Bacterial Phospholipid Fatty Acid Research Articles

Seasonal freeze‒thaw processes impact microbial communities of soil aggregates associated with soil pores on the Qinghai–Tibet Plateau

BackgroundSeasonal freeze‒thaw (FT) processes alter soil formation and cause changes in soil microbial communities, which regulate the decomposition of organic matter in alpine ecosystems. Soil aggregates are basic structural units and play a critical role in microbial habitation. However, the impact of seasonal FT processes on the distribution of microbial communities associated with soil pores in different aggregate fractions under climate change has been overlooked. In this study, we sampled soil aggregates from two typical alpine ecosystems (alpine meadow and alpine shrubland) during the seasonal FT processes (UFP: unstable freezing period, SFP: stable frozen period, UTP: unstable thawing period and STP: stable thawed period). The phospholipid fatty acid (PLFA) method was used to determine the biomass of living microbes in different aggregate fractions.ResultsThe microbial biomass of 0.25–2 mm and 0.053–0.25 mm aggregates did not change significantly during the seasonal FT process while the microbial biomass of > 2 mm aggregates presented a significant difference between the STP and UTP. Bacterial communities dominated the microbes in aggregates, accounting for over 80% of the total PLFAs. The microbial communities of soil aggregates in the surface layer were more sensitive to the seasonal FT process than those in other soil layers. In the thawing period, Gram positive bacteria (GP) was more dominant. In the freezing period, the ratio of Gram-positive to Gram-negative bacterial PLFAs (GP/GN) was low because the enrichment of plant litter facilitated the formation of organic matter. In the freezing process, pores of 30–80 μm (mesopores) favored the habitation of fungal and actinobacterial communities while total PLFAs and bacterial PLFAs were negatively correlated with mesopores in the thawing process.ConclusionsThe freezing process caused a greater variability in microbial biomass of different aggregate fractions. The thawing process increased the differences in microbial biomass among soil horizons. Mesopores of aggregates supported the habitation of actinobacterial and fungal communities while they were not conducive to bacterial growth. These findings provide a further comprehension of biodiversity and accurate estimation of global carbon cycle.

Long-term fertilization affects microbial necromass accumulation by regulating nutrient and enzymatic stoichiometry in a calcareous Fluvisol

Microbial necromass accumulation through rhizodeposition plays a critical role in increasing the stable soil organic carbon pool, which is greatly affected by fertilization. However, the legacy effects of long-term fertilization on microbial necromass accumulation remain unclear. Here, we selected a calcareous Fluvisol treated with no fertilizer (Ctrl), P and K fertilizers (PK), N and K fertilizers (NK), and N, P and K fertilizers (NPK) for 34 years and conducted a 12-week microcosm experiment with simulated daily rhizodeposition to disentangle the legacy effects of long-term fertilization on microbial necromass accumulation. We measured soil C, N and P contents and C-, N- and P-acquiring extracellular enzyme activities and analyzed phospholipid fatty acids (PLFAs) and amino sugars to indicate microbial biomass and necromass, respectively. We found that compared with the Ctrl and NK treatments, the PK and NPK treatments significantly decreased the C:N and C:P ratios and the net accumulation of microbial necromass but significantly increased the ratios of C- to N- and C- to P-acquiring enzyme activities and the fungal PLFAs abundance in soils. The net accumulation of microbial necromass was positively correlated with soil nutrient stoichiometry (mainly the C:N and C:P ratios) but negatively correlated with soil enzymatic stoichiometry (mainly the ratios of C- to N- and C- to P-acquiring enzyme activities) and the fungal to bacterial PLFA ratio. Taken together, these results suggest that long-term fertilization has legacy effects on microbial necromass accumulation and that fertilization-induced changes in nutrient and enzymatic stoichiometry regulate microbial necromass accumulation through rhizodeposition in the calcareous Fluvisol.

