Organic Layer Serves as a Hotspot of Microbial Activity and Abundance in Arctic Tundra Soils

Tundra ecosystem is of importance for its high accumulation of organic carbon and vulnerability to future climate change. Microorganisms play a key role in carbon dynamics of the tundra ecosystem by mineralizing organic carbon. We assessed both ecosystem process rates and community structure of Bacteria, Archaea, and Fungi in different soil layers (surface organic layer and subsurface mineral soil) in an Arctic soil ecosystem located at Spitsbergen, Svalbard during the summer of 2008 by using biochemical and molecular analyses, such as enzymatic assay, terminal restriction fragment length polymorphism (T-RFLP), quantitative polymerase chain reaction (qPCR), and pyrosequencing. Activity of hydrolytic enzymes showed difference according to soil type. For all three microbial communities, the average gene copy number did not significantly differ between soil types. However, archaeal diversities appeared to differ according to soil type, whereas bacterial and fungal diversity indices did not show any variation. Correlation analysis between biogeochemical and microbial parameters exhibited a discriminating pattern according to microbial or soil types. Analysis of the microbial community structure showed that bacterial and archaeal communities have different profiles with unique phylotypes in terms of soil types. Water content and hydrolytic enzymes were found to be related with the structure of bacterial and archaeal communities, whereas soil organic matter (SOM) and total organic carbon (TOC) were related with bacterial communities. The overall results of this study indicate that microbial enzyme activity were generally higher in the organic layer than in mineral soils and that bacterial and archaeal communities differed between the organic layer and mineral soils in the Arctic region. Compared to mineral soil, peat-covered organic layer may represent a hotspot for secondary productivity and nutrient cycling in this ecosystem.     

Drought‐resistant fungi control soil organic matter decomposition and its response to temperature

Microbial‐mediated decomposition of soil organic matter (SOM) ultimately makes a considerable contribution to soil respiration, which is typically the main source of CO₂ arising from terrestrial ecosystems. Despite this central role in the decomposition of SOM, few studies have been conducted on how climate change may affect the soil microbial community and, furthermore, on how possible climate‐change induced alterations in the ecology of microbial communities may affect soil CO₂ emissions. Here we present the results of a seasonal study on soil microbial community structure, SOM decomposition and its temperature sensitivity in two representative Mediterranean ecosystems where precipitation/throughfall exclusion has taken place during the last 10 years. Bacterial and fungal diversity was estimated using the terminal restriction fragment length polymorphism technique. Our results show that fungal diversity was less sensitive to seasonal changes in moisture, temperature and plant activity than bacterial diversity. On the other hand, fungal communities showed the ability to dynamically adapt throughout the seasons. Fungi also coped better with the 10 years of precipitation/throughfall exclusion compared with bacteria. The high resistance of fungal diversity to changes with respect to bacteria may open the controversy as to whether future ‘drier conditions’ for Mediterranean regions might favor fungal dominated microbial communities. Finally, our results indicate that the fungal community exerted a strong influence over the temporal and spatial variability of SOM decomposition and its sensitivity to temperature. The results, therefore, highlight the important role of fungi in the decomposition of terrestrial SOM, especially under the harsh environmental conditions of Mediterranean ecosystems, for which models predict even drier conditions in the future.     

Drying–Rewetting Cycles Affect Fungal and Bacterial Growth Differently in an Arable Soil

Drying and rewetting is a frequent physiological stress for soil microbial communities; a stress that is predicted to grow more influential with future climate change. We investigated the effect of repeated drying–rewetting cycles on bacterial (leucine incorporation) and fungal (acetate in ergosterol incorporation) growth, on the biomass concentration and composition (PLFA), and on the soil respiration. Using different plant material amendments, we generated soils with different initial fungal:bacterial compositions that we exposed to 6–10 repetitions of a drying–rewetting cycle. Drying–rewetting decreased bacterial growth while fungal growth remained unaffected, resulting in an elevated fungal:bacterial growth ratio. This effect was found irrespective of the initial fungal:bacterial biomass ratio. Many drying–rewetting cycles did not, however, affect the fungal:bacterial growth ratio compared to few cycles. The biomass response of the microbial community differed from the growth response, with fungal and total biomass only being slightly negatively affected by the repeated drying–rewetting. The discrepancy between growth- and biomass-based assessments underscores that microbial responses to perturbations might previously have been misrepresented with biomass-based assessments. In light of this, many aspects of environmental microbial ecology may need to be revisited with attention to what measure of the microbial community is relevant to study.     

