Linking soil N2O emissions with soil microbial community abundance and structure related to nitrogen cycle in two acid forest soils

Plant and Soil - Tree species and seasonal change influence N2O flux and microbial communities, but the mechanisms are unclear. We studied N2O flux in soils planted with slash pine and oil-seed...     

暖温带森林土壤微生物量、群落结构和活性对植物地下碳源的响应

该研究以典型的亚热带—温带过渡区森林为对象,采用野外过程监测和控制试验相结合的方法,利用磷脂脂肪酸和土壤胞外酶活性分别表征土壤微生物群落结构和活性,并结合微环境因子,重点探究土壤微生物生物量、群落结构和活性对植物地下碳输入的响应特征。结果表明：在观测周期内,处理均能显著降低三组年龄段林分的土壤微生物量碳,其变化幅度在－8.72％~－5.72％之间,其中在80年的林分中降幅最大,而在160年的林分中降幅最小;微生物量氮的变化规律与相应的微生物量碳的变化规律相似,但与对照相比其差异性均未达到显著性水平;另外,经壕沟处理2~4个月后,所有林分的土壤微生物量碳和氮与对照相比出现增加的现象。处理均能对三组年龄段林分的土壤微生物群落结构产生不同程度的影响,其中40年林分的土壤微生物群落对处理的响应程度要高于另外两个年龄段的林分;与对照相比,壕沟处理样方的腐生真菌的相对丰富度均下降明显,其中在40年和80年林分中的下降幅度达到显著水平,而细菌、放线菌和丛枝菌根真菌均无明显变化;壕沟处理样方的水解酶(β-葡萄糖苷酶和N-乙酰-葡萄糖苷酶)活性均显著下降,而氧化酶(酚氧化酶和过氧化物酶)活性的变化相对较小,除80年的林分外,其余林分均不显著。此外,处理均不能显著影响土壤的含水量和温度。该研究结果为初步阐明全球气候变化背景下森林土壤微生物结构及其功能的变化特征以及更加精确预测未来森林土壤碳的变化趋势提供了科学依据。     

Effects of wear and above ground forest site type characteristics on the soil microbial community structure in an urban setting

We studied the effects of wear on the understorey vegetation and the soil microbial community structure (phospholipid fatty acid pattern) in urban forests of medium fertility and of varying size in the capital area of Finland, Helsinki. These forests are important sites of recreation for a large number of residents. Consequently, the cover of understorey vegetation is affected by trampling. In the study, the cover of ground layer plant species (mosses) was found to be lower than in rural reference areas. We found that microbial activity, measured as soil respiration, was lower in the most worn forest patches as compared to less worn sites. Further, the microbial community structure of the humus layer changed due to the effects of wear. By comparing the PLFA pattern in trampled and un-trampled forest patches, we found out that the most important factors affecting the structure of microbial community were the dominant tree species (the proportion of broad-leaved tree species in relation to conifers), and the composition of the understorey vegetation. Thus, we could conclude that wear affects the microbial community structure through changes in vegetation, in the quality of litter shed, and through resultant changes in the humus pH, rather than only through soil compaction.     

长期不同施肥制度对潮棕壤微生物生物量碳、氮及细菌群落结构的影响

以沈阳生态站长期定位试验为研究平台,采用传统氯仿熏蒸方法和现代PCR-DGGE技术探讨了长期不同施肥制度对土壤微生物生物量碳和氮及细菌群落结构的影响.结果表明:在整个试验期,土壤微生物生物量碳和氮的动态变化趋势基本相同;长期施用有机肥可显著提高土壤有机碳和土壤微生物生物量碳和氮含量,而长期施用化肥明显降低土壤pH,土壤微生物生物量碳和氮含量也显著降低.DGGE图谱表明:不同施肥处理的细菌16S rDNA多数条带分布相同,28条带中有18条为共有条带,说明潮棕壤中细菌类群较稳定,但其数量受到施肥的影响;长期施用有机肥促进潮棕壤细菌群落结构的多样性,而施用化肥处理则降低了其多样性.     

