Dynamics of C, N, P and microbial community composition in particulate soil organic matter during residue decomposition

Decomposing residues can be an important source of nutrients for plants, especially of N and P, but the relationship between N and P release and microbial community dynamics have rarely been studied. Two pea (Pisum sativum L.) residues with contrasting chemical composition, shoots from flowering pea (Pea-Y) with 2.9 mg P and 36 mg N kg⁻¹ and from mature pea (Pea-M) with 0.3 mg P and 13 mg N kg⁻¹, were added at a rate of 20 g kg soil⁻¹ to a sandy soil low in nutrients. Particulate organic matter (POM) was isolated on days (d) 0, 5, 15, 28, 42 and 61 after residue addition and analysed for C, N, P and microbial community structure (fatty acid methyl ester analysis). The recovery of POM from residue-amended soils decreased over time to 30–40% of added amounts for both residues. Apart from d 0, the N concentration in POM was lower in residue-amended soil than in the control. Due to a rapid decrease in P concentration during the first 5 days in Pea-Y and a slow increase over the whole experiment in Pea-M, P concentrations in POM on d 61 were similar in all treatments. In Pea-Y, the dynamics of C, N and P were coupled, with amounts of C, N and P decreasing during the first 15 days and remaining stable thereafter. In Pea-M, a steady loss of C from POM was contrasted by a slight increase in P. As a result, the C/P ratio decreased from 1,330 on d 0 to 390 on d 61. The C/N ratio of Pea-M decreased only during the second phase of decomposition. The different nutrient dynamics in Pea-Y and Pea-M led to similar amounts of N and P in POM towards the end of the incubation. Microbial community composition in the POM in Pea-Y and Pea-M remained distinct from the control, even though it changed over time. POM was shown to be an important source of potentially available nutrients after addition of plant residues. In the unamended soil, stable nutrient amounts in POM suggested very low net nutrient release from native POM compared to POM after residue addition.     

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.     

凋落物多样性及组成对凋落物分解和土壤微生物群落的影响

凋落物分解是生态系统营养物质循环的核心过程,而土壤微生物群落在凋落物分解过程中扮演着极其重要且不可替代的角色。随着生物多样性的丧失日益严峻,探讨凋落物多样性及组成对凋落物分解和土壤微生物群落的影响,不仅有助于了解凋落物分解的内在机制,而且可为退化草原生态系统的恢复提供参考。以内蒙古呼伦贝尔草原退化恢复群落中的草本植物为研究对象,依据植物多度、盖度、频度和物种的重要值及其在群落中的恢复程度筛选出排序前4的羊草（Leymus chinensis）、茵陈蒿（Artemisia capillaris）、麻花头（Serratula centauroides）、二裂委陵菜（Potentilla bifurca）的凋落物为实验材料,通过设置3种凋落物多样性水平（1,2,4）,包括11种凋落物组合（单物种凋落物共4种,两物种凋落物混合共6种,四物种凋落物混合共1种）,利用磷脂脂肪酸（PLFA）方法来研究分解60 d后凋落物多样性及组成对凋落物分解和土壤微生物群落的影响。结果表明：（1）凋落物物种多样性仅对C残余率具有显著影响,表现在两物种混合凋落物C残余率显著低于单物种凋落物,而凋落物组成对所观测的4个凋落物分解参数（质量、C、N残余率以及C/N）均具有显著影响;（2）凋落物物种多样性对细菌（B）含量具有显著影响,而凋落物组成对真菌（F）含量具有显著影响,两者对F/B以及微生物总量均无显著影响;（3）冗余分析结果表明凋落物组成与凋落物分解相关指标（凋落物质量、C、N残余率及C/N）和土壤微生物（真菌、细菌含量）的相关关系高于凋落物多样性。（4）进一步建立结构方程模型（Structural Equation Model,SEM）发现,凋落物初始C含量对凋落物质量、C、N残余率及C/N有显著正的直接影响;凋落物木质素含量对凋落物质量、C、N残余率有显著正的直接影响;凋落物初始N含量对N残余率有显著正的直接影响,而对C残余率及C/N有显著负的直接影响;凋落物初始C/N对凋落物质量、N残余率有显著正的直接影响,而对C/N有显著负的直接影响。此外,凋落物初始C、N、木质素含量及C/N均对真菌含量具有显著正影响,并可通过真菌对凋落物质量分解产生显著负的间接影响。以上结果表明该退化恢复区域优势种凋落物分解以初始C、木质素为主导,主要通过土壤真菌影响凋落物的分解进程,这将减缓凋落物的分解速率进而减慢草原生态系统的进程。这些结果为凋落物多样性及组成对自身分解和土壤微生物群落的影响提供了实验依据,也为进一步分析凋落物分解内在机制以及草原生态系统的恢复提供了数据参考。     