Microbial necromass under global change and implications for soil organic matter

Microbial necromass is an important source and component of soil organic matter (SOM), especially within the most stable pools. Global change factors such as anthropogenic nitrogen (N), phosphorus (P), and potassium (K) inputs, climate warming, elevated atmospheric carbon dioxide (eCO₂), and periodic precipitation reduction (drought) strongly affect soil microorganisms and consequently, influence microbial necromass formation. The impacts of these global change factors on microbial necromass are poorly understood despite their critical role in the cycling and sequestration of soil carbon (C) and nutrients. Here, we conducted a meta-analysis to reveal general patterns of the effects of nutrient addition, warming, eCO₂, and drought on amino sugars (biomarkers of microbial necromass) in soils under croplands, forests, and grasslands. Nitrogen addition combined with P and K increased the content of fungal (+21%), bacterial (+22%), and total amino sugars (+9%), consequently leading to increased SOM formation. Nitrogen addition alone increased solely bacterial necromass (+10%) because the decrease of N limitation stimulated bacterial more than fungal growth. Warming increased bacterial necromass, because bacteria have competitive advantages at high temperatures compared to fungi. Other global change factors (P and NP addition, eCO₂, and drought) had minor effects on microbial necromass because of: (i) compensation of the impacts by opposite processes, and (ii) the short duration of experiments compared to the slow microbial necromass turnover. Future studies should focus on: (i) the stronger response of bacterial necromass to N addition and warming compared to that of fungi, and (ii) the increased microbial necromass contribution to SOM accumulation and stability under NPK fertilization, and thereby for negative feedback to climate warming.     

Mycorrhizal Hyphal Turnover as a Dominant Process for Carbon Input into Soil Organic Matter

The atmospheric concentration of CO₂ is predicted to reach double current levels by 2075. Detritus from aboveground and belowground plant parts constitutes the primary source of C for soil organic matter (SOM), and accumulation of SOM in forests may provide a significant mechanism to mitigate increasing atmospheric CO₂ concentrations. In a poplar (three species) plantation exposed to ambient (380 ppm) and elevated (580 ppm) atmospheric CO₂ concentrations using a Free Air Carbon Dioxide Enrichment (FACE) system, the relative importance of leaf litter decomposition, fine root and fungal turnover for C incorporation into SOM was investigated. A technique using cores of soil in which a C₄ crop has been grown (δ¹³C −18.1‰) inserted into the plantation and detritus from C₃ trees (δ¹³C −27 to −30‰) was used to distinguish between old (native soil) and new (tree derived) soil C. In-growth cores using a fine mesh (39 μm) to prevent in-growth of roots, but allow in-growth of fungal hyphae were used to assess contribution of fine roots and the mycorrhizal external mycelium to soil C during a period of three growing seasons (1999–2001). Across all species and treatments, the mycorrhizal external mycelium was the dominant pathway (62%) through which carbon entered the SOM pool, exceeding the input via leaf litter and fine root turnover. The input via the mycorrhizal external mycelium was not influenced by elevated CO₂, but elevated atmospheric CO₂ enhanced soil C inputs via fine root turnover. The turnover of the mycorrhizal external mycelium may be a fundamental mechanism for the transfer of root-derived C to SOM.     

Long-Term Phosphorus Fertilization Impacts Soil Fungal and Bacterial Diversity but not AM Fungal Community in Alfalfa

Soil function may be affected by cropping practices impacting the soil microbial community. The effect of different phosphorus (P) fertilization rates (0, 20, or 40 kg P₂O₅ ha⁻¹) on soil microbial diversity was studied in 8-year-old alfalfa monocultures. The hypothesis that P fertilization modifies soil microbial community was tested using denaturing gradient gel electrophoresis and phospholipids fatty acid (PLFA) profiling to describe soil bacteria, fungi, and arbuscular mycorrhizal (AM) fungi diversity. Soil parameters related to fertility (soil phosphate flux, soluble P, moisture, phosphatase and dehydrogenase assays, and carbon and nitrogen content of the light fraction of soil organic matter) were also monitored and related to soil microbial ribotype profiles. Change in soil P fertility with the application of fertilizer had no effect on crop yield in 8 years, but on the year of this study was associated with shifts in the composition of fungal and bacterial communities without affecting their richness, as evidenced by the absence of effect on the average number of ribotypes detected. However, variation in soil P level created by a history of differential fertilization did not significantly influence AM fungi ribotype assemblages nor AM fungi biomass measured with the PLFA 16:1ω5. Fertilization increased P flux and soil soluble P level but reduced soil moisture and soil microbial activity, as revealed by dehydrogenase assay. Results suggest that soil P fertility management could influence soil processes involving soil microorganisms. Seasonal variations were also recorded in microbial activity, soil soluble P level as well as in the abundance of specific bacterial and fungal PLFA indicators of soil microbial biomass.     

