Species-specific effects of epigeic earthworms on microbial community structure during first stages of decomposition of organic matter

Background: Epigeic earthworms are key organisms in organic matter decomposition because of the interactions they establish with microorganisms. The earthworm species and the quality and/or substrate availability are expected to be major factors influencing the outcome of these interactions. Here we tested whether and to what extent the epigeic earthworms Eisenia andrei, Eisenia fetida and Perionyx excavatus, widely used in vermicomposting, are capable of altering the microbiological properties of fresh organic matter in the short-term. We also questioned if the earthworm-induced modifications to the microbial communities are dependent on the type of substrate ingested. Methodology/Principal Findings: To address these questions we determined the microbial community structure (phospholipid fatty acid profiles) and microbial activity (basal respiration and microbial growth rates) of three types of animal manure (cow, horse and rabbit) that differed in microbial composition, after being processed by each species of earthworm for one month. No differences were found between earthworm-worked samples with regards to microbial community structure, irrespective of type of manure, which suggests the existence of a bottleneck effect of worm digestion on microbial populations of the original material consumed. Moreover, in mesocosms containing cow manure the presence of E. andrei resulted not only in a decrease in bacterial and fungal biomass, but also in a reduced bacterial growth rate and total microbial activity, while no such reduction was found with E. fetida and P. excavatus. Conclusions/Significance: Our results point to the species of earthworm with its associated gut microbiota as a strong determinant of the process shaping the structure of microbial communities in the short-term. This must nonetheless be weighed against the fact that further knowledge is necessary to evaluate whether the changes in the composition of microbiota in response to the earthworm species is accompanied by a change in the microbial community diversity and/or function.Ministerio de Ciencia e Innovación | Ref. CTM2009-0847

Adaptation of soil microbial communities to temperature: comparison of fungi and bacteria in a laboratory experiment

Temperature not only has direct effects on microbial activity, but can also affect activity indirectly by changing the temperature dependency of the community. This would result in communities performing better over time in response to increased temperatures. We have for the first time studied the effect of soil temperature (5–50 °C) on the community adaptation of both bacterial (leucine incorporation) and fungal growth (acetate‐in‐ergosterol incorporation). Growth at different temperatures was estimated after about a month using a short‐term assay to avoid confounding the effects of temperature on substrate availability. Before the experiment started, fungal and bacterial growth was optimal around 30 °C. Increasing soil temperature above this resulted in an increase in the optimum for bacterial growth, correlated to soil temperature, with parallel shifts in the total response curve. Below the optimum, soil temperature had only minor effects, although lower temperatures selected for communities growing better at the lowest temperature. Fungi were affected in the same way as bacteria, with large shifts in temperature tolerance at soil temperatures above that of optimum for growth. A simplified technique, only comparing growth at two contrasting temperatures, gave similar results as using a complete temperature curve, allowing for large scale measurements also in field situations with small differences in temperature

Epigeic earthworms exert a bottleneck effect on microbial communities through gut associated processes

Background: Earthworms play a critical role in organic matter decomposition because of the interactions they establish with microorganisms. The ingestion, digestion, assimilation of organic material in the gut and then casting is the first step in earthworm-microorganism interactions. The current knowledge of these direct effects is still limited for epigeic earthworm species, mainly those living in man-made environments. Here we tested whether and to what extent the earthworm Eisenia andrei is capable of altering the microbiological properties of fresh organic matter through gut associated processes; and if these direct effects are related to the earthworm diet. Methodology: To address these questions we determined the microbial community structure (phospholipid fatty acid profiles) and microbial activity (fluorescein diacetate hydrolysis) in the earthworm casts derived from three types of animal manure (cow, horse and pig manure), which differed in microbial composition. Principal Findings: The passage of the organic material through the gut of E. andrei reduced the total microbial biomass irrespective of the type of manure, and resulted in a decrease in bacterial biomass in all the manures; whilst leaving the fungi unaffected in the egested materials. However, unlike the microbial biomass, no such reduction was detected in the total microbial activity of cast samples derived from the pig manure. Moreover, no differences were found between cast samples derived from the different types of manure with regards to microbial community structure, which provides strong evidence for a bottleneck effect of worm digestion on microbial populations of the original material consumed. Conclusions/Significance: Our data reveal that earthworm gut is a major shaper of microbial communities, thereby favouring the existence of a reduced but more active microbial population in the egested materials, which is of great importance to understand how biotic interactions within the decomposer food web influence on nutrient cycling.Ministerio de Ciencia e Innovación | Ref. CTM2009-0847

Papel de las lombrices de tierra en la degradación del bagazo de uva: efectos sobre las características químicas y la microflora en las primeras etapas del proceso.

