Using landscape and depth gradients to decouple the impact of correlated environmental variables on soil microbial community composition

Simultaneously assessing shifts in microbial community composition along landscape and depth gradients allows us to decouple correlations among environmental variables, thus revealing underlying controls on microbial community composition. We examined how soil microbial community composition changed with depth and along a successional gradient of native prairie restoration. We predicted that carbon would be the primary control on both microbial biomass and community composition, and that deeper, low-carbon soils would be more similar to low-carbon agricultural soils than to high carbon remnant prairie soils. Soil microbial community composition was characterized using phospholipid fatty acid (PLFA) analysis, and explicitly linked to environmental data using structural equations modeling (SEM). We found that total microbial biomass declined strongly with depth, and increased with restoration age, and that changes in microbial biomass were largely attributable to changes in soil C and/or N concentrations, together with both direct and indirect impacts of root biomass and magnesium. Community composition also shifted with depth and age: the relative abundance of sulfate-reducing bacteria increased with both depth and restoration age, while gram-negative bacteria declined with depth and age. In contrast to prediction, deeper, low-C soils were more similar to high-C remnant prairie soils than to low-C agricultural soils, suggesting that carbon is not the primary control on soil microbial community composition. Instead, the effects of depth and restoration age on microbial community composition were mediated via changes in available phosphorus, exchangeable calcium, and soil water, together with a large undetermined effect of depth. Only by examining soil microbial community composition shifts across sites and down the soil column simultaneously were we able to tease apart the impact of these correlates environmental variables.     

Soil freeze-thaw cycle experiments: Trends, methodological weaknesses and suggested improvements

Although freeze-thaw cycles can alter soil physical properties and microbial activity, their overall impact on soil functioning remains unclear. This review addresses the effects of freeze-thaw cycles on soil physical properties, microorganisms, carbon and nutrient dynamics, trace gas losses and higher organisms associated with soil. I discuss how the controlled manipulation of freeze-thaw cycles has varied widely among studies and propose that, despite their value in demonstrating the mechanisms of freeze-thaw action in soils, many studies of soil freeze-thaw cycles have used cycle amplitudes, freezing rates and minimum temperatures that are not relevant to temperature changes across much of the soil profile in situ. The lack of coordination between the timing of soil collection and the season for which freeze-thaw cycles are being simulated is also discussed. Suggested improvements to future studies of soil freeze-thaw cycles include the maintenance of realistic temperature fluctuations across the soil profile, soil collection in the appropriate season and the inclusion of relevant surface factors such as plant litter in the fall or excess water in the spring. The implications of climate change for soil freeze-thaw cycles are addressed, along with the need to directly assess how changes in soil freeze-thaw cycle dynamics alter primary production.     

耕作对旱区坡耕地土壤碳素转化及冬小麦产量的影响

利用长期定位试验(1999开始保护性耕作,2004年采样测定),在豫西旱区坡耕地上进行了不同耕作对土壤有机碳、微生物态碳及水分利用效率的影响研究。结果表明:深松覆盖和免耕覆盖处理的耕层有机碳增加较明显,以深松覆盖有机碳含量最高为6.79gkg-1,比传统耕作高13.82%,其次是免耕,较传统高11.58%,而少耕却较传统降低了1.38%,随着土层的加深,土壤有机碳含量降低,0～60cm有机碳平均值,深松和免耕较传统分别增加了14.08%、5.41%,少耕较传统减少1.12%。土壤微生物碳对耕作敏感,其含量免耕>深松>传统>少耕,分别为206.87mgkg-1、138.43mgkg-1、115.42mgkg-1和112.57mgkg-1,较传统增加79.3%、19.9%和-2.5%。土壤有机碳和土壤微生物态碳都有坡下富集现象。少耕、免耕、深松和传统的SMBC/SOC的值分别为1.91%、3.11%、2.04%和1.93%,免耕和深松对培肥地力、改善环境有好的应用前景;同时免耕覆盖与深松覆盖可提高产量,增产分别达10.22%与9.26%;可提高水分利用效率。     

Combined microbial community level and single species biosensor responses to monitor recovery of oil polluted soil