Structural Stability,Microbial Biomass and Community Composition of Sediments Affected by the Hydric Dynamics of an Urban Stormwater Infiltration Basin

The sedimentary layer deposited at the surface of stormwater infiltration basins is highly organic and multicontaminated. It undergoes considerable moisture content fluctuations due to the drying and inundation cycles (called hydric dynamics) of these basins. Little is known about the microflora of the sediments and its dynamics; hence, the purpose of this study is to describe the physicochemical and biological characteristics of the sediments at different hydric statuses of the infiltration basin. Sediments were sampled at five time points following rain events and dry periods. They were characterized by physical (aggregation), chemical (nutrients and heavy metals), and biological (total, bacterial and fungal biomasses, and genotypic fingerprints of total bacterial and fungal communities) parameters. Data were processed using statistical analyses which indicated that heavy metal (1,841 μg/g dry weight (DW)) and organic matter (11%) remained stable through time. By contrast, aggregation, nutrient content (NH₄⁺, 53–717 μg/g DW), pH (6.9–7.4), and biological parameters were shown to vary with sediment water content and sediment biomass, and were higher consecutive to stormwater flows into the basin (up to 7 mg C/g DW) than during dry periods (0.6 mg C/g DW). Coinertia analysis revealed that the structure of the bacterial communities is driven by the hydric dynamics of the infiltration basin, although no such trend was found for fungal communities. Hydric dynamics more than rain events appear to be more relevant for explaining variations of aggregation, microbial biomass, and shift in the microbial community composition. We concluded that the hydric dynamics of stormwater infiltration basins greatly affects the structural stability of the sedimentary layer, the biomass of the microbial community living in it and its dynamics. The decrease in aggregation consecutive to rewetting probably enhances access to organic matter (OM), explaining the consecutive release of NH₄⁺, the bloom of the microbial biomass, and the change in structure of the bacterial community. These results open new perspectives for basin management since the risk of OM and pollutant transfer to the aquifer is greatly affected by alternating dry and flood periods.     

Elevated Atmospheric CO2 Alters Soil Microbial Communities Associated with Trembling Aspen (Populus tremuloides) Roots

Global atmospheric CO₂ levels are expected to double within the next 50 years. To assess the effects of increased atmospheric CO₂ on soil ecosystems, cloned trembling aspen (Populus tremuloides) seedlings were grown individually in 1 m³ open bottom root boxes under either elevated (720 ppm, ELEV) or ambient CO₂ (360 ppm, AMB). After 5 years, soil cores (40 cm depth) were collected from the root boxes and divided into 0–20 cm and 20–40 cm fractions. ELEV treatment resulted in significant decreases in both soil nitrate and total soil nitrogen in both the 0–20 cm and 20–40 cm soil fractions, with a 47% decrease in soil nitrate and a 50% decrease in total soil nitrogen occurring in the 0–20 cm fraction. ELEV treatment did not result in a significant change in the amount of soil microbial biomass. However, analysis of indicator phospholipid fatty acids (PLFA) indicated that ELEV treatment did result in significant increases in PLFA indicators for fungi and Gram-negative bacteria in the 0–20 cm fraction. Terminal restriction fragment length polymorphism (T-RFLP) analysis was used to analyze the composition of the soil bacterial communities (using primers targeting the 16SrRNA gene) and the soil fungal communities (using primers targeting the intergenic transcribed spacer region). T-RFLP analysis revealed shifts in both bacterial and fungal community structure, as well as increases in both bacterial and fungal species richness with ELEV treatment. These results indicated that increased atmospheric CO₂ had significant effects on both soil nutrient availability and the community composition of soil microbes associated with aspen roots.     