Comparison of Soil Microbial Community between Managed and Natural Vegetation Restoration along a Climatic Gradient in Karst Regions

Managed and natural vegetation restorations are two vital measures of land restoration; however, their effects on soil microbial communities at a large scale are not clearly understood. Hence, changes in the microbial community composition after 15 years of vegetation restoration along a climatic gradient in the subtropical karst region of Southwest China were assessed based on phospholipid fatty acids (PLFAs) profiles. Managed (plantation forest) and natural (naturally recovered to shrubbery) vegetation restoration types were compared, with cropland and mature forest serving as controls. Soil microbial community abundance was significantly higher under the two vegetation restoration types than in the cropland; however, it was lower than in the mature forest. The abundance, composition, and structure of soil microbial communities did not differ significantly between plantation forest and shrubbery. Soil organic carbon or total nitrogen was the primary factor positively affecting soil microbial abundance, whereas the mean annual temperature (MAT) was recognized as the primary factor contributing to the variation in the soil microbial community structure. Moreover, temperature had opposite effects on different indicators of microbial community structure. That is, it positively and negatively affected the ratios of gram-positive to gram-negative bacterial PLFAs (GP:GN) and fungal to bacterial PLFAs (F:B), respectively. Our results show that both vegetation restoration types have the ability to improve soil productivity in karst areas. Furthermore, shifts in soil microbial community structure (GP:GN and F:B ratios) induced by warming are likely to lead to a higher proportion of labile carbon, which is sensitive to soil tillage. Hence, more attention should be paid to ecological restoration in warmer karst areas to alleviate the severe loss of soil carbon in croplands.

Effects of Organic Materials and Their Incorporation Depths on Humus Substances Structure and Soil Microbial Communities’ Characteristics in a Chinese Mollisol

Organic material incorporation are important agricultural practices, which can influence soil organic carbon (SOC) sequestration and stabilization. However, the response of interaction between SOC structure and soil microbial to organic material incorporation management are still poorly understood. In 2021, we conducted a three years field experiment in Guangrong country, northeastern China. Five treatments were established: conventional tillage (CK), conventional tillage with straw incorporation (T1); subsoil tillage with straw incorporation (T2); subsoil tillage with straw and organic manure incorporation (T3) and subsoiling tillage with organic manure incorporation (T4). Fulvic–like and protein–like components were found in fulvic acid (FA) in a 0–15 cm soil layer, while fulvic–like components in humic acid (HA) were found in 0–15 cm and 15–35 cm soil layers. In the 15–35 cm soil layer, the bacterial, fungal and total phospholipid fatty acid (PLFA) contents were significantly higher by 159.62%, 687.00%, and 139.02% in T3 than CK, respectively. The fungal to bacterial PLFA ratios (F/B) were significantly higher by 97.46% and the Gram–positive bacteria to Gram–negative bacteria PLFA ratios (G+/G−) were lower by 20.99% in T3 than CK in the 15–35 cm soil layer. Therefore, subsoil tillage with straw and organic manure incorporation could be recommended to improve soil quality in Mollisol.

Long‐term grazing intensity by reindeer alters the response of the soil micro‐food web to simulated climate change in subarctic tundra

Top–down control by nematodes over soil microorganisms – considered to be stronger over bacteria than over fungi – may dampen microbial responses to global changes in tundra. To test whether large grazers alter the responses of belowground trophic networks to global changes, we employed factorial warming and nitrogen fertilization treatments in adjacent sites with different reindeer grazing intensities for the past 50 years. Lightly grazed tundra is dominated by dwarf shrubs and a more fungal‐based microbial community, while in heavily grazed tundra the high reindeer densities during autumn migration have induced a shift into graminoids and a more bacterial‐based microbial community. We analysed the soil micro‐food web (i.e. the nematode density, trophic structure and species composition) as well as fungal, bacterial and total phospholipid fatty acids (PLFAs) after four growing seasons of warming and fertilization both before and during reindeer migration. We predicted that bacterivore densities are higher and fungivore densities lower under heavy than light grazing (i.e. nematode populations before migration reflect grazing effects via the base of the food web), whereas reindeer migration induces a negative impact on nematode densities under heavy grazing (disturbance by trampling is the driving factor). We further predicted that nematodes negate treatment effects on microbial biomass to a stronger extent in the bacterial‐based heavily grazed tundra than in the fungal‐based lightly grazed tundra. Fungivore densities were higher under light than under heavy grazing, but nematodes did not respond to trampling. Warming increased fungivores and the fungal PLFAs irrespective of grazing and timing but, under heavy grazing, it increased bacterivores while the bacterial PLFAs remained steady. Fertilization increased carnivores and influenced nematode species composition, diversity and maturity interactively with warming. Our data suggest that large grazers affect tundra soil nematodes via bottom–up effects through microbial community composition and biomass, which in turn may alter the strength of their top–down control over soil bacteria under climate warming.