Understanding the effects of oil contamination on the composition and function of soil microbiota entails investigation of the effects of a mixture of hydrocarbons at the community level in a complex environmental matrix. One approach to this difficult problem is to ally a community-level fingerprinting approach with bioassays that have a physiological or functional implication. Two contrasting refined oils (paraffin and motor oil) were used to contaminate soil microcosms, and a simulated bioremediation treatment with nutrient-addition was applied. The indigenous microorganisms were monitored over 103 d using complementary community-level techniques (carbon source physiological profiling using Biolog^® microplates, and phospholipid fatty acid (PLFA) profiling). Changes in the toxicity of the applied oils were monitored using luminescent bacterial bioassays, including Vibrio fischeri and a hydrocarbon-degrading Pseudomonas putida strain. Distinct shifts in microbial community structure and C source utilization profiles were observed as a result of oil contamination. There was some evidence that bioremediated soils were returning to control values by the end of the experiment. This was supported by the bioassay results which showed an initial increase in toxicity as a result of the oil addition which had then decreased by the conclusion of the experiment. The two oils exhibited markedly different toxicity towards the bioassay organisms, with species-specific differences in response. This oil-specific difference was also found in the PLFA profiles which showed the two oil types selected different microbial communities.     

Diversity of rhizobia isolated from an agricultural soil in Argentina based on carbon utilization and effects of herbicides on growth

Seventy-six rhizobial isolates belonging to four different genera were obtained from the root nodules of several legumes (Vicia sativa, Vicia faba, Medicago sativa, Melilotus sp., Glycine max and Lotus corniculatus). The action of five commonly used herbicides [2,4-dichlorophenoxyacetic acid (2,4-D), glyphosate (GF), dicamba, atrazine and metsulfuron-methyl] on the growth of rhizobial strains was assessed. Subsequently, GF and 2,4-D were tested in a minimum broth as C and energy sources for 20 tolerant strains. The ability of these strains to metabolize different carbon sources was studied in order to detect further differences among them. Tolerance of the bacteria to agrochemicals varied; 2,4-D and GF in solid medium inhibited and diminished growth, respectively, in slow-growing rhizobial strains. Among slow-growing strains we detected Bradyrhizobium sp. SJ140 that grew well in broth + GF as the sole C and energy source. No strain was found which could use 2,4-D as sole C source. The 20 strains studied exhibited different patterns of C sources utilization. Cluster analysis revealed three groups, corresponding to four genera of rhizobia: Rhizobium (group I), Sinorhizobium (group II) and Mesorhizobium–Bradyrhizobium (group III). On the basis of the results obtained on responses to herbicides and C sources utilization by the isolates investigated, it was possible to differentiate them at the level of strains. These results evidenced a considerable diversity in rhizobial populations that had not been previously described for Argentinean soils, and suggested a physiological potential to use natural and xenobiotic C sources.     

Carbon cycling and sequestration opportunities in temperate grasslands

Abstract. Temperate grasslands account for c. 20% of the land area in Europe. Carbon accumulation in grassland ecosystems occurs mostly below ground and changes in soil organic carbon stocks may result from land use changes (e.g. conversion of arable land to grassland) and grassland management. Grasslands also contribute to the biosphere–atmosphere exchange of non-CO₂ radiatively active trace gases, with fluxes intimately linked to management practices. In this article, we discuss the current knowledge on carbon cycling and carbon sequestration opportunities in temperate grasslands. First, from a simple two-parameter exponential model fitted to literature data, we assess soil organic carbon fluxes resulting from land use change (e.g. between arable and grassland) and from grassland management. Second, we discuss carbon fluxes within the context of farming systems, including crop–grass rotations and farm manure applications. Third, using a grassland ecosystem model (PaSim), we provide estimates of the greenhouse gas balance, in CO₂ equivalents, of pastures for a range of stocking rates and of N fertilizer applications. Finally, we consider carbon sequestration opportunities for France resulting from the restoration of grasslands and from the de-intensification of intensive livestock breeding systems. We emphasize major uncertainties concerning the magnitude and non-linearity of soil carbon stock changes in agricultural grasslands as well as the emissions of N₂O from soil and of CH₄ from grazing livestock.     