Transport of Carbon and Nitrogen Between Litter and Soil Organic Matter in a Northern Hardwood Forest

We used sugar maple litter double-labeled with ¹³C and ¹⁵N to quantify fluxes of carbon (C) and nitrogen (N) between litter and soil in a northern hardwood forest and the retention of litter C and N in soil. Two cohorts of litter were compared, one in which the label was preferentially incorporated into non-structural tissue and the other structural tissue. Loss of ¹³C from this litter generally followed dry mass and total C loss whereas loss of ¹⁵N (20–30% in 1 year) was accompanied by large increases of total N content of this decaying litter (26–32%). Enrichment of ¹³C and ¹⁵N was detected in soil down to 10–15 cm depth. After 6 months of decay (November–May) 36–43% of the ¹³C released from the litter was recovered in the soil, with no differences between the structural and non-structural labeled litter. By October the percentage recovery of litter ¹³C in soil was much lower (16%). The C released from litter and remaining in soil organic matter (SOM) after 1 year represented over 30 g C m⁻² y⁻¹ of SOM accumulation. Recovery of litter ¹⁵N in soil was much higher than for C (over 90%) and in May ¹⁵N was mostly in organic horizons whereas by October it was mostly in 0–10 cm mineral soil. A small proportion of this N was recovered as inorganic N (2–6%). Recovery of ¹⁵N in microbial biomass was higher in May (13–15%) than in October (about 5%). The C:N ratio of the SOM and microbial biomass derived from the labeled litter was much higher for the structural than the non-structural litter and for the forest floor than mineral SOM, illustrating the interactive role of substrates and microbial activity in regulating the C:N stoichiometry of forest SOM formation. These results for a forest ecosystem long exposed to chronically high atmospheric N deposition (ca. 10 kg N ha⁻¹ y⁻¹) suggest possible mechanisms of N retention in soil: increased organic N leaching from fresh litter and reduced fungal transport of N from soil to decaying litter may promote N stabilization in mineral SOM even at a relatively low C:N ratio.     

氮沉降增加情景下植物-土壤-微生物交互对自然生态系统土壤有机碳的调控研究进展

大气氮沉降增加倾向于促进受氮限制陆地生态系统地上生物量,但是对地下碳过程和土壤碳截存的影响结果迥异,导致陆地生态系统“氮促碳汇”的评估存在很大的不确定性。大气氮沉降输入直接影响微生物活性或间接影响底物质量,改变凋落物和土壤有机质(SOM)的分解速率和分解程度,进而影响土壤有机碳(SOC)的积累与损耗过程。过去相关研究主要集中在土壤碳转化过程和碳储量动态方面,缺乏植物-微生物-SOM交互作用的理解,对土壤碳截存调控的生物化学和微生物学机理尚不清楚。本文以地下碳循环过程为主线,分别综述了氮沉降增加对植物地下碳分配、SOC激发效应、微生物群落碳代谢过程的影响,深入分析SOM化学稳定性与微生物群落动态的关系。该领域研究的薄弱环节体现在:(1)增氮倾向于降低根系的生长和周转,对根际沉积碳分配(数量和格局)的影响及驱动因素不明确;(2)虽然认识到氮素有效性影响土壤激发效应的方向和强度,但是氧化态NO-3和还原态NH+4输入对有机质激发效应的差异性影响及潜在机理知之甚少;(3)微生物碳利用效率(CUE)是微生物群落碳代谢的关键表征,能够很好地解释土壤碳的积累与损耗过程;由于缺乏适宜的测定方法,难以准确量化土壤微生物的CUE及微生物生物量的周转时间;(4)增氮会抑制土壤真菌群落及其胞外酶活性,对细菌群落组成的影响尚未定论,有关SOM化学质量与土壤微生物群落活性、组成之间的耦合关系尚不清楚。未来研究应基于长期的氮添加控制实验平台,结合碳氧稳定性同位素示踪、有机质化学、分子生物学和宏基因组学等方法,深入分析植物同化碳的地下分配规律、微生物碳代谢和周转、有机质化学结构与功能微生物群落的耦合关系等关键环节。上述研究将有助于揭示植物-土壤-微生物交互作用对SOC动态的调控机制,完善陆地生态系统碳-氮耦合循环模型,有效降低区域陆地碳汇评估的不确定性,并可为陆地生态系统应对全球变化提供科学依据。     

Soil Microbial Community Response to Drought and Precipitation Variability in the Chihuahuan Desert

