Mapping the niche space of soil microorganisms using taxonomy and traits

The biodiversity of microbial communities has important implications for the stability and functioning of ecosystem processes. Yet, very little is known about the environmental factors that define the microbial niche and how this influences the composition and activity of microbial communities. In this study, we derived niche parameters from physiological response curves that quantified microbial respiration for a diverse collection of soil bacteria and fungi along a soil moisture gradient. On average, soil microorganisms had relatively dry optima (0.3 MPa) and were capable of respiring under low water potentials (-2.0 MPa). Within their limits of activity, microorganisms exhibited a wide range of responses, suggesting that some taxa may be able to coexist by partitioning the moisture niche axis. For example, we identified dry-adapted generalists that tolerated a broad range of water potentials, along with wet-adapted specialists with metabolism restricted to less-negative water potentials. These contrasting ecological strategies had a phylogenetic signal at a coarse taxonomic level (phylum), suggesting that the moisture niche of soil microorganisms is highly conserved. In addition, variation in microbial responses along the moisture gradient was linked to the distribution of several functional traits. In particular, strains that were capable of producing biofilms had drier moisture optima and wider niche breadths. However, biofilm production appeared to come at a cost that was reflected in a prolonged lag time prior to exponential growth, suggesting that there is a trade-off associated with traits that allow microorganisms to contend with moisture stress. Together, we have identified functional groups of microorganisms that will help predict the structure and functioning of microbial communities under contrasting soil moisture regimes.     

Foliar absorption of intercepted rainfall improves woody plant water status most during drought

A large proportion of rainfall in dryland ecosystems is intercepted by plant foliage and is generally assumed to evaporate to the atmosphere or drip onto the soil surface without being absorbed. We demonstrate foliar absorption of intercepted rainfall in a widely distributed, continental dryland, woody-plant genus: Juniperus. We observed substantial improvement in plant water status, exceeding 1.0 MPa water potential for drought-stressed plants, following precipitation on an experimental plot that excluded soil water infiltration. Experiments that wetted shoots with unlabeled and with isotopically labeled water confirmed that water potential responded substantially to foliar wetting, that these responses were not attributable to re-equilibration with other portions of the xylem, and that magnitude of response increased with water stress. Foliar absorption is not included in most ecological, hydrological, and atmospheric models; has implications for interpreting plant isotopic signatures; and not only supplements water acquisition associated with increases in soil moisture that follow large or repeated precipitation events, but also enables plants to bypass soil water uptake and benefit from the majority of precipitation events, which wet foliage but do not increase soil moisture substantially. Foliar absorption of intercepted water could be more important than previously appreciated, especially during drought when water stress is greatest.     

山西芦芽山林线附近土壤水分空间分布特征及其影响因素

于2008年植被生长季,在芦芽山荷叶坪亚高山草甸及森林-草甸过渡带内布设观测样带,应用FDR土壤剖面水分测量仪测量10～40 cm深度土壤含水量,并分析其空间分布特征和影响因素。结果表明:(1)根据所处位置及地上植被状况可将样带分为林地样带和草甸样带,林地样带土壤含水量随深度增加呈先升高后降低的变化趋势,草甸样带则恰好相反。(2)10和40 cm深度为土壤含水量稳定层,20和30 cm深度为活跃层,且林地样带10 cm深度土壤含水量小于草甸样带,20、30和40 cm深度土壤含水量则大于草甸样带。(3)降雨发生后,阴坡上部树岛样带土壤含水量增幅最大,阳坡上、中、下部草甸样带土壤含水量增幅也较大;不同土层深度比较而言,10cm深度土壤含水量增幅最大,20、30和40 cm深度土壤含水量增幅较为接近,土壤含水量对降雨的响应存在1～2d的时滞。(4)10、20和30 cm土壤含水量变化值与坡度呈显著正相关,30、40 cm土壤含水量变化值与初始土壤含水量呈显著负相关,20、30 cm土壤含水量变化值与地形湿度指数呈显著负相关。研究区内土壤含水量空间分布格局及其动态变化受植被和降雨影响显著,初始土壤含水量、坡度以及地形湿度指数对其也有一定影响。     