The effects of stubble retention and nitrogen application on soil microbial community structure and functional gene abundance under irrigated maize

The effects of agronomic management practices on the soil microbial community were investigated in a maize production system in New South Wales, Australia. The site has been intensively studied to measure the impact of stubble management and N-fertilizer application on greenhouse gas emissions (CO(2) and N(2)O), N-cycling, pathology, soil structure and yield. As all of these endpoints can be regulated by microbial processes, the microbiology of the system was examined. Soil samples were taken after a winter fallow period and the diversity of the bacterial and fungal communities was measured using PCR-denaturing gradient gel electrophoresis. Stubble and N shifted the structure of bacterial and fungal communities with the primary driver being stubble addition on the fungal community structure (P<0.05 for all effects). Changes in C, N (total and NO(3)), K and Na, were correlated (P<0.05) with variation in the microbial community structure. Quantitative PCR showed that nifH (nitrogen fixation) and napA (denitrification) gene abundance increased upon stubble retention, whereas amoA gene numbers were increased by N addition. These results showed that the management of both stubble and N have significant and long-term impacts on the size and structure of the soil microbial community at phylogenetic and functional levels.     

干旱区高寒湿地逆行演替下土壤微生物群落结构的研究

【目的】探究高寒湿地逆行演替对土壤性质与微生物群落结构的影响。【方法】以新疆巴音布鲁克天鹅湖高寒湿地为研究对象,依托逆行演替典型样带(沼泽-沼泽化草甸-草甸),利用高通量测序技术分析各演替区土壤微生物群落结构。【结果】高寒湿地逆行演替改变了土壤微生物在分类操作单元(operational taxonomic unit,OTU)水平上的物种组成,致使草甸区的微生物ACE、Chao1、Simpson、Shannon多样性指数显著低于沼泽区和沼泽化草甸区(P<0.05);随着演替发生,变形菌门(Proteobacteria)、酸杆菌门(Acidobacteria)、拟杆菌门(Bacteroidetes)、子囊菌门(Ascomycota)的相对丰度均减少,放线菌门(Actinobacteria)、芽单胞菌门(Gemmatimonadetes)、担子菌门(Basidiomycota)、被孢霉门(Mortierellomycota)的相对丰度增加;主坐标法分析(principal coordinates analysis,PCoA)排序分析显示,土壤微生物群落在各逆行演替都出现不同程度的离散...     

Litter fingerprint on microbial biomass,activity, and community structure in the underlying soil

Aims

Little is known about how plant leaf litter decomposing on the soil surface is affecting microbial communities in the underlying soil. Here we examined the effects of decomposing leaf litter of different initial chemistry on biomass, stoichiometry, community structure and activity of microorganisms in the soil underneath the decaying litter layer.

Methods

Leaf litter from six different neotropical tree species with contrasted quality decomposed on top of a common tropical soil in a laboratory microcosm experiment over 98 days. At the end of the experiment we determined microbial biomass C, N, and P, microbial community structure (PLFA), and community level physiological profiles (CLPP) from the top soil.

Results

Despite growing in a common soil substrate, soil microorganisms were strongly affected by litter species, especially by the soluble litter fraction. While litters with low soluble C content did not affect the soil microbial community, litters with high soluble C content led to an increase of microbial biomass and to a structural shift to relatively more Gram-negative bacteria. Changing community structure resulted in changes of catabolic capacity of microorganisms to metabolize a range of different C substrates. The large differences in leachate N and P among litter species, in contrast, had no effect on soil microbial parameters.

Conclusions

Our data suggest that plant litter decomposing on the soil surface exhibit a strong and predictable leachate C-control over microbial community biomass, structure and function in the underlying soil.

     

Broad-scale approaches to the determination of soil microbial community structure: Application of the community DNA hybridization technique

Broad-scale approaches seek to integrate information on whole microbial communities. It is widely recognized that culture techniques are too selective and unrepresentative to allow a realistic assessment of the overall structure of microbial communities. Techniques based on fatty acid or metabolic profiles determine the phenotypic composition of the community. Complementary information about the genotypic structure of soil microbial communities necessitates analysis of community DNA. To determine broad-scale differences in soil microbial community structure (i.e., differences at the whole community level, rather than specific differences in species composition), we have applied a community hybridization technique to determine the similarity and relative diversity of two samples by cross hybridization. In previous studies this assay failed with whole-soil community DNA. Usable hybridization signals were obtained using whole-soil DNA, in this study, by digesting the DNA with restriction enzymes before the labeling with a random-primer reaction. The community hybridization technique was tested using a graded series of microbial fractions, increasing in complexity, all isolated from the same soil sample. This demonstrated that single bacterial species and a mixture of cultivable bacteria were less complex and only 5% similar to whole-community DNA or bacteria directly extracted from the soil. Extracted bacterial and whole-community DNA were 75% similar to each other and equally complex. When DNA was extracted from four different agricultural soils, their similarities ranged from 35 to 75%. The potential usefulness of community hybridization applied to soil microbial communities is discussed.     