Increases in the magnitude and variability of precipitation events have been predicted for the Chihuahuan Desert region of West Texas. As patterns of moisture inputs and amounts change, soil microbial communities will respond to these alterations in soil moisture windows. In this study, we examined the soil microbial community structure within three vegetation zones along the Pine Canyon Watershed, an elevation and vegetation gradient in Big Bend National Park, Chihuahuan Desert. Soil samples at each site were obtained in mid-winter (January) and in mid-summer (August) for 2 years to capture a component of the variability in soil temperature and moisture that can occur seasonally and between years along this watershed. Precipitation patterns and amounts differed substantially between years with a drought characterizing most of the second year. Soils were collected during the drought period and following a large rainfall event and compared to soil samples collected during a relatively average season. Structural changes within microbial community in response to site, season, and precipitation patterns were evaluated using fatty acid methyl ester (FAME) and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analyses. Fungal FAME amounts differed significantly across seasons and sites and greatly outweighed the quantity of bacterial and actinomycete FAME levels for all sites and seasons. The highest fungal FAME levels were obtained in the low desert scrub site and not from the high elevation oak–pine forests. Total bacterial and actinomycete FAME levels did not differ significantly across season and year within any of the three locations along the watershed. Total bacterial and actinomycete FAME levels in the low elevation desert-shrub and grassland sites were slightly higher in the winter than in the summer. Microbial community structure at the high elevation oak–pine forest site was strongly correlated with levels of NH₄ ⁺–N, % soil moisture, and amounts of soil organic matter irrespective of season. Microbial community structure at the low elevation desert scrub and sotol grasslands sites was most strongly related to soil pH with bacterial and actinobacterial FAME levels accounting for site differences along the gradient. DGGE band counts of amplified soil bacterial DNA were found to differ significantly across sites and season with the highest band counts found in the mid-elevation grassland site. The least number of bands was observed in the high elevation oak–pine forest following the large summer-rain event that occurred after a prolonged drought. Microbial responses to changes in precipitation frequency and amount due to climate change will differ among vegetation zones along this Chihuahuan Desert watershed gradient. Soil bacterial communities at the mid-elevation grasslands site are the most vulnerable to changes in precipitation frequency and timing, while fungal community structure is most vulnerable in the low desert scrub site. The differential susceptibility of the microbial communities to changes in precipitation amounts along the elevation gradient reflects the interactive effects of the soil moisture window duration following a precipitation event and differences in soil heat loads. Amounts and types of carbon inputs may not be as important in regulating microbial structure among vegetation zones within in an arid environment as is the seasonal pattern of soil moisture and the soil heat load profile that characterizes the location.     

Soil Organic Carbon Accumulation in Intensively Managed <Emphasis Type="Italic">Phyllostachys praecox</Emphasis> Stands

Area of bamboo forest (Phyllostachys praecox) has rapidly increased in southern China during the last 20 years due to its high economic value. Aims of this study were to analyse the temporal and spatial variations of soil organic matter (SOM) in heavily winter mulched bamboo stands and to estimate potential for carbon sequestration. Total of 60 soil profiles with 0–15 years of bamboo plantation were sampled from three towns in Lin’an County. Results showed that with increased plantation years, SOM decreased slightly at the beginning (1–5 years), and then rose up steadily. Based on the average of the three locations, the highest SOM content of 75.82 g/kg was the surface layer (0–10 cm) of the 15 years. As plantation year increased, the variation of SOM in the surface layer (0–10 cm) was represented by a parabolic shape, and in the second layer (10–20 cm), it was a similar mode, but less vigorous. Soil organic carbon (SOC) storage significantly increased during 5 to 15 years after it reached full production, and the calculated annual SOC increment in 0–40 cm soil profile was about 6.3 t C/ha/year. Therefore, extended Phyllostachys praecox forests can be considered as one option for countering CO₂ emissions and regional climate change.     

Pyrolysis-field ionization mass spectrometry of agricultural soils and humic substances: Effect of cropping systems and influence of the mineral matrix

