Co-accumulation of microbial residues and particulate organic matter in the surface layer of a no-till Oxisol under different crops

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Seasonal fluctuations of bacterial population and microbial activity in soils cultivated with eucalyptus and pinus

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Decomposition of the rubber tree Hevea brasiliensis litter at two depths

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Heavy metals and TPH effects on microbial abundance and diversity in two estuarine areas of the southern-central coast of São Paulo State, Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Soil property and management effects on grassland microbial communities across a latitudinal gradient in Germany

There is much interest in the identification of the main drivers controlling changes in the microbial community that may be related to sustainable land use. We examined the influence of soil properties and land-use intensity (N fertilization, mowing, grazing) on total phospholipid fatty acid (PLFA) biomass, microbial community composition (PLFA profiles) and activities of enzymes involved in the C, N, and P cycle. These relationships were examined in the topsoil of grasslands from three German regions (Schorfheide-Chorin (SCH), Hainich-Dun (HAI), Schwabische Alb (ALB)) with different parent material. Differences in soil properties explained 60% of variation in PLFA data and 81% of variation in enzyme activities across regions and land-use intensities. Degraded peat soils in the lowland areas of the SCH with high organic carbon (OC) concentrations and sand content contained lower PLFA biomass, lower concentrations of bacterial, fungal, and arbuscular mycorrhizal PLFAs, but greater enzyme activities, and specific enzyme activities (per unit microbial biomass) than mineral soils in the upland areas of the HAI and ALB, which are finer textured, drier, and have smaller OC concentrations. After extraction of variation that originated from large-scale differences among regions and differences in land-use intensities between plots, soil properties still explained a significant amount of variation in PLFA data (34%) and enzyme activities (60%). Total PLFA biomass and all enzyme activities were mainly related to OC concentration, while relative abundance of fungi and fungal to bacterial ratio were mainly related to soil moisture. Land-use intensity (LUI) significantly decreased the soil C:N ratio. There was no direct effect of LUI on total PLFA biomass, microbial community composition, N and P cycling enzyme activities independent of study region and soil properties. In contrast, the activities and specific activities of enzymes involved in the C cycle increased significantly with LUI independent of study region and soil properties, which can have impact on soil organic matter decomposition and nutrient cycling. Our findings demonstrate that microbial biomass and community composition as well as enzyme activities are more controlled by soil properties than by grassland management at the regional scale. (C) 2013 Elsevier B.V: All rights reserved.

The decomposition of starch grains in soils: implications for archaeological residue analyses

Recent research involving starch grains recovered from archaeological contexts has highlighted the need for a review of the mechanisms and consequences of starch degradation specifically relevant to archaeology. This paper presents a review of the plant physiological and soil biochemical literature pertinent to the archaeological investigation of starch grains found as residues on artefacts and in archaeological sediments. Preservative and destructive factors affecting starch survival, including enzymes, clays, metals and soil properties, as well as differential degradation of starches of varying sizes and amylose content, were considered. The synthesis and character of chloroplast-formed 'transitory' starch grains, and the differentiation of these from 'storage' starches formed in tubers and seeds were also addressed. Findings of the review include the higher susceptibility of small starch grains to biotic degradation, and that protective mechanisms are provided to starch by both soil aggregates and artefact surfaces. These findings suggest that current reasoning which equates higher numbers of starch grains on an artefact than in associated sediments with the use of the artefact for processing starchy plants needs to be reconsidered. It is argued that an increased understanding of starch decomposition processes is necessary to accurately reconstruct both archaeological activities involving starchy plants and environmental change investigated through starch analysis. (C) 2004 Elsevier Ltd. All rights reserved.