The effect of prescribed fires on abiotic and biotic factors in the southern region of Puerto Rico

Field fires can modify soil nutrient cycling and alter soil microbial communities (SMC), although the latter is not well understood. In the southern region of Puerto Rico, field fires have become a significant problem during the dry season. To mimic the effects of a field fire, we performed prescribed fires on a hillside at the Juana Díaz Agricultural Experiment substation in October 2015 and March 2017. A complete randomized block design was established in Yauco soil (Typic calciustolls) that included the following treatments: negative control (unburned), positive control (burned plots, no remediation), mulching treatment (burned plots remediated with Leucaena spp. mulch), and surfactant treatment (burned plots remediated with a surfactant). In the first burning (2015), soil samples were collected before burning and at 30, 180, and 420 days after burning (DAB). In the second burning (2017), soil samples were collected at 30, 90, and 270 DAb. soil physicochemical properties and microbial community structure were assessed using phospholipid fatty acid (PLFA) analysis. Overall, burning increased soil exchangeable Ca2+ (except after 30 DAB in the second burning) and decreased exchangeable K+ when compared to unburned soils. compared to unburned plots, total fungal PLFA was significantly lower in burned plots with or without mulch and surfactant treatments, and total bacterial PLFA did not differ between burned and unburned plots after 30 days. Total microbial biomass was significantly (P<0.05) higher in mulch and surfactant treated burned soil compared to unburned and burned plots without treatment after 90 DAB (2017) and 420 (2015) DAB. The use of mulch and surfactant treatments in prescribed burning fields increased microbial communities 90 DAB. This study emphasizes short-term changes in microbial communities and suggests they are highly resilient to disturbances after prescribed fires.

Variations in diversity, composition, and species interactions of soil microbial community in response to increased N deposition and precipitation intensity in a temperate grassland

BackgroundGlobal climate change has resulted in precipitation regimes exhibiting an increasing trend in rainfall intensity but a reduction in frequency. In addition, nitrogen (N) deposition occurs simultaneously in arid and semi-arid regions. Microbial biomass, diversity, composition, and species interactions are key determinants of ecological functions. We examined the effects of changes in precipitation intensity and N addition on the soil bacterial and fungal communities in a semi-arid grassland in Inner Mongolia, China.MethodsThe microbial biomass (bacterial PLFAs and fungal PLFAs) was determined through phospholipid fatty acid (PLFA) analysis, and microbial diversity (Shannon index and evenness index) was determined with high-throughput sequencing (16S and ITS). Species interactions were determined using a molecular ecological network analysis. The relationships between microbial community (bacterial community and fungal community) and environmental variables were examined by Mantel tests.ResultsWe found that N addition decreased fungal PLFA under moderate, high, and extreme precipitation intensity treatments and increased fungal community complexity under the high precipitation intensity treatment. Furthermore, N addition increased bacterial diversity under moderate and high precipitation intensity treatments. N addition caused greater environmental stress to the fungal community, which was dominated by deterministic processes.ConclusionsThe effects of N deposition on soil bacterial and fungal communities were altered by precipitation intensity. The changes in soil bacterial and fungal communities were different, implying that composition and functional traits adapt differently to projected global changes at a regional scale.

Differences in soil microbial communities with successional stage depend on vegetation coverage and soil substrates in alpine desert shrublands

In semiarid ecosystems, changes in plant communities are promoted under shrub canopies during restoration, but the link between shrub community restoration dynamics and changes in soil microbe communities is still unclear. We characterized the community structure and plant interactions of soil microbes by combining different methodological approaches (including high-throughput sequencing of the 16S rRNA gene and ITS gene, analysis of phospholipid fatty acids (PLFAs) and chloroform fumigation) and the key driving factors along a successional gradient of Sophora moorcroftiana shrub community in the middle reaches of the Yarlung Zangbo River. Soil microbial biomass carbon (MBC) and nitrogen (MBN), total PLFAs, and alpha diversity increased significantly as the successional stage advanced, and MBC and MBN were positively correlated with the carbon and nitrogen contents in the soil. Mantel test showed that successional stage-induced changes in soil microbial beta diversity were mainly associated with shrub coverage and soil physicochemical properties. The relative abundances of bacterial PLFAs, particularly those of gram-negative bacteria, such as Bacteroidetes, Alphaproteobacteria and Betaproteobacteria, significantly decreased with succession; the opposite was true for Acidobacteria, Planctomycetes, Gemmatimonadetes Deltaproteobacteria and Gammaproteobacteria. However, the proportion of fungi did not significantly differ among the four successional stages; the dominant phyla were Ascomycota and Basidiomycota. We suggest that shrubs directly shape soil microbial communities or indirectly affect such communities by altering soil substrates. Our findings advance the current understanding of sand-stabilizing plant–soil interactions during natural restoration and the reversal of desertification in stressful desert ecosystems.