Whole soil samples, extracted humic substances, the corresponding fulvic (FA) and humic acids (HA) and the extraction residues (humins) from long-term, agricultural test plots were investigated by in-source pyrolysis-field ionization mass spectrometry (Py-FIMS). For the soils distinct differences in the chemical composition of the organic matter in differently managed fields were observed. The FI mass spectra of the extracted humic substances gave complementary chemical information, as they cover a larger mass range compared to the whole soil spectra. The chemical, structural information of the conventional alkaline extraction residues was demonstrated by Py-FIMS spectra to be similar to that of the related soil samples. Influences of mineral matrix to organic matter ratios were studied on mixtures of extracted humic substances with defined mineral components such as quartz, basalt, iron oxide (Fe₂O₃), Ca-montmorillonite, kaolinite and illite. It was shown that in these mixtures the number of mass signals detected and the covered mass range decreased, when organic carbon concentrations (C_org) in this synthetic mineral matrix dropped below 2% (w/w). Limitations in the direct application of Py-FIMS might arise in the case of natural soil samples with C_org concentrations below 0.5% (w/w), high contents of swelling clay minerals and iron oxides. ei]{gnR}{fnMerckx}     

土壤有机质概念和分组技术研究进展

土壤有机质一直是土壤学研究领域的重点,在过去的50年里,对土壤质量可持续性观念的增强和寻找快速判断人为因素对土壤质量影响方向指标的强烈愿望导致了土壤有机质的研究重点发生了急剧变化：对农业措施反映慢的土壤腐殖质类物质的研究正在退出土壤有机质研究领域,而侧重点逐渐转向了土壤中未受微生物作用或正在受微生物降解的有机残体;也出现了新的土壤有机质研究概念和对应测试手段：土壤有机质的比重分组、与有机质结合的土壤颗粒大小分组、土壤团聚体中的POM和iPOM以及土壤水溶性有机质和微生物体C等概念和测试手段被相继提了出来,土壤有机质的研究重点正在从土壤微生物的作用产物(腐殖质)向土壤微生物作用前的、具有部分生物活性的有机质(轻组有机质、砂粒组和粗粉砂粒组中的有机质、POM和iPOM)和完全具有生物活性的有机质(微生物体C和水溶性有机质)转移,这一过程与土壤有机质概念的拓展密不可分。     

Microbial Protein in Soil: Influence of Extraction Method and C Amendment on Extraction and Recovery

The capacity to study the content and resolve the dynamics of the proteome of diverse microbial communities would help to revolutionize the way microbiologists study the function and activity of microorganisms in soil. To better understand the limitations of a proteomic approach to studying soil microbial communities, we characterized extractable soil microbial proteins using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Two methods were utilized to extract proteins from microorganisms residing in a Quitman and Benfield soil: (1) direct extraction of bulk protein from soil and (2) separation of the microorganisms from soil using density gradient centrifugation and subsequent extraction (DGC–EXT) of microbial protein. In addition, glucose and toluene amendments to soil were used to stimulate the growth of a subset of the microbial community. A bacterial culture and bovine serum albumin (BSA) were added to the soil to qualitatively assess their recovery following extraction. Direct extraction and resolution of microbial proteins using SDS-PAGE generally resulted in smeared and unresolved banding patterns on gels. DGC–EXT of microbial protein from soil followed by separation using SDS-PAGE, however, did resolve six to 10 bands in the Benfield but not the Quitman soil. DGC–EXT of microbial protein, but not direct extraction following the addition of glucose and toluene, markedly increased the number of bands (~40) on the gels in both Benfield and Quitman soils. Low recoveries of added culture and BSA proteins using the direct extraction method suggest that proteins either bind to soil organic matter and mineral particles or that partial degradation takes place during extraction. Interestingly, DGC may have been preferentially selected for actively growing cells, as gauged by the 10–100× lower cy19:0/18:1ω7 ratio of the fatty acid methyl esters in the isolated community compared to that for the whole soil. DGC can be used to isolate soil communities and provide microbial protein that can be characterized using PAGE.     

Anthropogenic N deposition alters soil organic matter biochemistry and microbial communities on decaying fine roots

Fine root litter is a primary source of soil organic matter (SOM), which is a globally important pool of C that is responsive to climate change. We previously established that ~20 years of experimental nitrogen (N) deposition has slowed fine root decay and increased the storage of soil carbon (C; +18%) across a widespread northern hardwood forest ecosystem. However, the microbial mechanisms that have directly slowed fine root decay are unknown. Here, we show that experimental N deposition has decreased the relative abundance of Agaricales fungi (?31%) and increased that of partially ligninolytic Actinobacteria (+24%) on decaying fine roots. Moreover, experimental N deposition has increased the relative abundance of lignin‐derived compounds residing in SOM (+53%), and this biochemical response is significantly related to shifts in both fungal and bacterial community composition. Specifically, the accumulation of lignin‐derived compounds in SOM is negatively related to the relative abundance of ligninolytic Mycena and Kuehneromyces fungi, and positively related to Microbacteriaceae. Our findings suggest that by altering the composition of microbial communities on decaying fine roots such that their capacity for lignin degradation is reduced, experimental N deposition has slowed fine root litter decay, and increased the contribution of lignin‐derived compounds from fine roots to SOM. The microbial responses we observed may explain widespread findings that anthropogenic N deposition increases soil C storage in terrestrial ecosystems. More broadly, our findings directly link composition to function in soil microbial communities, and implicate compositional shifts in mediating biogeochemical processes of global significance.     

