No-till soil management increases microbial biomass and alters community profiles in soil aggregates

Aggregation is important for soil functioning, providing physical protection of organic matter and microbial inhabitants. Tillage disrupts aggregates, increases wind and water erosion of soils and exposes formerly protected organic matter to decomposition and losses. Microbial biomass and community dynamics in dry-sieved aggregate-size classes from long-term no-till (NT) and conventionally tilled (CT) soils were examined using phospholipid fatty acid analysis (PLFA). Bacterial, fungal, and total biomass were up to 32% greater in NT compared to CT aggregates. Aggregate size also affected microbial biomass, which was highest in the 1–2 mm size class. Arbuscular mycorrhizal fungi (AMF) were particularly affected by tillage disturbance with increases of 40–60% among aggregate-size classes in NT vs. CT, but glomalin related soil protein concentration was not different between tillage treatments or among aggregate-size classes. Bacterial stress biomarkers were higher in CT than NT aggregates but were not significantly correlated with total C, total N or C:N ratio, indicating that the physiological status of bacteria within aggregates was not simply governed by the quantity of available resources. Ordination analysis of PLFA profiles demonstrated a shift in microbial community structure between NT and CT aggregates, correlated with AMF abundance in NT aggregates and increased bacterial stress biomarkers in CT aggregates. Our results demonstrated greater microbial biomass and altered microbial community structure in NT vs. CT aggregates. This work demonstrates that tillage management influences microbial community structure within aggregates and may provide a potential explanation for differences in process rates observed in NT vs. CT soils. Further research into the processes that govern community structure in aggregates from NT and tilled soils is needed to better understand how the interaction of microorganisms with their physical environment affects nutrient turnover and availability.     

Manipulation of the soil pore and microbial community structure in soil mesocosm incubation studies

Soil pore structure exerts a profound influence on distribution of moisture, O₂ and micro-organisms, thereby potentially controlling organic matter (OM) decomposition in soils. Although pore space is the habitat for soil micro-organisms and the actual location of soil biochemical processes, to date, very few studies looked into this relation mainly because of practical constraints. New experimental designs need to be developed which allow specific investigations of the relation between soil pore network structure, the microbial community and OM decomposition. We therefore subjected a sandy loam soil to a number of artificial manipulations namely i) compaction, ii) artificial change in particle size distribution, iii) addition of different substrates and iv) change in soil pH to manipulate soil pore structure and the decomposer community for use in lab incubation set-ups. Moisture retention data showed that compaction and artificial change in particle size distribution decreased volumes of large (9–300 μm) and small (<0.2 and 3–9 μm) pore size classes, respectively. PLFA signature analysis showed that acidification promoted fungi, while an effect of application of either sawdust or grass on the decomposer community was smaller. Acidification significantly reduced C mineralization and microbial biomass C. Surprisingly, the largest shift in microbial community (with promotion of fungi and protozoa relative to bacteria) over all treatments was observed in the treatments with artificially changed particle size distribution. We conclude that it is possible to ‘tailor’ soil pore structure and the decomposer community in soil mesocosm incubation experiments by such manipulations. However, non-targeted effects on microbial community structure, microbial biomass and gross C mineralization seem unavoidable.     

Relationships of soil respiration to microbial biomass, substrate availability and clay content

The roles of microbial biomass (MBC) and substrate supply as well as their interaction with clay content in determining soil respiration rate were studied using a range of soils with contrasting properties. Total organic C (TOC), water-soluble organic carbon, 0.5 M K₂SO₄-extractable organic C and 33.3 mM KMnO₄-oxidisable organic carbon were determined as C availability indices. For air-dried soils, these indices showed close relationship with flush of CO₂ production following rewetting of the soils. In comparison, MBC determined with the chloroform fumigation-extraction technique had relatively weaker correlation with soil respiration rate. After 7 d pre-incubation, soil respiration was still closely correlated with the C availability indices in the pre-incubated soils, but poorly correlated with MBC determined with three different techniques—chloroform fumigation extraction, substrate-induced respiration, and chloroform fumigation-incubation methods. Results of multiple regression analyses, together with the above observations, suggested that soil respiration under favourable temperature and moisture conditions was principally determined by substrate supply rather than by the pool size of MBC. The specific respiratory activity of microorganisms (CO₂-C/MBC) following rewetting of air-dried soils or after 7 d pre-incubation was positively correlated with substrate availability, but negatively correlated with microbial pool size. Clay content had no significant effect on CO₂ production rate, relative C mineralization rate (CO₂-C/TOC) and specific respiratory activity of MBC during the first week incubation of rewetted dry soils. However, significant protective effect of clay on C mineralization was shown for the pre-incubated soils. These results suggested that the protective effect of clay on soil organic matter decomposition became significant as the substrate supply and microbial demand approached to an equilibrium state. Thereafter, soil respiration would be dependent on the replenishment of the labile substrate from the bulk organic C pool.     