Microorganisms and physico-chemical properties of soils with different slope-protecting vegetation in Daguang Highway北大核心CSCD

In order to investigate the effect of different slope-protecting vegetation on soil restoration in the highways, we collected soils at depths of 0-10 cm, 10-20 cm, and 20-30 cm from areas planted with Amorpha fruticosa, Periploca sepium, and Paederia scandens for 6-7 years in the Daming road section of the Daguang Highway, in October 2016. The physico-chemical properties and microbial community of the soils were then analyzed. The soil microbial community was analyzed by terminal restriction fragment length polymorphism (T-RFLP). The correlation between the microbial community and the physico-chemical properties of the soils was determined by redundancy analysis (RDA). The results showed that (1) the physico-chemical properties were the best for soils with Paederia scandens; the nutrient content, water holding capacity, and porosity of the soils with the three types of slope-protecting vegetation were better in the 0-10 cm layer than in the other layers; (2) the contents of soil aggregates (diameter > 5 mm) were the highest in the 0-10 cm and 10-20 cm layers for the soil with Paederia scandens; (3) the dominant bacteria in the 0-10 cm layer and dominant fungi in the 0-10 cm, 10-20 cm, and 20-30 cm layers were higher in the soils with Pe. sepium and Pa. scandens than in the soil with A. fruticosa; and (4) results of RDA showed that the physical properties of the soils were the main factors that influenced the soil microbial community. The physical properties of the soils were sensitive to the change of soil quality. Soil quality can be improved by appropriate management measures, such as burying litter, which can subsequently improve the ecological environment of soils in sloping regions. © 2018 Science Press. All rights reserved.     

Microbial nitrogen limitation increases decomposition

With anthropogenic nutrient inputs to ecosystems increasing globally, there are long-standing, fundamental questions about the role of nutrients in the decomposition of organic matter. We tested the effects of exogenous nitrogen and phosphorus inputs on litter decomposition across a broad suite of litter and soil types. In one experiment, C mineralization was compared across a wide array of plants individually added to a single soil, while in the second, C mineralization from a single substrate was compared across 50 soils. Counter to basic stoichiometric decomposition theory, low N availability can increase litter decomposition as microbes use labile substrates to acquire N from recalcitrant organic matter. This "microbial nitrogen mining" is consistently suppressed by high soil N supply or substrate N concentrations. There is no evidence for phosphorus mining as P fertilization increases short- and long-term mineralization. These results suggest that basic stoichiometric decomposition theory needs to be revised and ecosystem models restructured accordingly in order to predict ecosystem carbon storage responses to anthropogenic changes in nutrient availability.     

Bioactivity,adsorption and persistence of pretilachlor in paddy field soils

The effects of environmental factors on bioactivity, adsorption and persistence of pretilachlor were studied in the laboratory and greenhouse using cucumber (Cucumis sativus L.) as the bioassay species. The three soils studied viz. Bernam, Selangor and Sabrang series were chosen for their different characteristics. The half‐life of pretilachlor decreased from 10.24 to 4.90 days as temperature increased from 25°C to 35°C in the Selangor Series soil and from 10.86 to 7.63 days in the Bernam Series soil at 60% field capacity. At the same moisture level, an increase of temperature from 25°C to 35°C also reduced the half‐life of pretilachlor in Sabrang soil from 8.87 to 2.59 days. The half‐life of pretilachlor also decreased with increasing moisture levels in Selangor and Sabrang series but not in Bernam series soils. The greatest adsorption of pretilachlor was observed in Bernam series, followed by Selangor and Sabrang series. No phytotoxic residue of pretilachlor was detected in the supernatant after 10 h incubation. Since the residue was strongly adsorbed in Bernam series, its biological activity was less than in the other soils studied.     