Impact of Ectomycorrhizosphere on the Functional Diversity of Soil Bacterial and Fungal Communities from a Forest Stand in Relation to Nutrient Mobilization Processes

The ectomycorrhizal symbiosis alters the physicochemical and biological conditions in the surrounding soil, thus creating a particular environment called ectomycorrhizosphere, which selects microbial communities suspected to play a role in gross production and nutrient cycling. To assess the ectomycorrhizosphere effect on the structure of microbial communities potentially involved in the mobilization of nutrients from the soil minerals in a poor-nutrient environment, we compared the functional diversity of soil and ectomycorrhizosphere bacterial communities in a forest stand. Two hundred and sixty-four bacterial strains and 107 fungal strains were isolated from the bulk soil of an oak (Quercus petraea) stand and from oak–Scleroderma citrinum ectomycorrhizosphere and ectomycorrhizae, in two soil organo-mineral horizons (0 to 3 cm and 5 to 10 cm). They were characterized using two in vitro tests related to their capacities to mobilize iron and phosphorus. We demonstrated that the oak–S. citrinum ectomycorrhizosphere significantly structures the culturable bacterial communities in the two soil horizons by selecting very efficient strains for phosphorus and iron mobilization. This effect was also observed on the diversity of the phosphate-solubilizing fungal communities in the lower soil horizon. A previous study already demonstrated that Laccaria bicolor–Douglas fir ectomycorrhizosphere structures the functional diversity of Pseudomonas fluorescens population in a forest nursery soil. Comparing to it, our work highlights the consistency of the mycorrhizosphere effect on the functional diversity of bacterial and fungal communities in relation to the mineral weathering process, no matter the fungal symbiont, the age and species of the host tree, or the environment (nursery vs forest). We also demonstrated that the intensity of phosphorus and iron mobilization by the ectomycorrhizosphere bacteria isolated from the lower soil horizon was significantly higher compared to that which was isolated from the upper horizon. This reveals for the first time a stratification of the functional diversity of the culturable soil bacterial communities as related to phosphorus and iron mobilization.     

Soil Water Content and Organic Carbon Availability Are Major Determinants of Soil Microbial Community Composition

Exploration of environmental factors governing soil microbial community composition is long overdue and now possible with improved methods for characterizing microbial communities. Previously, we observed that rice soil microbial communities were distinctly different from tomato soil microbial communities, despite management and seasonal variations within soil type. Potential contributing factors included types and amounts of organic inputs, organic carbon content, and timing and amounts of water inputs. Of these, both soil water content and organic carbon availability were highly correlated with observed differences in composition. We examined how organic carbon amendment (compost, vetch, or no amendment) and water additions (from air dry to flooded) affect microbial community composition. Using canonical correspondence analysis of phospholipid fatty acid data, we determined flooded, carbon-amended (+C) microcosm samples were distinctly different from other +C samples and unamended (–C) samples. Although flooding without organic carbon addition influenced composition some, organic carbon addition was necessary to substantially alter community composition. Organic carbon availability had the same general effects on microbial communities regardless of whether it was compost or vetch in origin. In addition, flooded samples, regardless of organic carbon inputs, had significantly lower ratios of fungal to bacterial biomarkers, whereas under drier conditions and increased organic carbon availability the microbial communities had higher proportions of fungal biomass. When comparing field and microcosm soil, flooded +C microcosm samples were most similar to field-collected rice soil, whereas all other treatments were more similar to field-collected tomato soil. Overall, manipulating water and carbon content selected for microbial communities similar to those observed when the same factors were manipulated at the field scale.     