The microbial ecology of cow slurry in vermiculture beds

The suitability of cow slurry as a substrate for vermicomposting by Eisenia fetida was investigated. Particular attention was given to the effects of the earthworm on the decomposition and stabilisation of the slurry; and to the interactions between E. fetida and the microflora of the substrate. Assessment of the chemical and microbiological changes in cow slurry stored under forced aeration, and subsequently in shallow trays, showed that neither method was suitable for the treatment of slurry. A comparison of two methods of vermicomposting showed that top-feeding of slurry was more efficient in promoting earthworm growth and cocoon production than the mixing of slurry with solid materials. Management practices were found to have an important influence on the efficiency of the process. An investigation o:f the effect of E. fetida. on the decomposition of slurry indicated that the presence of this earthworm enhanced the stabilisation of the substrate and increased the plant-available nitrogen content. Specific nutritional interactions were observed between E. fetida and micro-organisms in sand/cellulose microcosms. The earthworms were found to be feeding directly upon the cells of certain micro-organisms. Other species were found to be toxic to E. fetida.. A technique was developed :for the production of axenic E. fetida., and the use of such earthworms in :feeding experiments confirmed the importance of some micro-organisms in earthworm nutrition. The seeding of vermiculture beds with one such micro-organism stimulated earthworm growth and consumption of the substrate. Vermicomposted mixtures of cow slurry and spent mushroom compost were shown to have potential application as casing materials in mushroom cultivation. The findings of this study indicate the suitability of vermicomposting as a method for the stabilisation of intensively-produced cow slurry, and give some indication of the importance of micro-organisms in the nutrition of E. fetida.

Spatial and temporal stability of soil microbial properties in the Jena Experiment (Germany) from 2003-2014

The study was carried out on the main plots of a large grassland biodiversity experiment (the Jena Experiment). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. We tracked soil microbial basal respiration (BR; µlO2/g dry soil/h) and biomass carbon (Cmic; µgC/g dry soil) over a time period of 12 years (2003-2014) and examined the role of plant diversity and plant functional group composition for the spatial and temporal stability (calculated as mean/SD) of soil microbial properties (basal respiration and biomass) in bulk-soil. Our results highlight the importance of plant functional group composition for the spatial and temporal stability of soil microbial properties, and hence for microbially-driven ecosystem processes, such as decomposition and element cycling, in temperate semi-natural grassland.

Seawater carbonate chemistry and microbial polysaccharide degradation during experiments with phytoplankton Emiliania huxleyi (strain PML B92/11) and natural bacteria community, 2010

With the accumulation of anthropogenic carbon dioxide (CO2), a proceeding decline in seawater pH has been induced that is referred to as ocean acidification. The ocean's capacity for CO2 storage is strongly affected by biological processes, whose feedback potential is difficult to evaluate. The main source of CO2 in the ocean is the decomposition and subsequent respiration of organic molecules by heterotrophic bacteria. However, very little is known about potential effects of ocean acidification on bacterial degradation activity. This study reveals that the degradation of polysaccharides, a major component of marine organic matter, by bacterial extracellular enzymes was significantly accelerated during experimental simulation of ocean acidification. Results were obtained from pH perturbation experiments, where rates of extracellular alpha- and beta-glucosidase were measured and the loss of neutral and acidic sugars from phytoplankton-derived polysaccharides was determined. Our study suggests that a faster bacterial turnover of polysaccharides at lowered ocean pH has the potential to reduce carbon export and to enhance the respiratory CO2 production in the future ocean.

Degradation of Biofumigant Isothiocyanates and Allyl Glucosinolate in Soil and Their Effects on the Microbial Community Composition