Response of microbial community structure to natural and accelerated hydrarch successions in the boreal wetlands in northern Hokkaido, Japan

We estimated the effect of invading Sasa vegetation and accelerated terrestrialization on the microbial community structure in Sarobetsu-genya wetland (SGW) and Nakanominedaira wetland (NW) (original vegetation, Sphagnum). All examined peat-pore water samples were acidic. Electrical conductivity significantly differed between SGW and NW. Nonmetric multidimensional scaling (NMDS) and analysis of similarity based on denaturing gradient gel electrophoresis (DGGE) band patterns revealed differences in the bacterial community structure between the Sasa and Sphagnum vegetations at a depth of 10 cm in NW. In contrast, the bacterial NMDS profiles at all depths differed between the 2 wetlands rather than between the 2 vegetations. The archaeal community structure significantly differed between the wetlands at depths of 30 and 50 cm. The bacterial diversity index derived from the DGGE profiles significantly differed between the wetlands at all depths. The archaeal diversity index significantly differed between the wetlands at a depth of 50 cm. Sasa invasion affected the microbial community structure in the rhizosphere, up to a depth of 10 cm; this effect differed with the terrestrialization speed. These results suggest that in peat bogs subjected to artificially accelerated terrestrialization, the microbial community changes before the occurrence of the natural hydrarch ecological succession involving ground vegetation.     

Behaviour and recovery of the secondary metabolite batatasin-III from boreal forest humus: influence of temperature,humus type and microbial community

Batatasin-III (3,3′-dihydroxy-5-methoxybibenzyl) produced by Empetrum hermaphroditum has been identified as the main metabolite responsible for the chemical interference exerted by the shrub on the surrounding vegetation in the boreal forest of northern Sweden. In earlier studies, batatasin-III has been found to be present in both soil and soil solutions. However, to understand the actual mechanisms by which batatasin-III may interact, we need to know more about the fate and behaviour of the compound in soil. In order to achieve this, we firstly evaluated the efficiency of different extraction methods in recovering batatasin-III from Empetrum humus and found that the highest yield was obtained using ethyl acetate (6.57 ± 20 μg g⁻¹ HDM, least square mean ± SE). In contrast, no detectable amounts of batatasin-III were obtained when extracting the humus with distilled water, 0.125 M citric acid or 0.05 M NaOH. Secondly, we performed a series of experiments in which the recovery of batatasin-III was determined from humus samples exposed to different treatments. In summary, the recovery of batatasin-III was found to be initially strongly dependent on humus type (i.e. humus collected from under a cover of Empetrum, Vaccinium or forest herbs) as well as the temperature and the length of the incubation period. The amount of recovered batatasin-III was in general highest from the Empetrum humus and lowest from the herb humus, contrary to our hypothesis that microorganisms might be better adapted to batatasin-III in humus of the Empetrum origin than in humus of other origin. Regardless of humus type, the recovery was generally higher at +2 °C than at +18 °C suggesting that microbial degradation of batatasin-III did occur. However, when the recovery of batatasin-III from sterile and non-sterile humus was compared, microbial degradation was found to be of minor importance. In addition, no phenolic degradation products of batatasin-III were detected after batatasin-III had been added to non-sterile humus. The obtained results suggest that batatasin-III, when released into humus, becomes physically trapped by organic matter and metabolized by soil microbes to a less extent.     

Impact of the plant community composition on labile soil organic carbon, soil microbial activity and community structure in semi-natural grassland ecosystems of different productivity

Aims

The main objective was to describe the effects of plant litter on SOC and on soil microbial activity and structure in extensively managed grasslands in Central Germany that vary in biomass production and plant community composition.

Methods

The decomposition of shoot and root litter was studied in an incubation experiment. Labile C and N were isolated by hot water extraction (C_HWE, N_HWE), while functional groups of microbes were identified by PLFA analysis and microbial activity was measured using a set of soil exo-enzymes.

Results

The plant community composition, particulary legume species affected SOC dynamics and below-ground microbial processes, especially via roots. This was reflected in about 20% lower decomposition of root litter in low productivity grassland soil. The C_HWE soil pool was found to be a key driver of the below-ground food web, controlling soil microbial processes.

Conclusions

Below-ground responses appear to be related to the presence of legume species, which affected the microbial communities, as well as the ratio between fungal and bacterial biomass and patterns of soil enzyme activity. Low productivity fungal-dominated grasslands with slow C turnover rates may play an important role in SOC accumulation. The approach used here is of particular importance, since associated biological and biochemical processes are fundamental to ecosystem functioning.     

