Litter-fall and litter decomposition in a low Mediterranean shrubland

Annual production of litter by Cistus incanus (L.) and Myrtus communis (L.) and decomposition dynamics of leaf litter of these species was studied in a Mediterranean shrubland. Myrtus and Cistus produced 472 and 429 g dry weight litter m^-2 year^-1, respectively. Leaves were the predominant litter component for both species. The average decay constant of Myrtus and Cistus litters enclosed in litter bags, calculated over the whole study period (38 months), was 0.71 year^-1 and 0.31 year^-1 respectively. In green leaves the N content differed during growth seasons for both species, whereas the content of Ca, Mg, P, K, and Na did not show significant changes. Abscised leaves had lower N, P and K contents than green leaves, evidencing that a nutrient translocation before abscission occurred from senescent leaves. The nutrient contents of the leaves at abscission time, generally higher in Cistus than in Myrtus, allowed us to estimate the annual nutrient input to the soil. Phosphorus and K more than N were rapidly released by the decomposing litters after exposure. Nutrient limitation, in particular P, might be considered the main growth limiting factor for Myrtus and Cistus. Both species were adapted to recovery and rapidly recycle P more than N and K in the living biomass through retranslocation from green leaves before abscission and/or a high release rate from the decomposing litter. The former strategy was better used by Cistus, the latter by Myrtus.     

Plant regeneration functional groups modulate the response to fire of soil enzyme activities in a Mediterranean shrubland

Soil enzymes are critical to soil nutrient cycling function but knowledge on the factors that control their response to major disturbances such as wildfires remains very limited. We evaluated the effect of fire-related plant functional traits (resprouting and seeding) on the resistance and resilience to fire of two soil enzyme activities involved in phosphorus and carbon cycling (acid phosphatase and β-glucosidase) in a Mediterranean shrublands in SE Spain. Using experimental fires, we compared four types of shrubland microsites: SS (vegetation patches dominated by seeder species), RR (patches dominated by resprouter species), SR (patches co-dominated by seeder and resprouter species), and IP (shrub interpatches). We assessed pre- and post-fire activities of the target soil enzymes, available P, soil organic C, and plant cover dynamics over three years after the fire. Post-fire regeneration functional groups (resprouter, seeder) modulated both pre- and post-fire activity of acid phosphatase and β-glucosidase, with higher activity in RR and SR patches than in SS patches and IP. However, we found no major differences in enzyme resistance and resilience between microsite types, except for a trend towards less resilience in SS patches. Fire similarly reduced the activity of both enzymes. However, acid phosphatase and β-glucosidase showed contrasting post-fire dynamics. While β-glucosidase proved to be rather resilient to fire, fully recovering three years after fire, acid phosphatase showed no signs of recovery in that period. Overall, the results indicate a positive influence of resprouter species on soil enzyme activity that is very resistant to fire. Long-lasting decrease in acid phosphatase activity probably resulted from the combined effect of P availability and post-fire drought. Our results provide insights on how plant functional traits modulate soil biochemical and microbiological response to fire in Mediterranean fire-prone shrublands.     

Changes in soil microbial biomass and functional diversity with a nitrogen gradient in soil columns

