C, which may be due to their hyphal growth form allowing them to obtain rhizodeposited C more effectively. The mean turnover rates of rhizodeposited C in microbial groups ranged from 0.04 to 0.13 day−1. We did not detect significant differences in the turnover rates of rhizodeposited C among microbial groups. Based on the distribution and turnover rate of rhizodeposited C in different microbial groups, we further revealed that GN (31.2%) and fungi (25.8%) produced the most microbial residues via rhizodeposition-derived C. Our results provided quantitative information about the roles of different microbial functional groups in competing for and processing rhizodeposition-derived C, which could help refine parameter estimation in modeling microbial transformation of plant C into SOC under global changes.

The arbuscular mycorrhizal fungus Rhizophagus intraradices and other microbial groups affect plant species in a copper-contaminated post-mining soil

Background and aimArbuscular mycorrhizal fungi (AMF) have an important role in plant-microbe interactions. But, there are few studies in which the combined effect of AMF with a stress factor, such as the presence of a metal, on plant species were assessed. This study investigated the effect of arbuscular mycorrhizal (AM) fungus Rhizophagus intraradices and other soil microbial groups in the presence of copper on three plant species in a microcosm experiment. MethodsTwo grass species Poa compressa and Festuca rubra and one herb species Centaurea jacea were selected as model plants in a pot-design test in which soils were artificially contaminated with copper. Treatments were bacteria (control), saprophytic fungi, protists, and a combined treatment of saprophytic fungi and protists, all in the presence or absence of the AM fungal species. After sixty days, plants were harvested and the biomass of grass and herb species and microbial respiration were measured. ResultsThe results showed almost equal above- and belowground plant biomass and microbial respiration in the treatments in the presence or absence of R. intraradices. The herb species C. jecea responded significantly to the soil inoculation with AM fungus, while grass species showed inconsistent patterns. Significant effect of AMF and copper and their interactions was observed on plant biomass when comparing contaminated vs. non-contaminated soils. ConclusionStrong effect of AMF on the biomass of herb species and slight changes in plant growth with the presence of this fungal species in copper-spiked test soils indicates the importance of mycorrhizal fungi compared to other soil microorganisms in our experimental microcosms.

Non-monotonic and distinct temperature responses of respiration of soil microbial functional groups

The fate of soil carbon (C) under climatic warming predominantly depends on temperature sensitivity of soil microbial functioning, but it is poorly understood. Using temporal measurements of soil respiration in an incubation experiment with cross-inoculation of microbial communities to contrasting soils, we constrained a microbial-explicit C model to infer temperature responses of two general microbial functional groups: fast-growing r-vs slow-growing K-strategists. We found that the two groups exhibit distinct, non-monotonic temperature responses, and fast-growing r-strategists are more sensitive to temperature changes than slow-growing K-strategists. Both historical environments, under which the microbial communities were originated, and current environment, under which the microbial communities are colonized/adapted, significantly shape the temperature responses of the two groups. Our findings highlight the importance of combined effects of historical and current environment on microbial decomposition for regulating soil C dynamics under warming. We suggest that distinct, non-monotonic temperature responses of microbial functional groups may cause pronounced feedbacks between soil C dynamics and warming depending on climate-soil-microbe interactions.

Bacterial, fungal, and archaeal community assembly patterns and their determining factors across three subalpine stands at different stages of natural restoration after clear-cutting

The knowledge regarding how different soil microbial groups change in subalpine forest areas after clear-cutting is limited. To bridge this gap, we studied the change patterns of the different soil microbial community assemblies and their determining factors in subalpine areas. Field measurements and sampling were conducted in three stands at different stages of natural restoration (BF, broadleaf forest; MF, mixed coniferous and broadleaf forest; and PCF, primeval coniferous forest) after clear-cutting in western Sichuan Province, China. Three soil microbial group (bacteria, fungi, and archaea) community assemblies, edaphic properties, soil nematodes, tree diameter at breast height, plant richness, and understory vegetation biomass were examined and statistically analyzed. The α-diversity of the three microbial groups in the BF and MF stands was significantly higher than that in the PCF stand. The difference between the stands was greater than the difference within the stands for all three microbial groups. The changes in the three microbial groups were all significantly associated with shifts in soil carbon, soil total nitrogen, soil available nitrogen, and tree species composition. The bacterial and archaeal communities were also closely related to the bacterivore number. Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Basidiomycota, Ascomycota, and Thaumarchaeota were the main phyla that responded to environmental variation. The three soil microbial groups all showed regular trends across the three different stands. The changes in the soil microbial community assembly were mainly attributed to the differences in soil nutrients, tree species composition, and feeding traits of soil nematodes.

Soil microbiome-induced changes in the priming effects of 13C-labelled substrates from rice residues

Knowledge gap exists to understand the soil CO2 emission and microbial group response to substrates of whole plant residues and derived biochar. We used 13C-labelled substrates (rice straw, roots and biochar) to track influences of their decomposition on soil priming effect (PE) and phospholipid fatty acid (PLFA) composition during one-year incubation. Organic substrates at 1% (w/w) level increased soil pH, available nitrogen (AN) and available phosphorus (AP), especially during the first 45 days of incubation. After incubation, 44% of the added straw was mineralized to 13CO2, followed by roots (~35%) and biochar (~5%). Straw and roots amendment caused positive PE during 4–360 day of the incubation, where a lowest value of 41.9 mg C kg−1 was observed. Biochar amendment caused negative PE during 56–150 day of the incubation, where a largest value of −99.0 mg C kg−1 was observed. Analysis of 13C-labelled PLFA enabled the differentiation of microbial groups during substrates utilization. Gram positive bacteria (G+) and general bacteria groups were dominated in co-metabolizing both the native soil organic carbon (SOC) and substrates after straw and roots amendment. Gram negative bacteria (G−), especially identified by PLFA biomarkers cy17:0 and cy19:0, preferentially utilizes the 13C-labelled biochar but not promoting soil priming effect. Soil pH, SOC, AN and AP all explained changes of total and 13C-labelled PLFA contents (>75%, p < .05). Evidences showed that biochar is best in sequestering soil C pool, followed by straw and roots, and soil microbial groups in utilization of organic substances mediated SOC mineralization.

Sex-related responses in rhizosphere processes of dioecious Populus cathayana exposed to drought and low phosphorus stress

Extensive research has shown that dioecious plants exhibit sexual dimorphism under extreme environments. However, sex-specific differences in responses to drought, phosphorus (P) shortage or their combination are less known. In our study, impacts of drought, P shortage and their combination on the performance of Populus cathayana males and females were investigated. Drought and P deficiency caused a greater negative impact on female growth than on male growth. P application ameliorated the more negative effect of drought on the shoot dry matter accumulation and P concentration in male leaves, while smaller effects were observed in females. The concentration of citrate in the rhizosphere of males was higher under drought combined with P application than under adequate water availability, and the increase was greater in males than in females. Males also showed a higher abundance of main soil microbial groups, including bacteria, actinomycetes, arbuscular mycorrhizal fungi (AMF), and Gram+ and Gram- bacteria in the rhizosphere, resulting in a more resistant microhabitat. In contrast, the abundance of bacteria and AMF was less in the rhizosphere of females exposed to stress conditions, while saprophytic fungi increased significantly. P enhanced drought resistance more in stress-resistant males but less in females under relatively severe drought stress. Increased drought resistance by P in males might be associated with greater plasticity in rhizosphere processes when compared with females.