Brassicales species rich in glucosinolates are used for biofumigation, a process based on releasing enzymatically toxic isothiocyanates into the soil. These hydrolysis products are volatile and often reactive compounds. Moreover, glucosinolates can be degraded also without the presence of the hydrolytic enzyme myrosinase which might contribute to bioactive effects. Thus, in the present study the stability of Brassicaceae plant-derived and pure glucosinolates hydrolysis products was studied using three different soils ( model biofumigation). In addition, the degradation of pure 2-propenyl glucosinolate was investigated with special regard to the formation of volatile breakdown products. Finally, the influence of pure glucosinolate degradation on the bacterial community composition was evaluated using denaturing gradient gel electrophoresis of 16S rRNA gene amplified from total community DNA. The model biofumigation study revealed that the structure of the hydrolysis products had a significant impact on their stability in the soil but not the soil type. Following the degradation of pure 2-propenyl glucosinolate in the soils, the nitrile as well as the isothiocyanate can be the main degradation products, depending on the soil type. Furthermore, the degradation was shown to be both chemically as well as biologically mediated as autoclaving reduced degradation. The nitrile was the major product of the chemical degradation and its formation increased with iron content of the soil. Additionally, the bacterial community composition was significantly affected by adding pure 2-propenyl glucosinolate, the effect being more pronounced than in treatments with myrosinase added to the glucosinolate. Therefore, glucosinolates can have a greater effect on soil bacterial community composition than their hydrolysis products.

Effects of Soil Organic Matter Properties and Microbial Community Composition on Enzyme Activities in Cryoturbated Arctic Soils

Enzyme-mediated decomposition of soil organic matter (SOM) is controlled, amongst other factors, by organic matter properties and by the microbial decomposer community present. Since microbial community composition and SOM properties are often interrelated and both change with soil depth, the drivers of enzymatic decomposition are hard to dissect. We investigated soils from three regions in the Siberian Arctic, where carbon rich topsoil material has been incorporated into the subsoil (cryoturbation). We took advantage of this subduction to test if SOM properties shape microbial community composition, and to identify controls of both on enzyme activities. We found that microbial community composition (estimated by phospholipid fatty acid analysis), was similar in cryoturbated material and in surrounding subsoil, although carbon and nitrogen contents were similar in cryoturbated material and topsoils. This suggests that the microbial community in cryoturbated material was not well adapted to SOM properties. We also measured three potential enzyme activities (cellobiohydrolase, leucine-amino-peptidase and phenoloxidase) and used structural equation models (SEMs) to identify direct and indirect drivers of the three enzyme activities. The models included microbial community composition, carbon and nitrogen contents, clay content, water content, and pH. Models for regular horizons, excluding cryoturbated material, showed that all enzyme activities were mainly controlled by carbon or nitrogen. Microbial community composition had no effect. In contrast, models for cryoturbated material showed that enzyme activities were also related to microbial community composition. The additional control of microbial community composition could have restrained enzyme activities and furthermore decomposition in general. The functional decoupling of SOM properties and microbial community composition might thus be one of the reasons for low decomposition rates and the persistence of 400 Gt carbon stored in cryoturbated material.

Microbial community composition shapes enzyme patterns in topsoil and subsoil horizons along a latitudinal transect in Western Siberia

Soil horizons below 30 cm depth contain about 60% of the organic carbon stored in soils. Although insight into the physical and chemical stabilization of soil organic matter (SUM) and into microbial community composition in these horizons is being gained, information on microbial functions of subsoil microbial communities and on associated microbially-mediated processes remains sparse. To identify possible controls on enzyme patterns, we correlated enzyme patterns with biotic and abiotic soil parameters, as well as with microbial community composition, estimated using phospholipid fatty acid profiles. Enzyme patterns (i.e. distance-matrixes calculated from these enzyme activities) were calculated from the activities of six extracellular enzymes (cellobiohydrolase, leucine-amino-peptidase, N-acetylglucosaminidase, chitotriosidase, phosphatase and phenoloxidase), which had been measured in soil samples from organic topsoil horizons, mineral topsoil horizons, and mineral subsoil horizons from seven ecosystems along a 1500 km latitudinal transect in Western Siberia. We found that hydrolytic enzyme activities decreased rapidly with depth, whereas oxidative enzyme activities in mineral horizons were as high as, or higher than in organic topsoil horizons. Enzyme patterns varied more strongly between ecosystems in mineral subsoil horizons than in organic topsoils. The enzyme patterns in topsoil horizons were correlated with SUM content (i.e., C and N content) and microbial community composition. In contrast, the enzyme patterns in mineral subsoil horizons were related to water content, soil pH and microbial community composition. The lack of correlation between enzyme patterns and SUM quantity in the mineral subsoils suggests that SOM chemistry, spatial separation or physical stabilization of SUM rather than SUM content might determine substrate availability for enzymatic breakdown. The correlation of microbial community composition and enzyme patterns in all horizons, suggests that microbial community composition shapes enzyme patterns and might act as a modifier for the usual dependency of decomposition rates on SUM content or C/N ratios. (C) 2015 The Authors. Published by Elsevier Ltd.