Empirical evidence that soil carbon formation from plant inputs is positively related to microbial growth

Plant-carbon inputs to soils in the form of dissolved sugars, organic acids and amino acids fuel much of heterotrophic microbial activity belowground. Initial residence times of these compounds in the soil solution are on the order of hours, with microbial uptake a primary removal mechanism. Through microbial biosynthesis, the dissolved compounds become dominant precursors for formation of stable soil organic carbon. How the chemical class (e.g. sugar) of a dissolved compound influences stabilization in field soils is unknown and predictions from our understanding of microbial metabolism, turnover and identity are contradictory. We show that soil carbon formation, from chronic amendments of dissolved compounds to fertilized and unfertilized grasslands, is 2.4-times greater from a sugar than an amino acid. Formation rates are negatively correlated with respiration rates of the compounds, and positively correlated with their recovery in microbial biomass. These relationships suggest that the efficiency of microbial growth on a compound is positively related to formation rates of soil organic carbon. Fertilization does not alter these findings, but together nitrogen and phosphorus additions reduce soil carbon formation. Our results highlight the need to consider both nutrient enrichment and global-change induced shifts in the form of dissolved root inputs to soils to predict future soil carbon stocks and hence phenomena such as climate warming and food security to which these stock sizes are intimately tied.     

Dynamics of the methanogenic archaeal community during plant residue decomposition in an anoxic rice field soil

Incorporation of plant residues strongly enhances the methane production and emission from flooded rice fields. Temperature and residue type are important factors that regulate residue decomposition and CH(4) production. However, the response of the methanogenic archaeal community to these factors in rice field soil is not well understood. In the present experiment, the structure of the archaeal community was determined during the decomposition of rice root and straw residues in anoxic rice field soil incubated at three temperatures (15 degrees C, 30 degrees C, and 45 degrees C). More CH(4) was produced in the straw treatment than root treatment. Increasing the temperature from 15 degrees C to 45 degrees C enhanced CH(4) production. Terminal restriction fragment length polymorphism analyses in combination with cloning and sequencing of 16S rRNA genes showed that Methanosarcinaceae developed early in the incubations, whereas Methanosaetaceae became more abundant in the later stages. Methanosarcinaceae and Methanosaetaceae seemed to be better adapted at 15 degrees C and 30 degrees C, respectively, while the thermophilic Methanobacteriales and rice cluster I methanogens were significantly enhanced at 45 degrees C. Straw residues promoted the growth of Methanosarcinaceae, whereas the root residues favored Methanosaetaceae. In conclusion, our study revealed a highly dynamic structure of the methanogenic archaeal community during plant residue decomposition. The in situ concentration of acetate (and possibly of H(2)) seems to be the key factor that regulates the shift of methanogenic community.     

土壤微生物群落对枯落物输入的响应

枯落物分解在陆地生态系统物质循环能量流动中起着关键性作用,明确枯落物输入对土壤微生物群落的影响有助于理解土壤微生物生物多样性和陆地生态系统功能的相互关系。本文采用整合分析方法,以中国为研究区域,以不添加枯落物为对照组,探究土壤微生物(真菌、细菌、放线菌)及微生物生物量碳、生物量氮对枯落物输入的响应。结果表明:与不添加枯落物相比,添加枯落物后土壤微生物生物量碳、生物量氮分别显著增加3.9%和4.4%;土壤真菌PLFA、细菌PLFA及总微生物PLFA分别增加4.0%、3.1%和2.4%。枯落物输入对土壤微生物的影响受到气候条件、年降水量、植被类型及土壤酸碱度等因素的显著影响;不同气候类型下,土壤微生物对枯落物输入的响应呈现出亚热带季风气候区>温带季风气候区>温带大陆气候区的趋势,以及随着年降水量的增加呈现出先升高后降低的趋势;不同植被类型下,土壤微生物对枯落物输入的响应呈现出阔叶林>草地≈混交林>针叶林的趋势。     