Fertilization generates nutrient patches that may impact soil microbial activity. In this study, nitrogen patches were generated by adding ammonium sulfate or urea to soil columns (length 25 cm; internal diameter 7.2 cm). Changes in nitrogen transformation, soil microbial biomass, and microbial functional diversity with the nitrogen gradients were investigated to evaluate the response of microbial activity to chemical fertilizer nutrient patches. After applying of ammonium sulfate or urea, the added nitrogen migrated about 7 cm. Microbial biomass carbon (MBC) was lower in fertilized soil than in the control (CK) treatment at the same soil layers. MBC increased with soil depth while microbial biomass nitrogen (MBN) decreased. BIOLOG analysis indicated that the average well color development (AWCD) and functional diversity indices of the microbial communities were lower in the 1 cm and 2 cm soil layers after application of ammonium sulfate; the highest values were in the 3 cm soil layer. AWCD and Shannon indices from the 1 to 5 cm soil layers were higher than those from other soil layers under urea application. Both principal component analysis and carbon substrate utilization analysis showed significant separation of soil microbial communities among different soil layers under application of ammonium sulfate or urea. Microbial activity was substantially decreased when NH₄⁺-N concentration was higher than 528.5 mg kg⁻¹ (1–3 cm soil layer under ammonium sulfate application) or 536.8 mg kg⁻¹ (1 cm soil layer under urea application). These findings indicated that changes in soil microbial biomass and microbial functional diversity can occur with a nitrogen gradient. The extent of changes depends on the nitrogen concentration and the form of inorganic fertilizer.     

菇菜套作对土壤微生物群落的影响

套作是防治连作障碍的有效方法之一,但是蔬菜和可食用菌之间的套作机理研究鲜见报道,尤其是其土壤微生物学机制。本研究建立菇菜套作体系,利用实时荧光定量PCR和PCR-DGGE技术研究土壤细菌和真菌群落的变化。结果表明,菇菜套作显著提高了番茄生物量,且其番茄果实产量最高,硝酸盐含量最低。与对照相比,菇菜套作下土壤细菌和真菌基因拷贝数量均无显著变化;DGGE指纹图谱表明,不同处理下的细菌群落无明显差异,但是菇菜套作下真菌群落结构发生了分异,主要表现为尖孢镰刀菌(Fusarium oxysporum)和稻黑孢菌(Nigrospora oryzae)代表型条带的强度的下降。     

Changes in metabolic and structural diversity of a soil bacterial community in response to cadmium toxicity

Cadmium toxicity reduces the species diversity of soil microbial communities and their ability to metabolize different carbon substrates. However, it is not yet clear whether there is a relationship between loss of species diversity and the metabolic rates at which different substrates are used. In this research, the ability of a soil microbial community to metabolize 31 C substrates was examined using Biolog Ecoplates amended with Cd over a range of concentrations (0, 5, 10, 20, 50 g ml^–1). After 48 h growth, the bacterial communities that were produced on ten of the substrates were characterized in relation to their 16S rDNA profiles by PCR denaturing-gradient gel electrophoresis. Results showed that both the microbial growth rates and the numbers of substrates that were used were reduced with increasing Cd concentration. When examined across all substrates, approximately 30% of the 16S rDNA bands representing different bacterial species were eliminated by 5 g Cd ml^–1. However, there was considerable variation in the bacterial community responses with different C substrates. Both cluster analysis and discriminant analysis indicated that the bacterial community structures could be grouped into sensitive, moderately sensitive, and Cd-resistant communities.     

Substrate utilization patterns of desert soil microbial communities in response to xeric and mesic conditions

The Negev Desert is characterized by low soil moisture and organic matter content and an unpredictable rainfall amount, dispersion, and intensity. Water and nutrient availability are, therefore, the major limiting factors of biological activity in arid and semi-arid ecosystems. Plants have developed different ecophysiological adaptations in order to cope with the harsh conditions in this xeric environment, e.g., excretion of salt (Reaumuria negevensis) and chemical compounds (Artemisia sieberi) through the leaves. Microorganisms constitute a major part of these ecosystems' total biomass, and are diverse members of the soil food web, being primarily responsible for breaking down complex organic compounds, which are then recycled. They are also known to be very sensitive to abiotic changes and can time their activity to the environmental conditions.Soil samples were collected monthly from a 0 to 10 cm depth, under the canopies of A. sieberi, Noaea mucronata, and R. negevensis. Samples collected from inter-shrub spaces served as control. CO₂ evolution, microbial biomass, microbial functional diversity, and the physiological profile of the community, were determined by MicroResp™ analysis. A significant difference was found between the two dry periods in most of the examined parameters. The values of water, organic matter content, and total soluble nitrogen were higher in soil samples collected in the vicinity of R. negevensis than in samples collected in the vicinity of N. mucronata, A. sieberi, and the open area. A similar trend was found in CO₂ evolution, microbial biomass, and H' values, in which soil samples collected beneath the canopies of N. mucronata and R. negevensis and from open area had higher values during the wet periods (which were characterized by a mesic environment) and in samples collected beneath the A. sieberi in the wet 2006 and dry 2007 periods.     