Changes in vineyard soil parameters after repeated application of organic-inorganic amendments based on spent mushroom substrate

The changes of physicochemical and biochemical parameters of a silty loam (S1) and sandy loam (S2) vineyard soils added with spent mushroom substrate (SMS) or SMS composted with ophite (OF) as rock dust (SMS + OF) were studied. Two doses of SMS or SMS + OF (25 and 100 Mg ha−1) were applied for two consecutive years (2020–2021) and changes of soil physicochemical parameters, and dehydrogenase activity (DHA), respiration (RES), microbial biomass (BIO), and the phospholipid fatty acids (PLFAs) profile were assayed on a temporal basis. The results showed an increase in soil organic carbon (OC) content, total and mineralised N, P, and K, especially when the highest SMS dose was applied to soils. Repeated application caused OC content over time up to 2.3 times higher than initial content in the silty loam soil. This increase was not observed in sandy soil, possibly due to a higher bioavailability of OC, as indicated by the evolution of extractable humic acid/fulvic acid pools. In both soils, all biochemical parameters increased after amendment, being favoured both by the OC and by the presence of OF. Significant positive correlations were found between DHA, RES and BIO, and OC content especially in the first part and then levelled off after the second dose application. Total bacterial or fungal PLFAs patterns reflected the variation of BIO by SMS application. The higher growth of fungi vs. bacterial community in amended soils was recorded after the first SMS application, although the opposite effect occurred after the second application, with similar results in both soils. The findings indicate that the application of SMS or SMS + OF in vineyard soils could be an appropriate agronomic management practice for maintaining soil sustainability, although doses and application times of these amendments should first be evaluated depending on soil texture.

Vascular plant and cryptogam abundance as well as soil chemical properties shape microbial communities in the successional gradient of glacier foreland soils

In the glacier forelands, microbes play a fundamental role in soil development and shaping the vegetation structure. Such ecosystems represent various stages of soil development and are, therefore, an excellent place to study the interrelationship between soil, plants, and microorganisms. The aim of the study was to assess the effects of vegetation and soil physicochemical properties developing after glacier retreat on soil microbial communities. Specifically, abundance, species richness and the composition of arbuscular mycorrhizal fungi (AMF), as well as microbial biomass and community structure in soils were compared between plots established in 800-meter transects of three glacier forelands in northern Sweden. The cover of vascular plants and cryptogams, soil C content, AMF spore density and species richness, AMF biomass indicators, total microbial biomass, and bacterial phospholipid fatty acids (PLFA) were significantly and positively related to the distance from the glacier terminus. On the other hand, macronutrient concentrations and pH decreased along with increasing distance. No significant impact of the distance from the glacier terminus on the ratio fungal/bacterial PLFA was observed. Moreover, we found a significant effect of both glacier and the distance from the glacier terminus on the microbial community structure. AMF species richness and spore density in the glacier forelands were generally low, which is probably due to a limited supply of inoculum in primary successional ecosystems. Most microbial biochemical markers and AMF parameters were positively associated with the number of arbuscular mycorrhizal plant species and vascular plant and lichen cover as well as C content in soil, whereas negatively with soil macronutrients and pH. This could be related to an increase in plant cover and a decrease in soil nutrient levels as plant succession progresses. Our results showed that vegetation, soil C content, and microbial communities are interlinked and exhibit concordant patterns along successional gradients.