Nutritional enrichment of a microbial community: The effects on activity, elemental composition, community structure and virus production

Abstract Viruses are active members of the microbial community in natural waters but little is known about the factors that regulate their activity and production. In this study we have investigated the effects of increased availability of organic nutrients and inorganic phosphate on activity, elemental composition, community structure and virus production in a natural bacterial community. The fraction of active cells in the community as estimated from microautoradiography of cells assimilating ³H-labeled thymidine ranged from 0–22%, but changes in the elemental composition of the cells indicated that more than 90% of the cells were active. The increase in carbon and energy availability stimulated virus production more than bacterial biomass production, while the increase in phosphate availability stimulated biomass production rather than virus production. A decrease in morphological diversity of the bacterial community was paralleled by a reduction in the virus-to-bacteria ratio (VBR) but the relationship between bacterial diversity and viral activity is uncertain. Our general conclusion is that nutrient availability, in addition to the bacterial activity, also affects the viral activity, and that both of these may affect the structure and diversity of the bacterial community.     

生姜水浸液对生姜幼苗根际土壤酶活性、微生物群落结构及土壤养分的影响

本文以生姜为材料,研究生姜不同部位（根茎、茎和叶）、不同浓度（10、20、40和80 g L-1）的水浸液对生姜幼苗根际土的微生物数量、土壤酶活性及土壤养分含量的影响,并通过HPLC定量分析了生姜各部位水浸液中所含酚酸类（香草酸、丁香酸、对羟基苯甲酸、香豆酸和阿魏酸）、香豆素类（伞花内脂和7-甲氧基香豆素）化合物的含量。结果表明：三种生姜水浸液对所测六种土壤酶活性均产生了不同程度的影响,其中影响最大的是酸性磷酸酶和蔗糖酶,在10 g L-1 时就达到了显著性差异水平,并且所有酶均有随着水浸液浓度的增加而呈增大的趋势;相同部位的水浸液随着浓度的增加,细菌和真菌的数量呈增加趋势,而放线菌的数量呈减少趋势;三种生姜水浸液均随着浓度的增加降低了土壤中有机质的含量,加剧了土壤中硝态氮含量的积累,根茎水浸液对土壤有效磷、速效钾和铵态氮均显示出低浓度提高其含量而高浓度降低其含量的趋势,而茎和叶水浸液则随着浓度的增加均降低了其含量。生姜水浸液中主要化感成分包括：根茎水浸液主要是丁香酸和伞花内脂;茎水浸液主要是阿魏酸,且其含量最高为73.4 ug/g;叶水浸液除了阿魏酸,其他六种物质均被检测出,但含量较高的主要有丁香酸、伞花内脂和香豆酸。     

The influence of soil frost on the quality of dissolved organic carbon in a boreal forest soil: combining field and laboratory experiments

Riparian soils exert a major control on stream water dissolved organic carbon (DOC) in northern latitudes. As the winter climate in northern regions is predicted to be particularly affected by climate change, we tested the sensitivity of DOC formation to winter conditions in riparian soils using an 8?year field-scale soil frost manipulation experiment in northern Sweden. In conjunction with the field experiment, we also carried out a laboratory experiment based on three levels of four winter climatic factors: frost intensity, soil water content, frost duration and frequency of freeze–thaw cycles. We evaluated changes in lability of DOC in soil solution from lysimeter samples taken at different depths (10–80?cm) as well as from DOC extracted from soils in the laboratory, using carbon-specific ultraviolet absorbance at 254?nm (sUVA₂₅₄). In the field, significantly more labile DOC was observed during the spring and summer from upper horizons of frost-exposed soils, when compared to controls. In addition, the amount of labile DOC was positively correlated with frost duration at a soil depth of 10?cm. In the laboratory, frost intensity was the factor that had the greatest positive influence on DOC lability; it also reduced the C:N ratio which may indicate a microbial origin of the DOC. The laboratory experiment also demonstrated significant interactions between some of the applied climatic factors, such as frost intensity interacting with water content. In combination, field and laboratory experiments demonstrate that winter soil conditions have profound effects on DOC-concentration and quality during subsequent seasons.     