Long-term Effect of Municipal Solid Waste Amendment on Microbial Abundance and Humus-associated Enzyme Activities Under Semiarid Conditions

Microbial ecology is the key to understanding the function of soil biota for organic matter cycling after a single amendment of organic waste in semiarid soils. Therefore, in this paper, the long-term effect (17 years) of adding different doses of a solid municipal waste to an arid soil on humus–enzyme complexes, a very stable and long-lasting fraction of soil enzymes, as well as on microbial and plant abundance, was studied. Humic substances were extracted by 0.1 M pH 7 sodium pyrophosphate from soil samples collected in experimental plots amended with different doses of a solid municipal waste (0, 65, 130, 195, and 260 t/ha) 17 years before. The activity of different hydrolases related with the C (β-glucosidase), N (urease), and P (alkaline phosphatase) cycles and with the formation of humic substances (o-diphenol oxidase) were determined in this extract. The density and diversity of plant cover in the plots, as well as the fungal and bacterial biomass (by analyzing phopholipid fatty acids) were also determined. In general, the amended plots showed greater humic substance-related enzymatic activity than the unamended plots. This activity increased with the dose but only up to a certain level, above which it leveled off or even diminished. Plant diversity and cover density followed the same trend. Fungal and bacterial biomass also benefited in a dose-dependent manner. Different signature molecules representing gram+ and gram− bacteria, and those corresponding to monounsaturated and saturated fatty acids showed a similar behavior. The results demonstrate that organic amendment had a noticeable long-term effect on the vegetal development, humic substances-related enzyme activity and on the development of bacteria and fungi in semiarid conditions.     

Response of Oxidative Enzyme Activities to Nitrogen Deposition Affects Soil Concentrations of Dissolved Organic Carbon

Recent evidence suggests that atmospheric nitrate (NO ₃ ⁻ ) deposition can alter soil carbon (C) storage by directly affecting the activity of lignin-degrading soil fungi. In a laboratory experiment, we studied the direct influence of increasing soil NO ₃ ⁻ concentration on microbial C cycling in three different ecosystems: black oak–white oak (BOWO), sugar maple–red oak (SMRO), and sugar maple–basswood (SMBW). These ecosystems span a broad range of litter biochemistry and recalcitrance; the BOWO ecosystem contains the highest litter lignin content, SMRO had intermediate lignin content, and SMBW leaf litter has the lowest lignin content. We hypothesized that increasing soil solution NO ₃ ⁻ would reduce lignolytic activity in the BOWO ecosystem, due to a high abundance of white-rot fungi and lignin-rich leaf litter. Due to the low lignin content of litter in the SMBW, we further reasoned that the NO ₃ ⁻ repression of lignolytic activity would be less dramatic due to a lower relative abundance of white-rot basidiomycetes; the response in the SMRO ecosystem should be intermediate. We increased soil solution NO ₃ ⁻ concentrations in a 73-day laboratory incubation and measured microbial respiration and soil solution dissolved organic carbon (DOC) and phenolics concentrations. At the end of the incubation, we measured the activity of β-glucosidase, N-acetyl-glucosaminidase, phenol oxidase, and peroxidase, which are extracellular enzymes involved with cellulose and lignin degradation. We quantified the fungal biomass, and we also used fungal ribosomal intergenic spacer analysis (RISA) to gain insight into fungal community composition. In the BOWO ecosystem, increasing NO ₃ ⁻ significantly decreased oxidative enzyme activities (−30% to −54%) and increased DOC (+32% upper limit) and phenolic (+77% upper limit) concentrations. In the SMRO ecosystem, we observed a significant decrease in phenol oxidase activity (−73% lower limit) and an increase in soluble phenolic concentrations (+57% upper limit) in response to increasing NO ₃ ⁻ in soil solution, but there was no significant change in DOC concentration. In contrast to these patterns, increasing soil solution NO ₃ ⁻ in the SMBW soil resulted in significantly greater phenol oxidase activity (+700% upper limit) and a trend toward lower DOC production (−52% lower limit). Nitrate concentration had no effect on microbial respiration or β-glucosidase or N-acetyl-glucosaminidase activities. Fungal abundance and basidiomycete diversity tended to be highest in the BOWO soil and lowest in the SMBW, but neither displayed a consistent response to NO ₃ ⁻ additions. Taken together, our results demonstrate that oxidative enzyme production by microbial communities responds directly to NO ₃ ⁻ deposition, controlling extracellular enzyme activity and DOC flux. The regulation of oxidative enzymes by different microbial communities in response to NO ₃ ⁻ deposition highlights the fact that the composition and function of soil microbial communities directly control ecosystem-level responses to environmental change.