Relationships between soil properties, vegetation and soil biota in extremely sulfurized mine soils

The study aimed to assess the influence of high sulfur (S) contamination and the properties of the reclaimed (e.g. neutralization/liming of contamination) soil on the regeneration of soil vegetation and fauna in the example of the former sulfur mine. An attempt was also made to assess minimal conditions for the development of soil microorganisms and mesofauna depending on the type of cover (reforestation/herbaceous vegetation/bare soil). Thirty sample plots were situated on three mainland categories–– i) plant cover vegetated mainly Pinus sylvestris L. (Scots pine stand category), ii) Betula pendula Roth (silver birch stand category), and iii) degraded area with bare soil (Bare_Central – in the central place of the plot and Bare_Edge usually 5.5 m from Bare_Central, Veg – 1 m from Bare_Edge). Basic soil chemicals (as pH, electrical conductivity EC, total sulfur S, total nitrogen TN, total organic carbon TOC), biological parameters (e.g. fungal and bacterial phospholipid fatty acids PLFAs, GRAM+, GRAM−, actinobacteria, total microbial biomass TM), and mesofauna density were analyzed to assess the level of contamination and colonization of the area by plants and soil fauna. The PLFA and the presence of soil microorganisms, always increased from a central point (Bare_Central) to an outer one (Bare_Edge) that was very close (about 1 m) to the vegetation (Veg). However, the highest biological parameters was found in Veg near the bare soil than in the stands with Scots pine. It was found that the highest microbiological biomass was positively correlated with the occurrence of vegetation. Mesofauna was limited by a high content of sulfur in the soil and high EC. Silver birch stands, through the larger and more favorable properties of plant litter, create conditions in which the growth of microorganisms is much greater than under Scots pine stands. On the other hand grasses area with single Scots pine was characterized by higher biological parameters than with the silver birch. In the plots with tree stands it was quite the opposite. To properly restoration this type of place, it is necessary to ensure the accuracy of the technical measures performed. The best effects of activating soil microorganisms are the introduction of trees with appropriate density. The activity of soil microorganisms allows for the growth of herbaceous vegetation, which will be a start-up source of organic matter and nourishment for soil biota. Herbaceous vegetation will create a good mixture with hard decomposed pines litterfall.

Contrasting Effect of Thinning and Understory Removal on Soil Microbial Communities in a Subtropical Moso Bamboo Plantation

Thinning and understory clearance are among the two most popular forest management practices carried out to improve stand productivity in subtropical plantations. Unfortunately, studies have not fully explored the single and combination effect of thinning and understory clearance on soil microbial properties. By conducting a field manipulation experiment in a subtropical moso bamboo (Phyllostachys edulis) plantation in Southern China, we assessed the effects of thinning, understory clearance, and their combination on soil microbial phospholipid fatty acids (PLFAs) three years after treatments were first applied. We also examined the changes in soil properties after thinning and/or understory clearance. Thinning decreased soil fungal and bacterial PLFAs, and consequently soil total microbial PLFAs due to the increased soil NH4+-N, and NO3−N concentrations. Understory clearance decreased soil pH and soil water content resulting in increased soil fungal PLFAs and the ratio of soil fungal to bacterial (F:B). In addition, thinning and understory clearance caused apparent interactive effects on soil total microbial PLFAs and bacterial PLFAs, and the negative influence of thinning on soil total microbial and bacterial PLFAs were partly compensated by understory clearance. These results suggest the contrasting and interactive effect of thinning and understory clearance should be considered to assess the changes of soil microbial community and ecological processes in subtropical moso bamboo (Phyllostachys edulis) plantations in southern China.

Meta-analysis of the impacts of phosphorus addition on soil microbes

Soil microbes play a crucial role in myriad ecological processes in terrestrial ecosystem. With increasing nitrogen (N) loading, phosphorus (P) may become more limiting for soil microbes and these processes. However, it remains unclear to what extent P addition impacts soil microbial communities and respiration at global scale, especially under different N loadings. Therefore, we used a global meta-analysis to examine the effects of phosphorus addition on soil microbes based on 2293 paired observations from 129 studies in the world. Overall, P addition increased significantly total as well as fungal, bacterial, and actinomycete (ACT) phospholipid fatty acids (PLFAs), together with Gram+ bacteria (G+) and Gram- bacteria (G-) abundance regardless of N input or not. The increments were more pronounced under higher P addition rate or places with higher mean annual temperature or mean annual precipitation. Moreover, the fungi: bacteria ratio significantly decreased along elevational gradients. Furthermore, higher P addition frequency tended to have significantly more ACT PLFAs, as well as higher G+:G-, but significantly lower fungi: bacteria ratio (F:B). However, the responses of P addition on bacterial PLFAs and F:B were larger in forest than grassland, and cropland and varied with P fertilizer forms. In addition, the responses of soil organic carbon (SOC) contents was positively correlated with those of microbial biomass carbon (MBC) and bacterial PLFAs, and all these three parameters, in addition to fungal PLFAs, correlated positively with the response of soil respiration (Rs). Our results suggest that phosphorus addition had globally positive effects on soil microbes with different N loadings, and the positive effects of soil microbial abundance tended to promote heterotrophic respiration (Rh) and Rs. These results deepen our understanding of soil microbial community structure and function dynamics under increasing P deposition. They also provide extensive evidences and bases for parameterization of soil carbon cycling models incorporating microbial responses under global climate change.