The wine industry, of particular importance in various regions of Spain, generates vast amounts of organic waste during the different stages of wine production. Among the possible methodological alternatives available for its treatment, vermicomposting is one of the best-known processes for the biological stabilization of solid organic wastes by transforming them into safer and more stabilized materials suitable for application to soil. In this study we analyzed the chemical, biochemical and microbiological changes that occur in the first stages of the degradation of grape marc, an organic residue whose accumulation and management constitute an important environmental problem. After fifteen days of vermicomposting, a significant reduction in the fungal biomass measured as the ergosterol content was observed, as well as a reduction in microbial activity and cellulase and protease activities. The speed at which these transformations occurred makes vermicomposting a good system for studying the role of earthworms and their associated microflora in the first stages of grape marc degradation, providing important advances in the possible application of vermicomposting as an alternative for the treatment of organic residues derived from the wine industry.La industria vitivinícola, de gran importancia en varias regiones de España, genera una gran cantidad de residuos originados en las distintas etapas de la fabricación del vino. De las diversas alternativas para su tratamiento, el vermicompostaje constituye un proceso adecuado de estabilización de estos residuos, eliminando su contaminación potencial y permitiendo obtener un producto estable e inocuo con grandes posibilidades de utilización en la agricultura. En este trabajo estudiamos los cambios químicos, bioquímicos y microbiológicos que se producen a corto plazo en la degradación del bagazo de uva, un residuo orgánico cuya acumulación y gestión constituye un importante problema ambiental. Tras quince días de procesado por las lombrices, se observó una reducción significativa en la biomasa fúngica medida como el contenido de ergosterol, así como una disminución de la actividad microbiana y de las actividades enzimáticas celulasa y proteasa. La rapidez con que ocurrieron estas transformaciones hacen del proceso de vermicompostaje un buen sistema para estudiar el papel de las lombrices de tierra y su microflora asociada en la primeras etapas de la degradación del bagazo de uva; y proporcionan un importante avance de la posible aplicación del vermicompostaje como una alternativa para el tratamiento de residuos orgánicos derivados de la industria vitivinícola

Short-term stabilization of grape marc through earthworms

The winery industry generates vast amounts of organic waste during the various stages of wine production. Among the possible methodological alternatives available for its treatment, vermicomposting is one of the best-known processes for the biological stabilization of solid organic wastes by transforming them into safer and more stabilized materials suitable for application to soil. In this study we carried out a mesocosm experiment to evaluate the effectiveness of the active phase of vermicomposting for the stabilization of grape marc, an enriched lignocellulosic by-product obtained after the grape crushing and pressing stages in wine production. For this we analysed the chemical, biochemical and microbiological properties of the product resulting from this phase, in comparison with those in a control treatment. Earthworm activity reduced the abundance of both bacterial and fungal PLFA biomarkers. Decreases in microbial activity and in protease and cellulase activities were also attributed to the presence of earthworms. The differences in microbial communities were accompanied by a reduction in the labile C pool and the cellulose content. These results indicate that earthworms played a key role in the stabilization of the grape marc in the short-term, via its effects on organic matter decomposition and microbial biomass and activity.Xunta de Galicia | Ref. 09TAL012209PRMinisterio de Ciencia e Innovación | Ref. CTM2009-0847

Short-term effects of organic and inorganic fertilizers on soil microbial community structure and function: A field study with sweet corn

A field study was carried out to analyze the short-term impacts of replacing mineral by organic fertilizers on the microbial and biochemical parameters relevant for soil fertility and crop yield. Three types of fertilization regimes were compared: (1) conventional fertilizer regime with inorganic fertilizer, and combined integrated fertilizer regimes in which 25 % of the nutrients were supplied by either (2) rabbit manure or (3) vermicompost. The effects on microbial community structure and function (phospholipid fatty acid [PLFA] profiles, bacterial growth, fungal growth, basal respiration, β-glucosidase, protease and phosphomonoesterase activities), soil biochemical properties (total C, dissolved organic carbon [DOC], N-NH4 +, N-NO3 -, PO4, total K) and crop yield were investigated in the samples collected from the experimental soil at harvest, 3 months after addition of fertilizer. The integrated fertilizer regimes stimulated microbial growth, altered the structure of soil microbial community and increased enzyme activity relative to inorganic fertilization. Bacterial growth was particularly influenced by the type of fertilizer regime supplied, while fungal growth only responded to the amount of fertilizer provided. The use of manure produced a fast increase in the abundance of PLFA biomarkers for Gram-negative bacteria as compared to inorganic fertilizer. Nutrient supply and crop yield with organic fertilizers were maintained at similar levels to those obtained with inorganic fertilizer. The effects of the organic amendments were observed even when they involved a small portion of the total amount of nutrients supplied; thereby confirming that some of the beneficial effects of integrated fertilizer strategies may occur in the short term.Ministerio de Ciencia e Innovación | Ref. CTM2009-08477Xunta de GaliciaFundación Alfonso Martín Escuder