Strong functional stability of soil microbial communities under semiarid Mediterranean conditions and subjected to long-term shifts in baseline precipitation

We investigated the effect of soil microclimate on the structure and functioning of soil microbial communities in a Mediterranean Holm-oak forest subjected to 10 years of partial rain exclusion manipulations, simulating average drought conditions expected in Mediterranean areas for the following decades. We applied a high throughput DNA pyrosequencing technique coupled to parallel measurements of microbial respiration (R_H) and temperature sensitivity of microbial respiration (Q₁₀). Some consistent changes in the structure of bacterial communities suggest a slow process of community shifts parallel to the trend towards oligotrophy in response to long-term droughts. However, the structure of bacterial communities was mainly determined by short-term environmental fluctuations associated with sampling date (winter, spring and summer) rather than long-term (10 years) shifts in baseline precipitation. Moreover, long-term drought did not exert any chronic effect on the functioning of soil microbial communities (R_H and Q₁₀), emphasizing the functional stability of these communities to this long-term but mild shifts in water availability. We hypothesize that the particular conditions of the Mediterranean climate with strong seasonal shifts in both temperature and soil water availability but also characterized by very extreme environmental conditions during summer, was acting as a strong force in community assembling, selecting phenotypes adapted to the semiarid conditions characterizing Mediterranean ecosystems. Relations of climate with the phylogenetic structure and overall diversity of the communities as well as the distribution of the individual responses of different lineages (genera) to climate confirmed our hypotheses, evidencing communities dominated by thermotolerant and drought-tolerant phenotypes.     

菜-菌轮作模式下土壤微生物群落结构及多样性的变化

为明确菜-菌轮作模式对土壤微生物的影响,基于高通量测序技术,对4种轮作模式下的土壤微生物群落结构与多样性进行了研究,结果显示：不同轮作模式下土壤样品中真菌和细菌OUT总数分别是2298和15840条,相较于常规轮作模式A,菜-菌轮作模式B、C、D下真菌的OUT总数、ACE指数、Chao1指数、Shannon指数降低显著,Simpson指数增加明显,但细菌的各参数没有显著的差异;其土壤全氮、碱解氮、速效钾、有机质含量显著高于常规轮作模式A;真菌的优势群落是子囊菌门,相对丰度在66%以上,枝孢属、镰刀菌属两类致病菌群的丰度在菜-菌轮作模式B、C、D中降低明显;细菌的优势群落是变形菌门、放线菌门、绿弯菌门以及酸杆菌门,鞘氨醇单胞菌属、伯克霍尔德氏菌属丰度在菜-菌轮作模式B、C、D中显著提高;聚类分析表明菜-菌轮作模式C、D下微生物群落结构相似度最高,常规轮作模式A可划分为区别于菜-菌轮作模式B、C、D的单独类群。综上所述,菜-菌轮作可降低真菌群落丰度,改变土壤微生物群落的结构组成,同时提高土壤中有益菌群的丰度,降低有害菌群的丰度。     