Effects of soil nematodes communities on litter decomposition in urban forest of Dalian北大核心CSCD

In order to further expound the effect of soil nematodes on litter decomposition in urban forest, this study investigated the responses of soil nematodes communities to litter decomposition by litterbags technology at different mesh sizes in Dalian National Forest Park. Soil nematodes community composition, decomposition rate of litter and nutrient release were also analyzed. It found a total of 4 418 nematodes from 39 genera. Higher relative density of soil nematodes was found in the bags with 0.1 mm mesh size (1.55 individuals and 7.34 orders per g of dry litter) compared to the bags with 0.02 mm mesh size (0.21 individuals and 0.49 orders per g of dry litter). There were very few soil nematodes in the 0.02 mm litter bags. Thus we regarded that soil nematodes only affected the 0.1 mm litter bags. The mass loss rates as well as C and P release rates was higher in litter bags with 0.1 mm mesh size than in those with 0.02 mm mesh size, indicating a significant influence of soil nematodes on mass loss and nutrient release. The contribution of soil nematodes to the litter mass loss was about 24%. The effect of soil nematodes on the nutrient release rates differed among elements. The soil nematodes had a bigger influence on the release rate of N than that of other elements, whereas the influence on K release rate was the lowest. The results showed that soil nematodes communities has a significant effect on the litter decomposition and nutrient release of the forest litter in Dalian city, especially promoting the mass loss rates and N release rates.     

生物有机无机复合肥对土壤微生物活性的影响

进行了化肥、有机肥、生物堆肥、有机无机复合肥和生物有机无机复合肥的田间比较试验。结果表明 :生物有机无机复合肥显著提高土壤微生物活性。与不施肥处理比较 ,土壤细菌增加了 1 6 5 .3 8% ,真菌增加了1 89.4 7% ,放线菌增加了 4 8.72 % ,总量增加了 1 0 4 .0 7% ,其增加量高于其他处理。土壤蔗糖酶、脲酶、磷酸酶活性也都有明显提高 ,促进了土壤有机质的分解转化和速效养分的释放。     

Seasonal variations in plant species effects on soil N and P dynamics

It is well established that plant species influence ecosystem processes, but we have little ability to predict which vegetation changes will alter ecosystems, or how the effects of a given species might vary seasonally. We established monocultures of eight plant species in a California grassland in order to determine the plant traits that account for species impacts on nitrogen and phosphorus cycling. Plant species differed in their effects on net N mineralization and nitrification rates, and the patterns of species differences varied seasonally. Soil PO4- and microbial P were more strongly affected by slope position than by species. Although most studies focus on litter chemistry as the main determinant of plant species effects on nutrient cycling, this study showed that plant species affected biogeochemical cycling through many traits, including direct traits (litter chemistry and biomass, live-tissue chemistry and biomass) and indirect traits (plant modification of soil bioavailable C and soil microclimate). In fact, species significantly altered N and P cycling even without litter inputs. It became particularly critical to consider the effects of these multiple traits in order to account for seasonal changes in plant species effects on ecosystems. For example, species effects on potential rates of net N mineralization were most strongly influenced by soil bioavailable C in the fall and by litter chemistry in the winter and spring. Under field conditions, species effects on soil microclimate influenced rates of mineralization and nitrification, with species effects on soil temperature being critical in the fall and species effects on soil moisture being important in the dry spring. Overall, this study clearly demonstrated that in order to gain a mechanistic, predictive understanding of plant species effects on ecosystems, it is critical to look beyond plant litter chemistry and to incorporate the effects of multiple plant traits on ecosystems.     

Interactive effects of plant species diversity and elevated CO2 on soil biota and nutrient cycling

Terrestrial ecosystems consist of mutually dependent producer and decomposer subsystems, but not much is known on how their interactions are modified by plant diversity and elevated atmospheric CO2 concentrations. Factorially manipulating grassland plant species diversity and atmospheric CO2 concentrations for five years, we tested whether high diversity or elevated CO2 sustain larger or more active soil communities, affect soil aggregation, water dynamics, or nutrient cycling, and whether plant diversity and elevated CO2 interact. Nitrogen (N) and phosphorus (P) pools, symbiotic N2 fixation, plant litter quality, soil moisture, soil physical structure, soil nematode, collembola and acari communities, soil microbial biomass and microflora community structure (phospholipid fatty acid [PLFA] profiles), soil enzyme activities, and rates of C fluxes to soils were measured. No increases in soil C fluxes or the biomass, number, or activity of soil organisms were detected at high plant diversity; soil H2O and aggregation remained unaltered. Elevated CO2 affected the ecosystem primarily by improving plant and soil water status by reducing leaf conductance, whereas changes in C cycling appeared to be of subordinate importance. Slowed-down soil drying cycles resulted in lower soil aggregation under elevated CO2. Collembola benefited from extra soil moisture under elevated CO2, whereas other faunal groups did not respond. Diversity effects and interactions with elevated CO2 may have been absent because soil responses were mainly driven by community-level processes such as rates of organic C input and water use; these drivers were not changed by plant diversity manipulations, possibly because our species diversity gradient did not extend below five species and because functional type composition remained unaltered. Our findings demonstrate that global change can affect soil aggregation, and we advocate that soil aggregation should be considered as a dynamic property that may respond to environmental changes and feed back on other ecosystem functions.     