Changes in soil microbial community composition in response to fertilization of paddy soils in subtropical China

Repeated fertilizer applications to cultivated soils may alter the composition and activities of microbial communities in terrestrial agro-ecosystems. In this study, we investigated the effects of different long term fertilization practices (control (CK), three levels of mineral fertilizer (N₁P₁K₁, N₂P₂K₂, and N₃P₃K₃), and organic manure (OM)) on soil environmental variables and microbial communities by using phospholipid fatty acid (PLFA) biomarkers analysis in subtropical China. Study showed that OM treatment led to increases in soil organic carbon (SOC), total nitrogen (TN) and total phosphorus (TP) contents, while the mineral fertilizer treatment led to increases in dissolved organic carbon (DOC) content. Changes in soil microbial communities (eg. bacteria, actinomycetes) were more noticeable in soils subjected to organic manure applications than in the control soils or those treated with mineral fertilizer applications. Fungal PLFA biomarkers responded differently from the other PLFA groups, the numerical values of fungal PLFA biomarkers were similar for all the OM and mineral fertilizer treatments. PCA analysis showed that the relative abundance of most PLFA biomarkers increased in response to OM treatment, and that increased application rates of the mineral fertilizer changed the composition of one small fungal PLFA biomarker group (namely 18:3ω6c and 16:1ω5c). Further, from the range of soil environmental factors that we examined, SOC, TN and TP were the key determinants affecting soil microbial community. Our results suggest that organic manure should be recommended to improve soil microbial activity in subtropical agricultural ecosystems, while increasing mineral fertilizer applications alone will not increase microbial growth in paddy soils.     

Input related microbial carbon dynamic of soil organic matter in particle size fractions

This paper investigated the flow of carbon into different groups of soil microorganisms isolated from different particle size fractions. Two agricultural sites of contrasting organic matter input were compared. Both soils had been submitted to vegetation change from C3 (Rye/Wheat) to C4 (Maize) plants, 25 and 45 years ago. Soil carbon was separated into one fast-degrading particulate organic matter fraction (POM) and one slow-degrading organo-mineral fraction (OMF). The structure of the soil microbial community were investigated using phospholipid fatty acids (PLFA), and turnover of single PLFAs was calculated from the changes in their ¹³C content. Soil enzyme activities involved in the degradation of carbohydrates was determined using fluorogenic MUF (methyl-umbelliferryl phosphate) substrates.We found that fresh organic matter input drives soil organic matter dynamic. Higher annual input of fresh organic matter resulted in a higher amount of fungal biomass in the POM-fraction and shorter mean residence times. Fungal activity therefore seems essential for the decomposition and incorporation of organic matter input into the soil. As a consequence, limited litter input changed especially the fungal community favoring arbuscular mycorrhizal fungi. Altogether, supply and availability of fresh plant carbon changed the distribution of microbial biomass, the microbial community structure and enzyme activities and resulted in different priming of soil organic matter.Most interestingly we found that only at low input the OMF fraction had significantly higher calculated MRT for Gram-positive and Gram-negative bacteria suggesting high recycling of soil carbon or the use of other carbon sources. But on average all microbial groups had nearly similar carbon uptake rates in all fractions and both soils, which contrasted the turnover times of bulk carbon. Hereby the microbial carbon turnover was always faster than the soil organic carbon turnover and higher carbon input reduced the carbon storage efficiency from 51% in the low input to 20%. These findings suggest that microbial community preferentially assimilated fresh carbon sources but also used recycled existing soil carbon. However, the priming rate was drastically reduced under carbon limitation. In consequence at high carbon availability more carbon was respired to activate the existing soil carbon (priming) whereas at low carbon availability new soil carbon was formed at higher efficiencies.     