Changes in the microbial community structure of bacteria,archaea and fungi in response to elevated CO2 and warming in an Australian native grassland soil

The microbial community structure of bacteria, archaea and fungi is described in an Australian native grassland soil after more than 5 years exposure to different atmospheric CO₂ concentrations ([CO₂]) (ambient, + 550 ppm) and temperatures (ambient, + 2°C) under different plant functional types (C ₃ and C ₄ grasses) and at two soil depths (0–5 cm and 5–10 cm). Archaeal community diversity was influenced by elevated [CO₂], while under warming archaeal 16S rRNA gene copy numbers increased for C ₄ plant Themeda triandra and decreased for the C ₃ plant community (P < 0.05). Fungal community diversity resulted in three groups based upon elevated [CO₂], elevated [CO₂] plus warming and ambient [CO₂]. Overall bacterial community diversity was influenced primarily by depth. Specific bacterial taxa changed in richness and relative abundance in response to climate change factors when assessed by a high‐resolution 16S rRNA microarray (PhyloChip). Operational taxonomic unit signal intensities increased under elevated [CO₂] for both Firmicutes and Bacteroidetes, and increased under warming for Actinobacteria and Alphaproteobacteria. For the interaction of elevated [CO₂] and warming there were 103 significant operational taxonomic units (P < 0.01) representing 15 phyla and 30 classes. The majority of these operational taxonomic units increased in abundance for elevated [CO₂] plus warming plots, while abundance declined in warmed or elevated [CO₂] plots. Bacterial abundance (16S rRNA gene copy number) was significantly different for the interaction of elevated [CO₂] and depth (P < 0.05) with decreased abundance under elevated [CO₂] at 5–10 cm, and for Firmicutes under elevated [CO₂] (P < 0.05). Bacteria, archaea and fungi in soil responded differently to elevated [CO₂], warming and their interaction. Taxa identified as significantly climate‐responsive could show differing trends in the direction of response (‘+’ or ‘?’) under elevated CO₂ or warming, which could then not be used to predict their interactive effects supporting the need to investigate interactive effects for climate change. The approach of focusing on specific taxonomic groups provides greater potential for understanding complex microbial community changes in ecosystems under climate change.     

海南尖峰岭热带林土壤动物群落——群落结构的季节变化及其气候因素

对土壤原生动物、线虫和其它大中型土壤动物等3个部分,分别描述群落的季节变化,然后,综合分析气候因素对群落的影响。①原生动物群落的季节化表现为：种数在1、2月份最高,达43、44种;个体数量则在8月份和12月份（14万多和12万多/g.干土）。②线早的种数也在1月份最高,达67种;个体数则在9月份（88.3万/m^2）;DG指数显示出有9月份的大高峰（19.9）和1月份的小高峰（19.7）。③大中型土壤动物群落的季节变化幅度很大：类群数的大高峰在7月份（31个）,小高峰在12月份（17种）;个体数量则在6月份和11月份（5.8万个和1.05万个/m^2）。④气温与地表温度对群落变化的影响较小：对线虫的种数变化有显著负相关;对原生动物、大中型土壤动物种数变化也只有阶段性的相关。⑤土壤含水量对群落变化的影响较大：与原生动物丰度呈非常显著的相关（r=0.896,d?=10,r0.01=0.708）;与其它大中型土壤动物的类群数、总个体数及DG指数的影响则具有季节性差异,即在湿季呈显著的负相关。⑥降水量年内和年间的变化均具很大的不稳定性,暴雨又是土壤动物（除原生动物外）灾难性的因素。因此降水量的变化是造成群落跳跃式波动和大起大落的主要因素。     

The short-term effects of surface soil disturbance on soil bacterial community structure at an experimental site near Scott Base, Antarctica

Humans are visiting Antarctica in increasing numbers, and the ecological effect of rapid soil habitat alteration due to human-induced physical disturbance is not well understood. An experimental soil disturbance trial was set up near Scott Base on Ross Island, to investigate the immediate and short-term changes to bacterial community structure, following surface soil disturbance. Three blocks, each comprising an undisturbed control, and an area disturbed by removing the top 2 cm of soil, were sampled over a time series (0, 7, 14, 21, and 35 days), to investigate changes to bacterial community structure using DNA profiling by terminal restriction fragment length polymorphism. The simulated disturbance did not cause any major shifts in the structure of the bacterial communities over the 35-day sampling period. Ordination showed that the bacterial community composition correlated strongly with soil EC (R ² = 0.55) and soil pH (R ² = 0.67), rather than the removal of the top 2 cm of surface material. Although the replicate blocks were visually indistinguishable from one another, high local spatial variability of soil chemical properties was found at the study site and different populations of bacterial communities occurred within 2 m of one another, within the same landscape unit. Given the current knowledge of the drivers of bacterial community structure, that is, soil EC, soil pH, and soil moisture content, a follow-up investigation incorporating DNA and RNA-based analyses over a time frame of 2–3 years would lead to a greater understanding of the effects of soil disturbance on bacterial communities.