植物根际微生态区域中铝的环境行为研究进展

铝毒是酸性土壤(pH<5.0)中影响植物生长的重要因素.根系环境中的铝离子可影响矿物营养的获取,增加植物对铝胁迫的风险.植物通过根系分泌有机酸、生物酶和其他物质来解除或减轻铝的毒害.从铝胁迫对根系分泌系统的影响、根际微环境中铝的毒理效应和根际微环境中铝的抗毒机制等3个方面对植物根际微生态区域中铝的环境行为研究进展进行了综述,并对今后该领域的研究方向进行了展望.     

菌根在污染土壤生物修复中的作用

菌根是土壤真菌 -植物根系形成的共生体 ,广泛存在于自然界中 ,它能增强植物的吸收能力 ,改善植物的生长 ,提高植株的抗逆能力和耐受能力等。所以 ,菌根化植物可作为很好的生物修复载体。本文主要从无机、有机以及放射性污染 3方面对国内外关于菌根在污染土壤生物修复中的作用进行了综述     

Impact of litter removal on soil characteristics under a Pinus caribaea stand

ABSTRACT

Forest productivity is dependent on soil quality, which in turn is related to litter; yet there is limited understanding of the relationships between litter and soil quality. The effects of litter removal treatment on tree growth and soil properties were examined in a Pinus caribaea stand with the aim of providing an understanding of consequences of litter removal on soil patterns. This knowledge is important for planning appropriate long-term forest management. Three pairs of 30 × 30 m² plots (each pair a control and treatment) were established in the center of a P. caribaea stand in April 2002. The controls were left undisturbed with an intact litter layer, while litter was removed monthly from treated plots. The diameter and height of the P. caribaea decreased and soil quality was degraded over the experimental period in litter-removed (treated) plots. Litter removal also produced a significant increase in soil bulk density at 0–20 and 20–40 cm depths. The capillary porosity, capillary moisture capacity, and natural water content in controls at 0–20 and 20–40 cm depths were significantly greater than treated plots. The non-capillary porosity in controls at the 0–20 cm depth was also significantly higher than treated plots. The organic carbon, total nitrogen (N), total potassium (K) and alkalized N content in each layer, and available P and exchangeable K at 0–20 and 40–60 cm depths in control plots were significantly greater than litter-removed plots. The numbers of bacteria at 0–20 and 40–60 cm depths and of fungi at 20–40 and 40–60 cm depths were higher in control than treated plots. The number of actinomyces and urease, catalase, and acid phosphatase activities in controls at each depth were significantly greater than litter-removed plots.     

森林凋落物分解研究进展

森林凋落物是指森林生态系统内由生物组分产生,然后归还到林地表面的所有有机物质的总称。森林凋落物在促进森林生态系统正常的物质循环和养分平衡,维持生态系统功能中具有重要作用,其分解受多因素影响,且各因素之间相互交错。不同情况下,各因子的重要性可能不同。温度和湿度被认为是影响凋落物分解主要的气候因子。凋落物随着温度升高分解速率加快,增加土壤湿度对凋落物分解有积极作用。凋落物的化学性质中,C、N比和木质素含量被认为是最重要的指标。凋落物分解前期的分解速率受到养分含量、水溶性碳化合物和结构碳化合物含量的强烈影响,而后期则更多地受到木质素及纤维素/木质素比值的支配。土壤动物可以粉碎凋落物,土壤微生物也是促进凋落物分解的重要因素,人为活动也影响凋落物分解。N沉降、全球变暖和臭氧层破坏等全球变化对森林凋落物分解的影响已逐渐成为研究热点。未来凋落物分解的研究方向是统一研究方法,开展长期定位监测,加强对分解过程中有机碳含量和释放量的研究,以及N沉降对凋落物分解作用机理的研究。     