Land-use intensification and agroforestry in the Kenyan highland: Impacts on soil microbial community composition and functional capacity

This study investigates microbial communities in soil from sites under different land use in Kenya. We sampled natural forest, forest plantations, agricultural fields of agroforestry farms, agricultural fields with traditional farming and eroded soil on the slopes of Mount Elgon, Kenya. We hypothesised that microbial decomposition capacity, biomass and diversity (1) decreases with intensified cultivation; and (2) can be restored by soil and land management in agroforestry. Functional capacity of soil microbial communities was estimated by degradation of 31 substrates on Biolog EcoPlates™. Microbial community composition and biomass were characterised by phospholipid fatty acid (PLFA) and microbial C and N analyses. All 31 substrates were metabolised in all studied soil types, i.e. functional diversity did not differ. However, both the substrate utilisation rates and the microbial biomass decreased with intensification of land use, and the biomass was positively correlated with organic matter content. Multivariate analysis of PLFA and Biolog EcoPlate™ data showed clear differences between land uses, also indicated by different relative abundance of PLFA markers for certain microorganism groups. In conclusion, our results show that vegetation and land use control the substrate utilisation capacity and microbial community composition and that functional capacity of depleted soils can be restored by active soil management, e.g. forest plantation. However, although 20–30 years of agroforestry farming practises did result in improved soil microbiological and chemical conditions of agricultural soil as compared to traditional agricultural fields, the change was not statistically significant.     

Establishment of macro-aggregates and organic matter turnover by microbial communities in long-term incubated artificial soils

The study of interactions between minerals, organic matter (OM) and microorganisms is essential for the understanding of soil functions such as OM turnover. Here, we present an interdisciplinary approach using artificial soils to study the establishment of the microbial community and the formation of macro-aggregates as a function of the mineral composition by using artificial soils. The defined composition of a model system enables to directly relate the development of microbial communities and soil structure to the presence of specific constituents. Five different artificial soil compositions were produced with two types of clay minerals (illite, montmorillonite), metal oxides (ferrihydrite, boehmite) and charcoal incubated with sterile manure and a microbial community derived from a natural soil. We used the artificial soils to analyse the response of these model soil systems to additional sterile manure supply (after 562 days). The artificial soils were subjected to a prolonged incubation period of more than two years (842 days) in order to take temporally dynamic processes into account. In our model systems with varying mineralogy, we expected a changing microbial community composition and an effect on macro-aggregation after OM addition, as the input of fresh substrate will re-activate the artificial soils. The abundance and structure of 16S rRNA gene and internal transcribed spacer (ITS) fragments amplified from total community DNA were studied by quantitative real-time PCR (qPCR) and denaturing gradient gel electrophoresis (DGGE), respectively. The formation of macro-aggregates (>2 mm), the total organic carbon (OC) and nitrogen (N) contents, the OC and N contents in particle size fractions and the CO₂ respiration were determined. The second manure input resulted in higher CO₂ respiration rates, 16S rRNA gene and ITS copy numbers, indicating a stronger response of the microbial community in the matured soil-like system. The type of clay minerals was identified as the most important factor determining the composition of the bacterial communities established. The additional OM and longer incubation time led to a re-formation of macro-aggregates which was significantly higher when montmorillonite was present. Thus, the type of clay mineral was decisive for both microbial community composition as well as macro-aggregation, whereas the addition of other components had a minor effect. Even though different bacterial communities were established depending on the artificial soil composition, the amount and quality of the OM did not show significant differences supporting the concept of functional redundancy.     

Microbial community structure varies in different soil zones of a potato field

Analyses of phosholipid fatty acids (PLFA) and phospholipid etherlipids (PLEL) revealed differences in size and structure of microbial communities in the three soil zones of a potato field: ridge (RS), uncompacted interrow (IS), and tractor‐compacted interrow soil (CS). The quantity of phosholipid biomarker concentrations (= microbial biomass) showed large differences among different zones, when lipid contents were related to fresh soil volume instead of soil dry matter. Compaction of interrow soil caused an increase in bacterial and eukaryotic biomass, expressed as total PLFA concentration, as well as an increase in total archaeal biomass, expressed as total PLEL concentration and caused a decrease in the fungi‐to‐bacteria ratio. Due to the higher waterfilled pore space (an indirect measure for reduced O₂ availability) in CS, a more pronounced anaerobic microbial community was estimated than in IS, which serves as an explanation for the elevated N₂O fluxes in this soil zone. Apart from the effect of O₂ availability, microbial communities, especially populations of aerobic bacteria, ascinomycetes, fungi, algae, protozoa, and aerobic archaea responded to organic matter composition in the individual zones. Only in RS PLEL derived cyclic isoprenoids were found, which presumably indicate root‐colonizing archaea. Following principal component analyses of specific biomarker profiles, the assumed substrate effect had the strongest influence on the differences in microbial community structure between the three soil zones.     