Tritrophic interactions in a soil community enhance decomposition rates

Microbivorous soil fauna can influence decomposition rates by regulating biomass and composition of the microbial community. The idea that predators at higher trophic levels regulate population densities of microbivorous fauna and thus indirectly increase microbial growth and activity has often been suggested but rarely examined in soil ecosystems. In this paper the effects of tritrophic interactions on decomposition processes in the soil are studied and expressed as soil respiration, hyphal lengths, cellulase and chitinase activities. The experiments were carried out in soil microcosms in a factorial design with three fungal species ( Alternaria alternata , Fusarium oxysporum , Trichoderma viride ), the fungivorous collembolan Folsomia fimetaria and the predatory mite Hypoaspis aculeifer . The respiration rate was significantly higher with three trophic levels than in those with two and lowest in those with only fungi present. This indicates that a low level of grazing stimulates microbial respiration more than a high level or no grazing at all. The effect was similar for all three fungal species but most pronounced in microcosms with the fungus A. alternata which was a preferred food source by the collembolans. Hyphal lengths were in all cases but with T. viride reduced in the presence of collembolans and predatory mites. T. viride had a slightly higher chitinase activity than the other fungi but increased numbers of trophic levels did not affect the enzymatic activities of any of the fungi.     

Increases in soil respiration following labile carbon additions linked to rapid shifts in soil microbial community composition

Organic matter decomposition and soil CO₂ efflux are both mediated by soil microorganisms, but the potential effects of temporal variations in microbial community composition are not considered in most analytical models of these two important processes. However, inconsistent relationships between rates of heterotrophic soil respiration and abiotic factors, including temperature and moisture, suggest that microbial community composition may be an important regulator of soil organic matter (SOM) decomposition and CO₂ efflux. We performed a short-term (12-h) laboratory incubation experiment using tropical rain forest soil amended with either water (as a control) or dissolved organic matter (DOM) leached from native plant litter, and analyzed the effects of the treatments on soil respiration and microbial community composition. The latter was determined by constructing clone libraries of small-subunit ribosomal RNA genes (SSU rRNA) extracted from the soil at the end of the incubation experiment. In contrast to the subtle effects of adding water alone, additions of DOM caused a rapid and large increase in soil CO₂ flux. DOM-stimulated CO₂ fluxes also coincided with profound shifts in the abundance of certain members of the soil microbial community. Our results suggest that natural DOM inputs may drive high rates of soil respiration by stimulating an opportunistic subset of the soil bacterial community, particularly members of the Gammaproteobacteria and Firmicutes groups. Our experiment indicates that variations in microbial community composition may influence SOM decomposition and soil respiration rates, and emphasizes the need for in situ studies of how natural variations in microbial community composition regulate soil biogeochemical processes.     

植物、土壤及土壤管理对土壤微生物群落结构的影响

土壤微生物是土壤生态系统的重要组成部分,对土壤微生物群落结构多样性的研究是近年来土壤生态学研究的热点。本文综述了有关植物、土壤类型以及土壤管理措施对土壤微生物群落结构影响的最新研究结果,指出植物的作用因植物群落结构多样性、植物种类、同种植物不同的基因型,甚至同一植物不同根的区域而异;而土壤的作用与土壤质地和有机质含量等因素有关;植物和土壤类型在对土壤微生物群落结构影响上的作用存在互作关系。不同的土壤管理措施对土壤微生物群落结构影响较大,长期连作、大量的外援化学物质的应用降低了土壤微生物的多样性;而施用有机肥、免耕可以增加土壤微生物群落结构多样性,有利于维持土壤生态系统的功能。     

Mycorrhizal mediation of plant N acquisition and residue decomposition: Impact of mineral N inputs

Mycorrhizas are ubiquitous plant–fungus mutualists in terrestrial ecosystems and play important roles in plant resource capture and nutrient cycling. Sporadic evidence suggests that anthropogenic nitrogen (N) input may impact the development and the functioning of arbuscular mycorrhizal (AM) fungi, potentially altering host plant growth and soil carbon (C) dynamics. In this study, we examined how mineral N inputs affected mycorrhizal mediation of plant N acquisition and residue decomposition in a microcosm system. Each microcosm unit was separated into HOST and TEST compartments by a replaceable mesh screen that either prevented or allowed AM fungal hyphae but not plant roots to grow into the TEST compartments. Wild oat (Avena fatua L.) was planted in the HOST compartments that had been inoculated with either a single species of AM fungus, Glomus etunicatum, or a mixture of AM fungi including G. etunicatum. Mycorrhizal contributions to plant N acquisition and residue decomposition were directly assessed by introducing a mineral ¹⁵N tracer and ¹³C‐rich residues of a C₄ plant to the TEST compartments. Results from ¹⁵N tracer measurements showed that AM fungal hyphae directly transported N from the TEST soil to the host plant. Compared with the control with no penetration of AM fungal hyphae, AM hyphal penetration led to a 125% increase in biomass ¹⁵N of host plants and a 20% reduction in extractable inorganic N in the TEST soil. Mineral N inputs to the HOST compartments (equivalent to 5.0 g N m^?2 yr^?1) increased oat biomass and total root length colonized by mycorrhizal fungi by 189% and 285%, respectively, as compared with the no‐N control. Mineral N inputs to the HOST plants also reduced extractable inorganic N and particulate residue C proportion by 58% and 12%, respectively, in the corresponding TEST soils as compared to the no‐N control, by stimulating AM fungal growth and activities. The species mixture of mycorrhizal fungi was more effective in facilitating N transport and residue decomposition than the single AM species. These findings indicate that low‐level mineral N inputs may significantly enhance nutrient cycling and plant resource capture in terrestrial ecosystems via stimulation of root growth, mycorrhizal functioning, and residue decomposition. The long‐term effects of these observed alterations on soil C dynamics remain to be investigated.     