Riparian reforestation: are there changes in soil carbon and soil microbial communities?

Reforestation of pastures in riparian zones has the potential to decrease nutrient runoff into waterways, provide both terrestrial and aquatic habitat, and help mitigate climate change by sequestering carbon (C). Soil microbes can play an important role in the soil C cycle, but are rarely investigated in studies on C sequestration. We surveyed a chronosequence (0-23years) of mixed-species plantings in riparian zones to investigate belowground (chemical and biological) responses to reforestation. For each planting, an adjacent pasture was surveyed to account for differences in soil type and land-use history among plantings. Two remnant woodlands were included in the survey as indicators of future potential of plantings. Both remnant woodlands had significantly higher soil organic C (SOC) content compared with their adjacent pastures. However, there was no clear trend in SOC content among plantings with time since reforestation. The substantial variability in SOC sequestration among plantings was possibly driven by differences in soil moisture among plantings and the inherent variability of SOC content among reference pastures adjacent to plantings. Soil microbial phospholipid fatty acids (PLFA, an indicator of microbial biomass) and activities of decomposition enzymes (β-glucosidase and polyphenol oxidase) did not show a clear trend with increasing planting age. Despite this, there were positive correlations between total SOC concentration and microbial indicators (total PLFA, fungal PLFA, bacterial PLFA and activities of decomposition enzymes) across all sites. The soil microbial community compositions (explored using PLFA markers) of older plantings were similar to those of remnant woodlands. There was a positive correlation between the soil carbon:nitrogen (C:N) and fungal:bacterial (F:B) ratios. These data indicate that in order to maximise SOC sequestration, we need to take into account not only C inputs, but the microbial processes that regulate SOC cycling as well.

Plant-mediated effects on microbial diversity in mesocosms of an oligotrophic bog

Globally, peatlands occupy a small portion of terrestrial land area but contain up to one-third of all soil organic carbon. This carbon pool is vulnerable to increased decomposition under projected climate change scenarios but little is known about how plant functional groups will influence microbial communities responsible for regulating carbon cycling processes. Here we examined initial shifts in microbial community structure within two sampling depths under plant functional group manipulations in mesocosms of an oligotrophic bog. Microbial community composition for bacteria and archaea was characterized using targeted 16S rRNA Illumina gene sequencing. We found statistically distinct spatial patterns between the more shallow 10-20 cm sampling depth and the deeper 30-40 cm depth. Significant effects by plant functional groups were found only within the 10-20 cm depth, indicating plant-mediated microbial community shifts respond more quickly near the peat surface. Specifically, the relative abundance of Acidobacteria decreased under ericaceous shrub treatments in the 10-20 cm depth and was replaced by increased abundance of Gammaproteobacteria and Bacteroidetes. In contrast, the sedge rhizosphere continued to be dominated by Acidobacteria but also promoted an increase in the relative recovery of Alphaproteobacteria and Verrucomicrobia. These initial results suggest microbial communities under ericaceous shrubs may be limited by anaerobic soil conditions accompanying high water table conditions, while sedge aerenchyma may be promoting aerobic taxa in the upper peat rhizosphere regardless of ambient soil oxygen limitations.