Drivers of microbial respiration and net N mineralization at the continental scale

The dominant pools of C and N in the terrestrial biosphere are in soils, and understanding what factors control the rates at which these pools cycle is essential in understanding soil CO₂ production and N availability. Many previous studies have examined large scale patterns in decomposition of C and N in plant litter and organic soils, but few have done so in mineral soils, and fewer have looked beyond ecosystem specific, regional, or gradient-specific drivers. In this study, we examined the rates of microbial respiration and net N mineralization in 84 distinct mineral soils in static laboratory incubations. We examined patterns in C and N pool sizes, microbial biomass, and process rates by vegetation type (grassland, shrubland, coniferous forest, and deciduous/broadleaf forest). We also modeled microbial respiration and net N mineralization in relation to soil and site characteristics using structural equation modeling to identify potential process drivers across soils. While we did not explicitly investigate the influence of soil organic matter quality, microbial community composition, or clay mineralogy on microbial process rates in this study, our models allow us to put boundaries on the unique explanatory power these characteristics could potentially provide in predicting respiration and net N mineralization. Mean annual temperature and precipitation, soil C concentration, microbial biomass, and clay content predicted 78% of the variance in microbial respiration, with 61% explained by microbial biomass alone. For net N mineralization, only 33% of the variance was explained, with mean annual precipitation, soil C and N concentration, and clay content as the potential drivers. We suggest that the high R² for respiration suggests that soil organic matter quality, microbial community composition, and clay mineralogy explain at most 22% of the variance in respiration, while they could explain up to 67% of the variance in net N mineralization.     

Substrate inputs and pH as factors controlling microbial biomass, activity and community structure in an arable soil

Our aim was to determine whether the smaller biomasses generally found in low pH compared to high pH arable soils under similar management are due principally to the decreased inputs of substrate or whether some factor(s) associated with pH are also important. This was tested in a soil incubation experiment using wheat straw as substrate and soils of different pHs (8.09, 6.61, 4.65 and 4.17). Microbial biomass ninhydrin-N, and microbial community structure evaluated by phospholipid fatty acids (PLFAs), were measured at 0 (control soil only), 5, 25 and 50 days and CO₂ evolution up to 100 days. Straw addition increased biomass ninhydrin-N, CO₂ evolution and total PLFA concentrations at all soil pH values. The positive effect of straw addition on biomass ninhydrin-N was less in soils of pH 4.17 and 4.65. Similarly total PLFA concentrations were smallest at the lowest pH. This indicated that there is a direct pH effect as well as effects related to different substrate availabilities on microbial biomass and community structure. In the control soils, the fatty acids 16:1ω5, 16:1ω7c, 18:1ω7c&9t and i17:0 had significant and positive linear relationships with soil pH. In contrast, the fatty acids i15:0, a15:0, i16:0 and br17:0, 16:02OH, 18:2ω6,9, 17:0, 19:0, 17:0c9,10 and 19:0c9,10 were greatest in control soils at the lowest pHs. In soils given straw, the fatty acids 16:1ω5, 16:1ω7c, 15:0 and 18:0 had significant and positive linear relationships with pH, but the concentration of the monounsaturated 18:1ω9 PLFA decreased at the highest pHs. The PLFA profiles indicative of Gram-positive bacteria were more abundant than Gram-negative ones at the lowest pH in control soils, but in soils given straw these trends were reversed. In contrast, straw addition changed the microbial community structures least at pH 6.61. The ratio: [fungal PLFA 18:2w6,9]/[total PLFAs indicative of bacteria] indicated that fungal PLFAs were more dominant in the microbial communities of the lowest pH soil. In summary, this work shows that soil pH has marked effects on microbial biomass, community structure, and response to substrate addition.     