Silicon-rich soil amendments impact microbial community composition and the composition of arsM bearing microbes

Plant and Soil - Arsenic (As) cycling in flooded rice paddies is driven by soil microbes which among other transformations can cause conversion between inorganic and organic As species. Silicon...     

罕山土壤微生物群落组成对植被类型的响应

选取分布在中国东北部地区的阔叶林-针叶林-亚高山草甸这一明显的植被垂直带谱来研究植被类型对土壤微生物群落组成的影响。选取5种植被类型-山杨(Populus davidiana)(1250—1300 m),山杨(P.davidiana)与白桦(Betula platyphylla)的混交林(1370—1550 m),白桦(B.platyphylla)(1550—1720 m),落叶松(Larix principis-rupprechtii)(1840—1890 m),亚高山草甸(1900—1951 m),采用磷脂脂肪酸(Phopholipid Fatty Acids,PLFAs)分析方法测定不同植被类型下的土壤微生物群落组成。分别采用主成分分析(Principal Components Analysis,PCA)以及冗余分析(Redundancy Analysis,RDA)来解释单种特征PLFAs的分异以及土壤理化指标与微生物PLFAs指标间的相关性。结果表明不同植被类型下土壤有机碳(SOC)对土壤微生物PLFAs总量,各类群(真菌(f)、细菌(b)、革兰氏阳性菌(G+)、革兰氏阴性菌(G-))生物量以及群落结构影响显著;土壤微生物PLFAs总量及各类群的生物量随土层加深总体上表现降低趋势,G+/G-和f/b分别随土层加深总体上表现升高趋势。不同植被类型下,阔叶混交林土壤PLFAs总量及各类群生物量总体上最高;针叶林比阔叶林下的f/b和G+/G-高;亚高山草甸下低的p H值对有机碳的可利用性有一定的抑制作用,导致f/b和G+/G-的值相对较高。总之,不同植被类型下SOC对土壤微生物群落组成的影响最为显著,而较低的p H对有机碳的可利用性有一定的抑制作用;真菌对植被类型的变化比细菌更敏感,而细菌更易受可利用性养分和p H变异的影响,这对预测不同林型下的土壤微生物群落组成有重要的启示作用。     

Links between plant community composition,soil organic matter quality and microbial communities in contrasting tundra habitats

Plant communities, soil organic matter and microbial communities are predicted to be interlinked and to exhibit concordant patterns along major environmental gradients. We investigated the relationships between plant functional type composition, soil organic matter quality and decomposer community composition, and how these are related to major environmental variation in non-acid and acid soils derived from calcareous versus siliceous bedrocks, respectively. We analysed vegetation, organic matter and microbial community compositions from five non-acidic and five acidic heath sites in alpine tundra in northern Europe. Sequential organic matter fractionation was used to characterize organic matter quality and phospholipid fatty acid analysis to detect major variation in decomposer communities. Non-acidic and acidic heaths differed substantially in vegetation composition, and these disparities were associated with congruent shifts in soil organic matter and microbial communities. A high proportion of forbs in the vegetation was positively associated with low C:N and high soluble N:phenolics ratios in soil organic matter, and a high proportion of bacteria in the microbial community. On the contrary, dwarf shrub-rich vegetation was associated with high C:N and low soluble N:phenolics ratios, and a high proportion of fungi in the microbial community. Our study demonstrates a strong link between the plant community composition, soil organic matter quality, and microbial community composition, and that differences in one compartment are paralleled by changes in others. Variation in the forb-shrub gradient of vegetation may largely dictate variations in the chemical quality of organic matter and decomposer communities in tundra ecosystems. Soil pH, through its direct and indirect effects on plant and microbial communities, seems to function as an ultimate environmental driver that gives rise to and amplifies the interactions between above- and belowground systems. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Influence of soil pollution on the composition of a microbial community