多氯联苯复合污染土壤的微生物群落结构多样性变化

土壤微生物群落结构多样性是指示土壤生态系统稳定性及其功能的重要传感器。采用磷脂脂肪酸（Phospholipid fatty acids,PLFAs）方法,对长江三角洲地区某POPs高风险区PCBs长期复合污染土壤的微生物群落结构多样性进行了初步研究。结果表明,PCBs重度污染土壤中格兰氏阴性菌（16：1w9、cy17：0等）和厌氧微生物（18：1w7）的PLFAs组分含量较多,而格兰氏阳性菌（如i15：0、i17：0等）、放线菌（16：0（10Me））及真菌（18：2ω6,9）和好氧性微生物的PLFAs含量较低,表明PCBs污染土壤中微生物群落结构与组成发生了明显变化。这一结果为PCBs降解微生物资源的定向筛选提供了科学依据。     

Interactive effects of warming, soil humidity and plant diversity on litter decomposition and microbial activity

Human activity has induced a multitude of global changes that are likely to affect the functioning of ecosystems. Although these changes act in concert, studies on interactive effects are scarce. Here, we conducted a laboratory microcosm experiment to explore the impacts of temperature (9, 12 and 15 °C), changes in soil humidity (moist, dry) and plant diversity (1, 4, 16 species) on soil microbial activity and litter decomposition.We found that changes in litter decomposition did not mirror impacts on microbial measures indicating that the duration of the experiment (22 weeks) may not have been sufficient to determine the full magnitude of global change effects. However and notably, changes in temperature, humidity and plant litter diversity/composition affected in a non-additive way the microbial parameters investigated. For instance, microbial metabolic efficiency increased with plant diversity in the high moisture treatment but remained unaffected in low moisture treatment suggesting that climate changes may mask beneficial effects of biodiversity on ecosystem functioning. Moreover, litter decomposition was unaffected by plant litter diversity/composition but increased with increasing temperature in the high moisture treatment, and decreased with increasing temperature in the low moisture treatment.We conclude that it is inevitable to perform complex experiments considering multiple global change agents in order to realistically predict future changes in ecosystem functioning. Non-additive interactions highlight the context-dependency of impacts of single global change agents.     

模拟增温和降水调控对土壤微生物碳氮、群落基质利用模式及群落组成的短期影响

Soil microorganisms are major drivers of soil carbon(C) cycling;however,the response of these microorganisms to climate change remains unclear.In the present study,we investigated how 18 months of multifactor climate treatments(warmed air temperature by 3℃ and decreased or increased precipitation manipulation by 30%) affected soil microbial biomass C and nitrogen(N),community substrate utilization patterns,and community composition.Decreased and increased precipitation significantly reduced microbial biomass C by 13.5% and 24.9% and microbial biomass N by 22.9% and 17.6% in unwarmed plots,respectively(P0.01).Warming enhanced community substrate utilization by 89.8%,20.4%,and 141.4% in the natural,decreased,and increased precipitation plots,respectively.Particularly,warming significantly enhanced the utilization of amine and carboxylic acid substrates among all precipitation manipulation plots.Compared with the natural air temperature with natural precipitation treatment,other treatments affected fungal community richness by -0.9% to 33.6% and reduced the relative abundance of the dominant bacterial and fungal groups by 0.5% to 6.8% and 4.3% to 10.7%,respectively.The warming and/or precipitation manipulation treatments significantly altered Zygomycota abundance(P0.05).Our results indicate that climate change drivers and their interactions may cause changes in soil microbial biomass C and N,community substrate utilization patterns,and community composition,particularly for the fungal community,and shifts in the microorganism community may further shape the ecosystems function.     

Interannual and seasonal changes in the soil exchange rates of monoterpenes and other VOCs in a Mediterranean shrubland