Effects of land use on soil microbial community structure and diversity in the Yellow River floodplain

Abstract Soil microorganisms and their diversity are important bioindicators of soil carbon and nutrient cycling. Land use type is a major determining factor that influences soil microbial community composition in floodplain ecosystems. However, how the structure and diversity of soil microbial communities respond to specific changes in land use, as well as the main drivers of these changes, are still unclear. This study was conducted in the Yellow River floodplain to examine the effects of land use type on soil microbial communities. Four land use types (shrubland, farmland, grassland and forest) were selected, wherein shrubland served as the baseline. We measured soil microbial structure and diversity using phospholipid fatty acids (PLFAs). Land use type significantly affected total, bacterial and fungal PLFAs, and the gram-positive/negative bacterial PLFAs. Compared with shrubland, peanut farmland had higher total and bacterial PLFAs and forest had higher fungal PLFAs. Soil pH and phosphorus were the predominate drivers of microbial PLFAs, explaining 37% and 26% of the variability, respectively. Soil total nitrogen and nitrate nitrogen were the main factors increasing microbial community diversity. Peanut farmland had the highest soil carbon content, soil carbon stock, total PLFAs and microbial diversity, suggesting that farmland has great potential as a carbon sink. Our findings indicated that peanut farmland in the Yellow River floodplain is critical for maintaining soil microbial communities and soil carbon sequestration.

Soil nutrients and nutrient ratios influence the ratios of soil microbial biomass and metabolic nutrient limitations in mountain peatlands

Soil microbes regulate the storage of carbon (C) in peatlands, which is facilitated by nutrients. To date, few researchers have examined the spatial distribution of soil microbial biomass, microbial community structure, and their metabolic nutrient limitations in mountain peatlands at different altitudes. This study aimed to improve the knowledge of how and why soil microbial biomass and their metabolic nutrient limitations varied with altitude. We investigated the phospholipid fatty acids (PLFAs) and enzymatic stoichiometry in surface (0–20 cm) and subsurface (20–50 cm) soil from peatlands with different types of vegetation in the Changbai Mountains. Overall, the soil microbial PLFAs were higher in the sedge-dominated peatlands than in the shrub/Sphagnum-dominated peatlands. The soil microbial PLFAs in the sedge-dominated peatlands were elevated at high altitudes but decreased with altitude in the shrub/Sphagnum-dominated peatlands. The soil fungal/bacterial ratios (F/B) in the surface soil increased with altitude in the sedge-dominated peatlands but not in the shrub/Sphagnum-dominated peatlands. The Gram-positive/Gram-negative bacteria ratios (G+/G−) in the surface soil decreased with altitude in the sedge-dominated and shrub/Sphagnum-dominated peatlands. The soil F/B ratios were higher, but the G+/G− ratios were lower in the shrub/Sphagnum-dominated peatlands than in the sedge-dominated peatlands. The soil pH and nutrient ratios explained most of the differences in soil bacterial and fungal PLFAs, respectively. However, the total nutrients of soil were the primary regulators of soil F/B and G+/G−. The soil microbial activities suffered from C- and phosphorus (P)- limitations in the mountain peatlands. The limitations were worse in the shrub/Sphagnum-dominated peatlands than in the sedge-dominated peatlands. The P limitations were greater at high altitude than at low altitude in both types of peatlands. The C and P limitations on soil microbial metabolism were primarily controlled by soil physical properties and nutrient ratios, respectively.