The abundance dynamics and composition of indigenous soil microbial communities were studied in soils polluted with naphthalene, dioctyl phthalate, diesel fuel, and crude oil. DGGE analysis of the 16S rRNA genes amplified from the total soil DNA revealed that the bacterial community of uncontaminated soil was more diverse and included no dominant species. In the soil samples polluted with the crude oil, diesel fuel, or dioctyl phthalate, Pseudomonas became the dominant bacteria since the third day of the experiment. In the soil polluted with naphthalene, two genera of bacteria (Pseudomonas and Paenibacillus) were dominant in population on the third day of the experiment, while on the 21th day of the experiment Arthrobacter became dominant. During the experiment, the average number of indigenous bacterial degraders increased approximately by two orders of magnitude. While the key genes of naphthalene catabolism, nahAc and nahH, were not detected in the pristine soil, they were found in a significant amount on the third day after naphthalene addition. Three degrader strains harboring the plasmids of naphthalene biodegradation (IncP-9 group) were isolated on the third day from the soil polluted with naphthalene. Two of these plasmids, although isolated from various degraders, were shown to be identical.     

Intensive allochthonous inputs along the Ganges River and their effect on microbial community composition and dynamics

Little is known about microbial communities in the Ganges River, India and how they respond to intensive anthropogenic inputs. Here we applied shotgun metagenomics sequencing to study microbial community dynamics and function in planktonic samples collected along an approximately 700 km river transect, including urban cities and rural settings in upstream waters, before and after the monsoon rainy season. Our results showed that 11%–32% of the microbes represented terrestrial, sewage and human inputs (allochthonous). Sewage inputs significantly contributed to the higher abundance, by 13-fold of human gut microbiome (HG) associated sequences and 2-fold of antibiotic resistance genes (ARGs) in the Ganges relative to other riverine ecosystems in Europe, North and South America. Metagenome-assembled genome sequences (MAGs) representing allochthonous populations were detectable and tractable across the river after 1–2 days of (downstream) transport (> 200 km apart). Only approximately 8% of these MAGs were abundant in U.S. freshwater ecosystems, revealing distinct biodiversity for the Ganges. Microbial communities in the rainy season exhibited increased alpha-diversity and spatial heterogeneity and showed significantly weaker distance-decay patterns compared with the dry season. These results advance our understanding of the Ganges microbial communities and how they respond to anthropogenic pollution.     

三种种植方式对土壤微生物群落组成的影响

土壤微生物是表征土壤质量变化的敏感指标之一。借助长期定位试验, 采用磷脂脂肪酸分析方法研究了3种种植方式(玉米(Zea mays)连作、玉米非连作和撂荒)对土壤微生物群落组成的影响。结果表明, 在不同的种植方式下, 土壤微生物群落组成有明显的差异。玉米连作的土壤中总磷脂脂肪酸和细菌磷脂脂肪酸含量最低, 分别为33.12 nmol·g^-1和18.09 nmol·g^-1。非连作的土壤真菌磷脂脂肪酸和真菌/细菌分别为0.61 nmol·g^-1和3.06%, 显著低于撂荒和连作(p < 0.05), 非连作方式下, 革兰氏阳性细菌/革兰氏阴性细菌增大。撂荒土壤的总磷脂脂肪酸和细菌磷脂脂肪酸分别为42.98和24.68 nmol·g^-1, 高于耕作处理。 同时, 在撂荒方式下, 革兰氏阳性细菌和革兰氏阴性细菌的含量增加, 革兰氏阳性细菌/革兰氏阴性细菌降低。主成分分析结果表明: 耕作处理(玉米连作和非连作)分布第一主成分负方向上, 第一主成分得分系数分别为-2.48和-1.84; 撂荒分布第一主成分正方向上, 第一主成分得分系数为2.31, 与连作和非连作差异显著(p < 0.05)。冗余分析(RDA)表明: 土壤pH、总氮、有效磷和土壤>0.25 mm水稳性团聚体含量与磷脂脂肪酸呈正相关, 并且土壤pH和土壤>0.25 mm水稳性团聚体含量对土壤微生物群落的影响最大。