施肥对中国农田土壤微生物群落结构与酶活性影响的整合分析

【目的】 施肥能直接或间接改变农田生态系统的养分平衡,从而影响土壤的物理、化学和生物学特性。本研究探讨不同种植制度和土壤条件下施肥对农田土壤生物学特性的影响程度,为合理施肥和土壤肥力提升提供科学依据。 【方法】 通过收集近10年 (2008—2018年) 来发表的文献,建立了包含185组微生物量及群落结构等相关内容的数据库。采用整合分析方法(Meta-analysis),定量分析了施肥对土壤微生物量、群落结构以及酶活性的影响。 【结果】 与不施肥相比,施肥显著提高了土壤微生物磷脂脂肪酸 (PLFA) 和微生物量碳、氮含量,提高幅度分别为28.5%、30.9%和41.6%。施用 (单施或配施) 有机物料对土壤微生物总PLFA含量及微生物量碳、氮含量的提高幅度分别为47.3%、50.4%和58.7%,相当于施用化肥的2.8、2.4和3.9倍。与不施肥相比,施肥均能增加各类微生物菌群PLFA含量,对细菌、真菌及放线菌的提高幅度为23.8%～30.4%,对革兰氏阴性菌(G–)和革兰氏阳性菌 (G+) 的提高幅度为37.8%～43.2%,且施用有机物料处理对各类微生物菌群PLFA含量的提高幅度显著高于施化肥处理。施用化肥对土壤微生物总PLFA含量的提高幅度在一年两熟制区为17.9%,在水田和水旱轮作条件下为18.3%～27.6%,而在一年一熟制区及旱地条件下对土壤微生物总PLFA含量无显著影响。在不同pH的土壤中,施用有机物料对微生物总PLFA的提高幅度均显著高于施化肥处理。在pH < 6与pH > 8的土壤上施用化肥对微生物总PLFA含量无明显影响。施肥显著提高了与土壤有机质分解相关的β-葡萄糖苷酶(42.4%)和乙酰氨基葡萄糖苷酶(174.5%)的活性,对与氮循环相关的亮氨酸氨基肽酶活性无显著影响。统计分析还表明,施肥并未改变土壤微生物的真菌细菌比(F∶B)和革兰氏阳性菌革兰氏阴性菌比(G +∶G–)。 【结论】 在不同种植制度、土地利用类型和土壤pH下,施肥显著改变了土壤微生物量和与有机质分解相关的酶活性,但未改变土壤微生物的真菌细菌比(F∶B)和革兰氏阳性菌革兰氏阴性菌比(G+∶G–)。单施或配施有机物料均有利于提高农田土壤微生物总量及各类菌群的生物量,效果显著好于单施化肥。      

Microbial community abundance and structure are determinants of soil organic matter mineralisation in the presence of labile carbon

Altered rates of native soil organic matter (SOM) mineralisation in the presence of labile C substrate (‘priming’), is increasingly recognised as central to the coupling of plant and soil-biological productivity and potentially as a key process mediating the C-balance of soils. However, the mechanisms and controls of SOM-priming are not well understood. In this study we manipulated microbial biomass size and composition (chloroform fumigation) and mineral nutrient availability to investigate controls of SOM-priming. Effects of applied substrate (¹³C-glucose) on mineralisation of native SOM were quantified by isotopic partitioning of soil respiration. In addition, the respective contributions of SOM-C and substrate-derived C to microbial biomass carbon (MBC) were quantified to account for pool-substitution effects (‘apparent priming’). Phospholipid fatty acid (PLFA) profiles of the soils were determined to establish treatment effects on microbial community structure, while the ¹³C-enrichment of PLFA biomarkers was used to establish pathways of substrate-derived C-flux through the microbial communities. The results indicated that glucose additions increased SOM-mineralisation in all treatments (positive priming). The magnitude of priming was reduced in fumigated soils, concurrent with reduced substrate-derived C-flux through putative SOM-mineralising organisms (fungi and actinomycetes). Nutrient additions reduced the magnitude of positive priming in non-fumigated soils, but did not affect the distribution of substrate-derived C in microbial communities. The results support the view that microbial community composition is a determinant of SOM-mineralisation, with evidence that utilisation of labile substrate by fungal and actinomycete (but not Gram-negative) populations promotes positive SOM-priming.     