Interactions of bacteria and fungi on decomposing litter: differential extracellular enzyme activities

Fungi and bacteria are key agents in plant litter decomposition in freshwater ecosystems. However, the specific roles of these two groups and their interactions during the decomposition process are unclear. We compared the growth and patterns of degradative enzymes expressed by communities of bacteria and fungi grown separately and in coexistence on Phragmites leaves. The two groups displayed both synergistic and antagonistic interactions. Bacteria grew better together with fungi than alone. In addition, there was a negative effect of bacteria on fungi, which appeared to be caused by suppression of fungal growth and biomass accrual rather than specifically affecting enzyme activity. Fungi growing alone had a high capacity for the decomposition of plant polymers such as lignin, cellulose, and hemicellulose. In contrast, enzyme activities were in general low when bacteria grew alone, and the activity of key enzymes in the degradation of lignin and cellulose (phenol oxidase and cellobiohydrolase) was undetectable in the bacteria-only treatment. Still, biomass-specific activities of most enzymes were higher in bacteria than in fungi. The low total activity and growth of bacteria in the absence of fungi in spite of apparent high enzymatic efficiency during the degradation of many substrates suggest that fungi provide the bacteria with resources that the bacteria were not able to acquire on their own, most probably intermediate decomposition products released by fungi that could be used by bacteria.     

超积累植物和化学改良剂联合修复锌镉污染土壤后的微生物特征

通过盆栽试验,观察分析不同的土壤改良配方对重金属超积累植物东南景天盆栽土壤中细菌、真菌和放线菌数量、Cmic及Nmic的影响,以此来筛选出最优的促进东南景天修复锌镉污染土壤的改良剂配方。结果显示:细菌、真菌和放线菌数量,与土壤Zn、Cd的去除率、东南景天植株干质量、Cmic及Cmic/Nmic两两之间都呈现极显著正相关关系(但Cmic/Nmic与真菌数量仅呈显著相关)。添加了土壤改良剂后,细菌、放线菌、真菌的数量都有不同程度的增加,其中以细菌数量的增加最为显著,放线菌次之,真菌则对各种土壤处理相对较不敏感;在各种土壤配方中,添加了6 g赤泥、15 g污泥和15 g沸石的T7处理最有利于各类土壤微生物的生长,微生物量碳达到345.64 mg.kg-1,与其它处理之间都达到显著差异。因此,可以利用土壤微生物作为污染土壤改良情况的生物指标。该研究为下阶段研究化学改良剂-植物-微生物修复技术奠定了基础。     

森林土壤氧化（吸收）甲烷研究进展

甲烷是一种重要的温室气体,对全球气候变暖的贡献仅次于CO2,约为25%。大气甲烷可以被土壤中甲烷氧化细菌在有氧条件下吸收利用,陆地生态系统森林土壤氧化吸收甲烷的研究已有大量报道。甲烷氧化菌是以甲烷作为唯一的碳源和能源的一类细菌的总称。但森林土壤在全球甲烷核算中具有一定的不确定性,取决于产甲烷菌和甲烷氧化菌的相对活性。甲烷氧化菌的研究集中在环境对氧化能力的影响和自身氧化能力上。大气甲烷氧化过程为高氧化能力低亲力氧化,受到一些因子,如土壤温度、土壤通气状况、pH、氮肥等的影响,具体机理的研究还有待进一步深入。土壤通气状况受土壤质地与土壤水分影响,土地利用类型可能改变土壤容重、土壤结构和土壤水分,进而影响土壤甲烷氧化。植物可以通过自身对生境的作用或化感作用影响土壤甲烷氧化。土壤动物的研究则相对较少,目前排放清单中仅有白蚁是全球甲烷核算所包括的。从甲烷氧化菌的分类出发,对甲烷氧化菌氧化甲烷的机理、菌的生态分布及甲烷氧化的影响因素、时空异质性、观测方法等作出了综述,为正确认识和准确预测森林土壤在一定气候和土地利用类型条件下的甲烷氧化强度提供理论依据。     