Linking the B ring hydroxylation pattern of condensed tannins to C, N and P mineralization. A case study using four tannins

Condensed tannins (CTs) are a major component of litter inputs, but little is known about the effects of tannin structural variations on soil biological processes and organic matter development. Four different CTs extracted from balsam fir, western red cedar, kalmia and black spruce were added to Corsican pine litter and subsequently incubated for 16 weeks in order to investigate the effect of the B ring hydroxylation pattern on C, N and P transformations. While for C mineralization the chain length and stereochemistry of the CTs seemed to be a more important parameter, net N and P mineralization rates were clearly reduced compared with non-amended litter. With regard to the B ring hydroxylation, the prodelphinidin (PD) CTs having predominantly three hydroxy groups at the B ring (balsam fir and western red cedar) exhibited significantly lower mineralization rates than the procyanidin (PC) CTs having two OH groups (kalmia and black spruce). The same was true for net nitrification, but this process was only slightly affected by the CTs. Although based on only four CTs, this study indicates that B ring hydroxylation is an important variable determining net N and P mineralization rates. Our results support previous suggestions that PD tannins bind to or react more strongly with soil organic matter. Therefore, more than PC tannins, they reduce the availability of organic N for mineralization as well as their own detectability by standard methods for soil CT.     

Nutrient spatial variability in biogenic structures of Nasutitermes (Termitinae; Isoptera) in a gallery forest of the Colombian ‘Llanos’

By definition ‘ecosystem engineers’ are those organisms capable to modify physically the environment by producing ‘biogenic’ structures (BS). Large macroinvertebrates like termites, earthworms and ants produce BS with distinguishable physico-chemical properties. We measured total C_org, and contents in the BS produced by two species of Neotropical termites (subfamily Nasutermitinae) in a gallery forest (GF) of the Eastern Plains of Colombia. We sampled from the top of the BS to the edge at proportional distances, i.e. 20-100% for the largest BS in the soil surface and 50-100% for the smallest arboricole BS. Control soil was sampled 1 m apart from the BS. Values of total C_org were high in the BS produced by Nasutitermes sp1 (epigeic mound), while a high N mineralization process was observed in the same BS and in the Nasutitermes sp2 arboreal nest. The role of these two ecosystem engineers in nutrient cycling is discussed.     

The effect of increased atmospheric carbon dioxide concentration on emissions of nitrous oxide, carbon dioxide and methane from a wheat field in a semi-arid environment in northern China

There are no reports on the effects of elevated carbon dioxide [CO₂] on the fluxes of N₂O, CO₂ and CH₄ from semi-arid wheat cropping systems. These three soil gas fluxes were measured using closed chambers under ambient (420 ± 18 μmol mol⁻¹) and elevated (565 ± 37 μmol mol⁻¹) at the Free-Air Carbon dioxide Enrichment experimental facility in northern China. Measurements were made over five weeks on a wheat crop (Triticum aestivum L. cv. Zhongmai 175). Elevated [CO₂] increased N₂O and CO₂ emission from soil by 60% and 15%, respectively, but had no significant effect on CH₄ flux. There was no significant interaction between [CO₂] and N application rate on these gas fluxes, probably because soil N was not limiting. At least 22% increase in C storage is required to offset the observed increase in greenhouse gas emissions under elevated [CO₂].     

Earthworm ecological groupings based on C analysis

We report the first use of ¹⁴C isotope analysis to investigate the ecological grouping of earthworms. Mature endogeic (Allolobophora caliginosa), mature epigeic (Lumbricus rubellus), and semimature anecic worms (A. longa) were collected in September 2002 from a woodland site at Lancaster, UK. Because anecic worms are known to have a variable feeding behaviour and can show dietary changes during ontogeny, additional immature and mature specimens of A. longa were also collected from the same site in January 2004. Epigeic earthworms showed the lowest radiocarbon concentration (0-3-years old), implying that they assimilated more recently fixed carbon than the anecic or endogeic earthworms. The age of carbon assimilated in mature anecic species (5-7-years old) was closer to that of endogeic species (5-8-years old) than to epigeics, suggesting that a greater proportion of older, more mineralised organic matter may form part of the diet of the anecic earthworms than previously thought. These results suggest that ¹⁴C approaches are useful in the study of the feeding behaviour of detritivorous animals by providing in situ information on the age of the carbon assimilated by the worms. This can then be related to their role in ecosystem functioning, particularly in carbon cycling.