Information about soil VOC inventories and exchange rates in different soils is very scarce. Seasonality of soil VOC exchange rates is also largely unknown, despite the increasing interest in some soil volatile compounds, such as monoterpenes, because of their important role in soil ecology. We aimed to explore and quantify soil VOC exchange rates in a Mediterranean shrubland and their seasonality. Measurements of soil VOC exchange were taken using GC‐MS and PTR‐MS techniques, together with soil temperature, soil moisture and soil CO₂ efflux measurements, during two annual campaigns with contrasting precipitation. Methanol, acetic acid, ethyl acetate, acetaldehyde, acetone, C₃ and C₄ carbonyls (such as methyl ethyl ketone), α‐pinene and limonene, showed the highest emission rates. Maximum soil monoterpene emission rates were very low (0.003 nmol m^?2 s^?1) compared with foliar monoterpene emission rates. The emission rates of the other VOCs were also low (maximum 0.8 nmol m^?2 s^?1) except for methanol (1.2 nmol m^?2 s^?1). Maximum soil uptake rates for some VOCs, such as methanol and acetonitrile (ranging from ?0.1 to ?0.5 nmol m^?2 s^?1) were, however, comparable with foliar uptake rates. Further studies are needed to corroborate these results and the possible importance of the soil VOC sink in regional chemistry‐climate models. Long‐term severe drought increased soil monoterpene emission rates in this Mediterranean shrubland. The increases seem to be linked to changes in the soil’s physical properties induced by low soil moisture. Unlike monoterpenes, other soil VOC emission rates decreased when soil moisture was low. The results suggest a seasonal control of soil temperature on the emission rates of monoterpenes and other VOCs. The emission rates increase with soil temperature. Positive correlations between the VOC exchange rates and the soil CO₂ fluxes suggest that phenology of roots and microorganisms also controls seasonal changes in soil VOCs in this Mediterranean shrubland.     

Responses of soil microbial community to nitrogen fertilizer and precipitation regimes in a semi-arid steppe

Purpose

Changes of nitrogen (N) cycle caused by N fertilization and precipitation regimes have affected the key ecosystem structure and functions in temperate steppe, which may modify the structure of soil microbial communities involved in N transformation. This paper was designated to examine the response of soil ammonia oxidizers and denitrifiers to the N fertilization and precipitation regimes in a semi-arid steppe where N and water contents are major limiting factors of the grassland productivity.

Materials and methods

This study was based on a long-term N fertilization and precipitation regimes experiment in Inner Mongolia (116° 17′ 20″ E, 42° 2′ 29″ N). The treatments including CK (control), R (reduced precipitation), W (30% increase in precipitation), N (10 g N m^?2 y^?1), RN (reduced precipitation and 10 g N m^?2 y^?1), and WN (30% increase in precipitation and 10 g N m^?2 y^?1). Soil basic chemical properties and microbial activities were analyzed. Molecular methods were applied to determine the abundance, structure and diversity of ammonia oxidizers and denitrifiers. Statistical analysis detected the main and interactive effect of treatments on soil microbial communities and revealed the relationship between soil microbial community structures and environmental factors.

Results and discussion

N fertilization significantly increased ammonia-oxidizing bacteria (AOB) abundance. Ammonia-oxidizing archaea (AOA) community structure was markedly changed in N fertilizer treatment and strongly affected by soil pH, while soil nitrate and water content correlated with AOB community structure. Soil nitrate was the key factor influencing nirK gene community structure, while soil pH and water content explained much of the variations of nosZ gene community. AOB-amoA and nosZ gene community diversities were influenced by precipitation regimes and interaction of N fertilization and precipitation regimes, respectively.

Conclusions

N fertilization and precipitation regimes had significant influences on the changes of soil properties and microbial functional communities. Soil nitrification was mainly driven by AOB in the semi-arid grassland. Changes of substrate content and soil pH were the key factors in shifting functional microbial communities. The non-synergistic effects of N fertilization and precipitation regimes on the microbial functional groups indicated that the negative effect of lower pH induced by N fertilization would be alleviated by precipitation regimes, which should be well considered in grassland restoration.

     

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.     