Responses of soil organic matter and microorganisms to freeze-thaw cycles

Soil organic matter (SOM) biomarker methods were utilized in this study to investigate the responses of fungi and bacteria to freeze-thaw cycles (FTCs) and to examine freeze-thaw-induced changes in SOM composition and substrate availability. Unamended, grass-amended, and lignin-amended soil samples were subject to 10 laboratory FTCs. Three SOM fractions (free lipids, bound lipids, and lignin-derived phenols) with distinct composition, stability and source were examined with chemolysis and biomarker Gas Chromatography/Mass Spectrometry methods and the soil microbial community composition was monitored by phospholipid fatty acid (PLFA) analysis. Soil microbial respiration was also measured before and during freezing and thawing, which was not closely related to microbial biomass in the soil but more strongly controlled by substrate availability and quality. Enhanced microbial mineralization (CO₂ flush), considered to be derived from the freeze-thaw-induced release of easily decomposable organic matter from microbial cell lyses, was detected but quickly diminished with successive FTCs. The biomarker distribution demonstrated that free lipids underwent a considerable size of decrease after repeated FTCs, while bound lipids and lignin compounds remained stable. This observation indicates that labile SOM may be most influenced by increased FTCs and that free lipids may contribute indirectly to the freeze-thaw-induced CO₂ flush from the soil. PLFA analysis revealed that fungal biomass was greatly reduced while bacteria were unaffected through the lab-simulated FTCs. Microbial community shifts may be caused by freezing stress and competition for freeze-thaw-induced substrate release. This novel finding may have an impact on carbon and nutrient turnover with predicted increases in FTCs in certain areas, because fungi and bacteria have different degradation patterns of SOM and the fungi-dominated soil community is considered to have a higher carbon storage capacity than a bacteria-dominated community.     

Microbial community structure and nutrient availability in oil sands reclaimed boreal soils

Alberta has one of the largest oil reserves in the world, some of which is extracted by surface mining representing a large scale disturbance to forest soils. We examined ecosystem function in reclaimed soils by measuring microbial community structure with phospholipid fatty acid (PLFA) analysis and nutrient availability with plant root simulator (PRS?) probes. Samples were taken from three slope positions, at three sites, on three dates (June and August 2005, and August 2006), and non-metric multi-dimensional scaling ordination was used to examine trends in the data. Repeated measures ANOVA was used to examine trends over time in key response variables identified by ordination. Ordination results revealed distinct differences between the spring and summer microbial community structure across sites, although large site differences were also found between fall measurements in the two consecutive years. Total microbial biomass (TMB) and the fungal to bacterial ratio (FBR) emerged as key response variables for microbial community structure, and repeated measures ANOVA indicated significant site differences for these parameters. Soil nutrient availability was predominantly affected by site, but was also greatly affected by season and by year of sampling. The key response variables for nutrient availability were NH₄⁺ and NO₃^?, which also varied significantly by site and season, with high NH₄⁺ availability in the spring on vegetated/fertilized sites and high NO₃^? availability year round on the non-vegetated site. Slope position had an inconsistent effect on the measured parameters which may indicate that these reclaimed soils are not characterized by near surface lateral flow. Seasonal fluctuations in nitrogen and boron availability, reflected in microbial community PLFA profiles, point at possible mechanistic linkages between the functioning of microbial communities and soil mineral nutrient availability.     

Soil texture affects soil microbial and structural recovery during grassland restoration