No evidence that conifer biochar impacts soil functioning by serving as microbial refugia in boreal soils

AbstractIt is well established that application of biochar to soils can promote soil fertility, which ultimately may enhance plant growth. While many mechanisms have been proposed to explain this, one specific mechanism, the “microbial refugia hypothesis,” suggests that biochar may provide physical protection for soil microbe from soil microfauna that otherwise exert top‐down control on microbial biomass and activity. We tested the microbial refugia hypothesis by incubating two boreal soils with and without biochar derived from a wood mixture of boreal tree species (Picea abies and Pinus sylvestris), and with and without soil nematodes. We measured phospholipid fatty acids (PLFA) as a relative measure of microbial biomass, and several variables indicative of microbial activity, including extractable nutrient concentrations (NH4+, NO3−, and PO4−), heterotrophic N2‐fixation, and soil respiration. Contrary to our expectations, we found that biochar by itself did not stimulate microbial biomass or activity. Furthermore, we found that nematode addition to soil stimulated rather than depressed the biomass of several bacterial PLFA groups. Finally, interactive effects between the nematode treatment and biochar never worked in a way that supported the microbial refugia hypothesis. Our findings suggest that a typical boreal biochar applied to boreal soils may not have the same stimulatory effect on microbial biomass and activity that has been shown in some other ecosystems, and that enhanced plant growth in response to biochar addition sometimes observed in boreal environments is likely due to other mechanisms, such as direct nutrient supply from biochar or amelioration of soil pH.

Co-application of spent mushroom substrate and PGPR alleviates tomato continuous cropping obstacle by regulating soil microbial properties

Continuous cropping of tomato (Solanum lycopersicum L.) in China has contributed to the decline of crop quality and yield. The aims of this study were to evaluate the integrated effect of plant growth-promoting rhizobacteria (PGPR) Bacillus sp. HW27 and spent mushroom substrate (SMS) on tomato plant growth and microbiological properties of rhizosphere soil. Bacillus sp. HW27 showed indole-3-acetic acid (IAA) and siderophore production, phosphate solubilization, and root colonization capacity in vitro assays. A pot experiment was carried out with four treatments: (1) CK: unamended control, (2) PGPR, (3) SMS, and (4) PGPR + SMS: combined application of strain HW27 and SMS. The enzyme activities, the abundances of beneficial microbes Bacillus and Pseudomonas and soil-borne pathogenic Fusarium oxysporum (using real-time PCR), the microbial functional diversity (using Biolog Ecoplates), and microbial community (using phospholipid fatty acid (PLFA) analysis) in rhizosphere soil were studied 20, 40 and 60 days after transplantation. At the end of the 60-day pot experiment, the results showed that the PGPR + SMS treatment performed best in improving tomato plants growth, which significantly (p < 0.05) increased the shoot length, root length, shoot dry weight and root dry weight by 34.4, 78.4, 93.5 and 82.4%, respectively, compared to the CK treatment. The enzyme activities of β-1,4-glucosidase, β-d-cellobiosidase, β-1,4-N-acetyl-glucosaminidase, protease and acid phosphatase were higher in the SMS and/or PGPR application treatments than in the CK treatment in the order PGPR < SMS < SMS + PGPR. The SMS + PGPR treatment showed the highest abundances of Bacillus and Pseudomonas, and the lowest abundance of Fusarium oxysporum. Furthermore, the application of SMS and/or PGPR stimulated microbial functional diversity and microbial growth (total PLFAs, bacterial, and Gram (+) and Gram (−) bacterial PLFAs), in which SMS + PGPR treatment had the greatest effect. Consequently, this study showed that co-application of PGPR and SMS expressed synergistic effect to increase tomato plant growth, enzyme activities and microbial biomass in continuous cropping greenhouse soil.

How do climate warming affect soil aggregate stability and aggregate-associated phosphorus storage under natural restoration?

The responses of soil aggregation and aggregate-associated phosphorus (P) fractions under natural restoration to climate warming remain unclear. Here, we conducted an eight-year mesocosm experiment wherein farmland soil from a colder site was transplanted to a warmer site to simulate climate warming and established continuous soybean cultivation and natural restoration treatments at each site. We investigated soil aggregate stability and the associated P fractions and soil properties under two land-use systems in a warming climate. Our results revealed that natural restoration significantly increased macroaggregates and macroaggregate-associated NaHCO3-Pi, NaOH-Po, and TP, but warming impeded the increases of these P fractions without changing soil aggregation. Although TP within microaggregates and the silt and clay fractions remained consistent across treatments, warming resulted in higher NaHCO3-Pi concentrations in both fractions and lower NaHCO3-Po and NaOH-Po within microaggregates in restored land. Bacterial community and alkaline phosphatase activity may be responsible for organic P mineralization within microaggregates. The enrichment of NaHCO3-Pi in smaller-sized aggregates and non-aggregate particles with warming likely increased the risk for P loss. Fungal and bacterial phospholipid fatty acid explained the most variation in the P fractions within macroaggregates and microaggregates, respectively, suggesting that biological processes are involved in determining P distribution. Our study indicates that the distribution of P fractions in differently sized aggregates during natural restoration can be significantly influenced by warming and highlights that incorporating the responses of soil microorganisms and enzymes will improve our understanding of the P cycling in a warming climate.