Tree species and mycorrhizal associations influence the magnitude of rhizosphere effects

Previous research on the effects of tree species on soil processes has focused primarily on the role of leaf litter inputs. We quantified the extent to which arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) tree species influence soil microbial activity and nutrient availability through rhizosphere effects. Rhizosphere soil, bulk soil, and fine roots were collected from 12 monospecifc plots (six AM and six ECM tree species) planted on a common soil at the Turkey Hill Plantations in Dryden, New York. Rhizosphere effects were estimated by the percentage difference between rhizosphere and bulk soil samples for several assays. Rhizosphere effects on soil microbes and their activities were significant for ECM species but in only a few cases for AM species. In AM tree species, microbial biomass, net N mineralization, and phosphatase enzyme activity in the rhizosphere were 10-12% greater than in bulk soil. In ECM tree species, rhizosphere effects for microbial biomass, C mineralization rates, net N mineralization, and phosphatase activity were 25-30% greater than bulk soil, and significantly greater than AM rhizosphere effects. The magnitude of rhizosphere effects was negatively correlated with the degree of mycorrhizal colonization in AM tree species (r = -0.83) and with fine root biomass (r = -0.88) in ECM tree species, suggesting that different factors influence rhizosphere effects in tree species forming different mycorrhizal associations. Rhizosphere effects on net N mineralization and phosphatase activity were also much greater in soils with pH < 4.3 for both AM and ECM tree species, suggesting that soil pH and its relation to nutrient availability may also influence the magnitude of rhizosphere effects. Our results support the idea that tree roots stimulate nutrient availability in the rhizosphere, and that systematic differences between AM and ECM may result in distinctive rhizosphere effects for C, N, and P cycling between AM and ECM tree species.     

The effect of imazethapyr on soil microbes in soybean fields in northeast China

Large quantities of herbicides are used on agricultural soils, but the effects of herbicides on the structure of the soil microbial community have not been well investigated. In this study, soil from three soybean fields was investigated. The herbicide imazethapyr was applied in one year to soil 1 and in two sequential years to soil 2. Control soil received no imazethapyr. Microbial biomass and community structure were characterised using chloroform fumigation–extraction and phospholipid fatty acid (PLFA) determination. The imazethapyr residue was 1.62 μ g·kg^?1 in soil 1 and 1.79 μ g·kg^?1 in soil 2. The microbial biomass carbon and total PLFAs for soil 2 were much higher than for the other soils. PLFA profiles showed that fatty acids for Gram-negative and Gram-positive bacteria, as well as total bacteria and total fungi in soil 2 were higher than in other samples. Principal component analysis of the PLFAs showed that the structure of the microbial community differed substantially among the three different soybean field soils. Application of the herbicide imazethapyr to soybean fields clearly changed the soil microbial biomass and shifted the structure of the microbial community.     

Tropical forest soil microbial communities couple iron and carbon biogeochemistry

We report that iron-reducing bacteria are primary mediators of anaerobic carbon oxidation in upland tropical soils spanning a rainfall gradient (3500-5000 mm/yr) in northeast Puerto Rico. The abundant rainfall and high net primary productivity of these tropical forests provide optimal soil habitat for iron-reducing and iron-oxidizing bacteria. Spatially and temporally dynamic redox conditions make iron-transforming microbial communities central to the belowground carbon cycle in these wet tropical forests. The exceedingly high abundance of iron-reducing bacteria (up to 1.2 x 10(9) cells per gram soil) indicated that they possess extensive metabolic capacity to catalyze the reduction of iron minerals. In soils from the higher rainfall sites, measured rates of ferric iron reduction could account for up to 44% of organic carbon oxidation. Iron reducers appeared to compete with methanogens when labile carbon availability was limited. We found large numbers of bacteria that oxidize reduced iron at sites with high rates of iron reduction and large numbers of iron reducers. The coexistence of large populations of iron-reducing and iron-oxidizing bacteria is evidence for rapid iron cycling between its reduced and oxidized states and suggests that mutualistic interactions among these bacteria ultimately fuel organic carbon oxidation and inhibit CH4 production in these upland tropical forests.