Many biotic and abiotic factors influence recovery of soil communities following prolonged disturbance. We investigated the role of soil texture in the recovery of soil microbial community structure and changes in microbial stress, as indexed by phospholipid fatty acid (PLFA) profiles, using two chronosequences of grasslands restored from 0 to 19 years on silty clay loam and loamy fine sand soils in Nebraska, USA. All restorations were formerly cultivated fields seeded to native warm-season grasses through the USDA’s Conservation Reserve Program. Increases in many PLFA concentrations occurred across the silty clay loam chronosequence including total PLFA biomass, richness, fungi, arbuscular mycorrhizal fungi, Gram-positive bacteria, Gram-negative bacteria, and actinomycetes. Ratios of saturated:monounsaturated and iso:anteiso PLFAs decreased across the silty clay loam chronosequence indicating reduction in nutrient stress of the microbial community as grassland established. Multivariate analysis of entire PLFA profiles across the silty clay loam chronosequence showed recovery of microbial community structure on the trajectory toward native prairie. Conversely, no microbial groups exhibited a directional change across the loamy fine sand chronosequence. Changes in soil structure were also only observed across the silty clay loam chronosequence. Aggregate mean weighted diameter (MWD) exhibited an exponential rise to maximum resulting from an exponential rise to maximum in the proportion of large macroaggregates (>2000 μm) and exponential decay in microaggregates (<250 μm and >53 μm) and the silt and clay fraction (<53 μm). Across both chronosequences, MWD was highly correlated with total PLFA biomass and the biomass of many microbial groups. Strong correlations between many PLFA groups and the MWD of aggregates underscore the interdependence between the recovery of soil microbial communities and soil structure that may explain more variation than time for some soils (i.e., loamy fine sand). This study demonstrates that soil microbial responses to grassland restoration are modulated by soil texture with implications for estimating the true capacity of restoration efforts to rehabilitate ecosystem functions.     

Soil microbial biomass and activity in Chinese tea gardens of varying stand age and productivity

Tea (Camellia sinensis) is a globally important crop and is unusual because it both requires an acid soil and acidifies soil. Tea stands tend to be extremely heavily fertilized in order to improve yield and quality, resulting in a great potential for diffuse pollution. The microbial ecology of tea soils remains poorly understood; an improved understanding is necessary as processes affecting nutrient availability and loss pathways are microbially mediated. We therefore examined the relationships between soil characteristics (pH, organic C, total N, total P, available P, exchangeable Al), the soil microbial biomass (biomass C, biomass ninhydrin-N, ATP, phospholipid fatty acids—PLFAs) and its activities (respiration, net mineralization and nitrification). At the Tea Research Institute, Hangzhou (TRI), we compared fields of different productivity levels (low, medium and high) and at Hongjiashan village (HJS) we compared fields of different stand age (9, 50 and 90 years). At both sites tea soils were compared with adjacent forest soils. At both sites, soil pH was highest in the forest soil and decreased with increasing productivity and age of the tea stand. Soil microbial biomass C and biomass ninhydrin-N were significantly affected by tea production. At TRI, microbial biomass C declined in the order forest>low>high>middle production and at HJS in the order stand age 50>age 9>forest>age 90. Soil pH had a strong influence on the microbial biomass, demonstrated by positive linear correlations with: microbial biomass C, microbial biomass ninhydrin-N, the microbial biomass C:organic C ratio, the microbial biomass ninhydrin-N:total N ratio, the respiration rate and specific respiration rate. Above pH_(KCl) 3.5 there was net N mineralization and nitrification, and below this threshold some samples showed net immobilization of N. A principal component (PC) analysis of PLFA data showed a consistent shift in the community composition with productivity level and stand age. The ratio of fungal:bacterial PLFA biomarkers was negatively and linearly correlated with specific respiration in the soils from HJS (r²=0.93, p=0.03). Our results demonstrate that tea cultivation intensity and duration have a strong impact on the microbial community structure, biomass and its functioning, likely through soil acidification and fertilizer addition.     

The seasonal pattern of soil microbial community structure in mesic low arctic tundra

Soil microorganisms are critical to carbon and nutrient fluxes in terrestrial ecosystems. Understanding the annual pattern of soil microbial community structure and how it corresponds to soil nutrient availability and plant production is a fundamental first step towards being able to predict impacts of environmental change on ecosystem functioning. We investigated the composition, structure and nutrient stoichiometry of the soil microbial community in mesic arctic tundra on 9 sample dates in 6 months from winter to fall using phospholipid fatty acid analysis (PLFA), quantitative polymerase chain reaction (qPCR), epifluorescent microscopy and chloroform-fumigation–extraction (CFE). PLFA analysis indicates that the winter microbial community was fungal-dominated, cold-adapted and associated with high C, N and P in the soil solution and microbial biomass. The microscopy data suggest that both bacteria and fungi were active and growing in soils between −5 °C and 0 °C. A significant shift occurred in the PLFA data, qPCR patterns, microscopy and microbial biogeochemistry after the thaw period, resulting in a distinct community that persisted through our spring, summer and fall sample dates, despite large changes in plant productivity. This shift was characterised by increasing relative abundances of certain bacteria (especially Gram +ves) as well as a decline in fungal biomass, and corresponded with decreasing C, N and P in the soil solution. The summer period of low substrate availability (plant–microbe competition) was associated with microbial indicators of nutritional stress. Overall, our results indicate that tundra microbial communities are clearly differentiated according to the changes in soil nutrient status and environmental conditions that occur between winter and post-thaw, and that those changes reflect functionally important adaptations to those conditions.     