Diversity and Effect of Increasing Temperature on the Activity of Methanotrophs in Sediments of Fildes Peninsula Freshwater Lakes, King George Island, Antarctica.

Global warming has a strong impact on polar regions. Particularly, the Antarctic Peninsula and nearby islands have experienced a marked warming trend in the past 50 years. Therefore, higher methane (CH4) emissions from this area could be expected in the future. Since mitigation of these emissions can be carried out by microbial oxidation, understanding this biological process is crucial since to our knowledge, no related studies have been performed in this area before. In this work, the aerobic CH4 oxidation potential of five freshwater lake sediments of Fildes Peninsula (King George Island, South Shetland Islands) was determined with values from 0.07 to 10 μmol CH4 gdw–1 day–1 and revealed up to 100-fold increase in temperature gradients (5, 10, 15, and 20°C). The structure and diversity of the bacterial community in the sediments were analyzed by next-generation sequencing (Illumina MiSeq) of 16S rRNA and pmoA genes. A total of 4,836 ASVs were identified being Proteobacteria, Actinobacteriota, Acidobacteriota, and Bacteroidota the most abundant phyla. The analysis of the pmoA gene identified 200 ASVs of methanotrophs, being Methylobacter Clade 2 (Type I, family Methylococcaceae) the main responsible of the aerobic CH4 oxidation. Moreover, both approaches revealed the presence of methanotrophs of the classes Gammaproteobacteria (families Methylococcaceae and Crenotrichaceae), Alphaproteobacteria (family Methylocystaceae), Verrucomicrobia (family Methylacidiphilaceae), and the candidate phylum of anaerobic methanotrophs Methylomirabilota. In addition, bacterial phospholipid fatty acids (PLFA) biomarkers were studied as a proxy for aerobic methane-oxidizing bacteria and confirmed these results. Methanotrophic bacterial diversity was significantly correlated with pH. In conclusion, our findings suggest that aerobic methanotrophs could mitigate in situ CH4 emissions in a future scenario with higher temperatures in this climate-sensitive area. This study provides new insights into the diversity of methanotrophs, as well as the influence of temperature on the CH4 oxidation potential in sediments of freshwater lakes in polar regions of the southern hemisphere.

Long-term warming reduced microbial biomass but increased recent plant-derived C in microbes of a subarctic grassland

Long-term soil warming and nitrogen (N) availability have been shown to affect microbial biomass and community composition. Altered assimilation patterns of recent plant-derived C and changes in soil C stocks following warming as well as increased N availability are critical in mediating the direction and magnitude of these community shifts. A 13C pulse labelling experiment was done on a warming gradient in an Icelandic grassland (Sigurdsson et al., 2016), to investigate the role of recent plant-derived C and warming on the microbial community structure and size. We observed an overall increase of microbial 13C (e.g., root-exudate) uptake, while warming led to significant microbial biomass loss in all microbial groups. The increase of microbial 13C uptake with warming differed between microbial groups: an increase was only observed in the general and Gram-positive bacterial phospholipid fatty acid (PLFA) markers and in the PLFA and neutral lipid fatty acid (NLFA) markers of arbuscular mycorrhizal fungi (AMF). Nitrogen addition of 50 kg ha−1 y−1 for two years had no effect on the microbial uptake, microbial biomass or community composition, indicating that microbes were not N limited, and no plant-mediated N addition effects occurred. Additionally, we show that both warming and soil C depletion were responsible for the microbial biomass loss. Soil warming caused stronger loss in microbial groups with higher 13C uptake. In our experiment, warming caused a general reduction of microbial biomass, despite a relative increase in microbial 13C uptake, and altered microbial community composition. The warming effects on microbial biomass and community composition were partly mediated through soil C depletion with warming and changes in recent plant-derived C uptake patterns of the microbial community.