Post-fire mineral N allocation and stabilisation in soil particle size fractions in Mediterranean grassland and shrubland

In the Mediterranean region, long-term post-fire soil N dynamics may be relevant in the stabilisation of soil organic matter and N cycling in the plant-soil system. Post-fire recycling of N may be retained by the retention of N in physically and/or chemically protected fractions of soil organic matter. We studied the allocation of post-fire ¹⁵N-tracer among different soil organic matter fractions (coarse sand, fine sand, coarse silt and fine silt + clay) and ¹⁵N-tracer dynamics for 12 years after prescribed fires in three different Mediterranean plant communities (grassland, mixed shrub-grassland and shrubland). We selected 6 plots for each community and we set experimental fires. Directly after the fires, we applied ¹⁵NH₄⁺-N and we monitored the fate of ¹⁵N-tracer over a period of 12 years. For this purpose, we carried out a physical size fractionation and we analysed the biochemical recalcitrance of N and ¹⁵N by acid hydrolysis in the size fractions obtained. In both burned and unburned plots the finest soil particles (<20 μm) accounted for most soil N. Fire promoted N increases in the medium size fractions while the N pool in the finest and coarsest fractions did not change after the fires. Interestingly, ¹⁵N-tracer was quickly incorporated into fine fractions from which, in the case of plant communities free of legumes, it was remobilised in the following years. Fire did not promote changes in recalcitrant N, but shrubland showed marked decreases in N recalcitrance 6 years after the fires. Despite the fact that the primary effects on soil fractions were detected just after the fires, these persisted for 12 years post-fire. Newly incorporated ¹⁵N-tracer was less recalcitrant than total N and, surprisingly, fine fractions had very low recalcitrant ¹⁵N values, similar to the coarse fractions. Apparently, the N transformations in the finest fraction (<20 μm) were mainly regulated by the quality of the ¹⁵N compounds retained in the fraction.     

不同利用方式下红壤微生物生物量及代谢功能多样性的变化

研究了不同农林利用方式下红壤微生物生物量和代谢功能多样性等土壤质量指标的变化.结果表明:不同利用方式对土壤质量各指标造成了显著的影响;稻田的微生物生物量碳、氮最高,林地和草地微生物生物量次之,旱地的微生物生物量碳、氮最低(分别是稻田利用方式的4.3% 和 13.7%);稻田的微生物代谢功能多样性最高,旱地、林地和草地的细菌代谢功能多样性较低,旱地的真菌代谢功能多样性最低;微生物生物量和代谢功能多样性可以作为反映土壤质量变化的早期敏感的指标,用来衡量管理措施的改变对土壤质量造成的影响.     

Spatial patterns of microbial denitrification genes change in response to poultry litter placement and cover crop species in an agricultural soil

Subsurface-banding manure and winter cover cropping are farming techniques designed to reduce N loss. Little is known, however, about the effects of these management tools on denitrifying microbial communities and the greenhouse gases they produce. Abundances of bacterial (16S), fungal (ITS), and denitrification genes (nirK, nirS, nosZ-I, and nosZ-II) were measured in soil samples collected from a field experiment testing the combination of cereal rye and hairy vetch cover cropping with either surface-broadcasted or subsurface-banded poultry litter. The spatial distribution of genes was mapped to identify potential denitrifier hotspots. Spatial distribution maps showed increased 16S rRNA genes around the manure band, but no denitrifier hotspots. Soil depth and nitrate concentration were the strongest drivers of gene abundance, but bacterial gene abundance also differed by gene, soil characteristics, and management methods. Gene copy number of nirK was higher under cereal rye than hairy vetch and positively associated with soil moisture, while nirS gene copies did not differ between cover crop species. The nirS gene copies increased when manure was surface broadcasted compared to subsurface banded and was positively associated with pH. Soil moisture and pH were positively correlated to nosZ-II but not to nosZ-I gene copy numbers. We observed stronger correlations between nosZ-I and nirS, and nosZ-II and nirK gene copies compared to the reverse pairings. Agricultural management practices differentially affect spatial distributions of genes coding for denitrification enzymes, leading to changes in the composition of the denitrifying community.