Use of C-labelled plant materials and ergosterol, PLFA and NLFA analyses to investigate organic matter decomposition in Antarctic soil

The relationship between organic matter decomposition and changes in microbial community structure were investigated in Antarctic soils using ¹³C-labelled plant materials. Soils with and without labelled Deschampsia antarctica (a native Antarctic grass) were incubated for 42 days and sampled at 0, 7, 14, 21, 28 and 42 days. Changes in microbial community structure were assessed using phospholipid fatty acid analysis (PLFA) and an analysis of the fatty acids associated with the neutral lipid fraction (NLFA). These studies showed that there were no significant changes in PLFA or NLFA profiles over time suggesting no change in microbial community structure during residue decomposition. There was a marked increase however, in ergosterol levels in these soils indicative of growth of the fungal biomass. Analysis of this ergosterol using gas chromatography-mass spectrometry confirmed the transformation of the plant residue by showing the incorporation of ¹³C-plant C into the ergosterol. This incorporation of ¹³C into the ergosterol increased over the incubation period. Importantly, these changes associated with fungal growth were not evident in the analysis of either the PLFA or NLFA fractions thus questioning the reliability of such approaches for studying changes in microbial communities associated with the decomposition of plant residues.     

Soil organic matter turnover as a function of the soil clay content: consequences for model applications

Based on a literature review including 201 surface soils from wet, mild, mid-latitude climates and 290 soils from the Lower Saxony soil monitoring programme (Germany), we investigated the relationship between soil clay content and soil organic matter turnover. The relationship was then used to evaluate the clay modifier for microbial decomposition in the organic matter module of the soil-plant-atmosphere model DAISY. A positive relationship was found between soil clay content and soil microbial biomass (SMB) C. Furthermore, a negative relationship was found between soil clay content and metabolic quotient (qCO₂) as an indicator of specific microbial activity. Both findings support the hypothesis of a clay dependent capacity of soils to protect microbial biomass. Under the differing conditions of practical agriculture and forestry, no or only very weak relationships were found between soil clay content and non-living soil organic matter C (humus C). It is concluded that the stabilising effect of clay is much stronger for SMB than for humus. This is in contrast to the DAISY clay modifier assuming the same negative relationship between soil clay content, on the one hand, and turnover of SMB and turnover of soil humus on the other. There is a positive relationship between SMB and microbial decomposition activity under steady-state conditions (microbial growth≈microbial death). The original concept of a biomass-independent simulation of organic matter turnover in the DAISY model must therefore be rejected. In addition to the original modifiers of organic matter turnover, a modifier based on the pool size of decomposing organisms is suggested. Priming effects can be simulated by applying this modifier. When using this approach, the original modifiers are related to specific microbial activity. The DAISY clay modifier is a useful approximation of the relationship between the metabolic quotient (qCO₂) as an indicator of specific microbial activity and soil clay content.     

Does biochar interfere with standard methods for determining soil microbial biomass and phenotypic community structure?

Due to its high sorption affinity for organic compounds, biochar may interfere with extraction procedures involving such compounds used for microbially-related assays commonly applied to soils. Here we assessed the impact of two biochars (derived from pine bark and produced at 300 and 600 °C) at three concentrations (0, 12.5, and 50 g kg⁻¹) in three distinct arable soils with contrasting textural classes (loamy sand, sandy loam, and clay) on the determination of soil microbial biomass C by fumigation–extraction, fungal biomass by ergosterol analysis, and microbial community structure as defined by phospholipid fatty acid (PLFA) profiling. Biochar did not affect the apparent concentration of soil microbial biomass C and had no significant impact on apparent PLFA profiles. By contrast, the apparent extraction efficiency of ergosterol was affected dependent on soil type, biochar production temperature, and biochar concentration. Nonetheless, ergosterol contents of biochar-amended soils can be accurately estimated by correcting for reduced recovery using an ergosterol spike.