Microcosm enrichment of 1,3-dichloropropene-degrading soil microbial communities in a compost-amended soil

AIMS: A microcosm-enrichment approach was used to investigate bacterial populations that may represent 1,3-dichloropropene (1,3-D)-degrading micro-organisms in compost-amended soil. METHODS AND RESULTS: After 8 weeks of incubation, with repeated application of 1,3-D, volatilization fluxes were much lower for compost-amended soil (CM) than with the unamended soils, indicating accelerated degradation due to addition of compost, or development of new microbial populations with enhanced degradation capacity. Denaturing gradient gel electrophoresis (DGGE) profiles of the PCR-amplified region of 16S rDNA genes were used to identify dominant bacterial populations in the fumigant-degrading soil. The DGGE results indicated that specific bacterial types had been enriched, and a more diverse fingerprint was observed in the community derived from the compost-amended soil compared with the unamended soil. Fragments from 16 different DGGE bands were cloned, sequenced and compared with published 16S rDNA sequences. Two clones, designated E1 and E4, were unique to all soils to which compost was added, and corresponded to strains of Pseudomonas and Actinomadura, respectively. CONCLUSIONS: The results show that the addition of compost to soil increases specific microbial populations and results in the accelerated degradation of fumigants. SIGNIFICANCE AND IMPACT OF THE STUDY: Application of compost manure to soil can help degrade soil fumigants at a faster rate.     

Redox and temperature-sensitive changes in microbial communities and soil chemistry dictate greenhouse gas loss from thawed permafrost

Shelf seas and their associated benthic habitats represent key systems in the global carbon cycle. However, the quantification of the related stocks and flows of carbon are often poorly constrained. To address benthic carbon storage in the North–West European continental shelf, we have spatially predicted the mass of particulate organic carbon (POC) stored in the top 10 cm of shelf sediments in parts of the North Sea, English Channel and Celtic Sea using a Random Forest model, POC measurements on surface sediments from those seas and relevant predictor variables. The presented model explains 78% of the variance in the data and we estimate that approximately 250 Mt of POC are stored in surficial sediments of the study area (633,000 km²). Upscaling to the North–West European continental shelf area (1,111,812 km²) yielded a range of 230–882 Mt of POC with the most likely estimate being on the order of 476 Mt. We demonstrate that the largest POC stocks are associated with coarse-grained sediments due to their wide-spread occurrence and high dry bulk densities. Our results also highlight the importance of coastal sediments for carbon storage and sequestration. Important predictors for POC include mud content in surficial sediments, annual average bottom temperature and distance to shoreline, with the latter possibly a proxy for terrestrial inputs. Now that key variables in determining the spatial distribution of POC have been identified, it is possible to predict future changes to the POC stock, with the presented maps providing an accurate baseline against which to assess predicted changes.     

Temperature fluctuation facilitates coexistence of competing species in experimental microbial communities

1. Temperature fluctuation is a general phenomenon affecting many, if not all, species in nature. While a few studies have shown that temperature fluctuation can promote species coexistence, little is known about the effects of different regimes of temperature fluctuation on coexistence. 2. We experimentally investigated how temperature fluctuation and different regimes of temperature fluctuation ('red' environments in which temperature series exhibited positive temporal autocorrelation vs. 'white' environments in which temperature series showed little autocorrelation) affected the coexistence of two ciliated protists, Colpidium striatum Stein and Paramecium tetraurelia Sonneborn, which competed for bacterial resources. 3. We have previously shown that the two species differed in their growth responses to changes in temperature and in their resource utilization patterns. The two species were not always able to coexist at constant temperatures (22, 24, 26, 28 and 30 degrees C), with Paramecium being competitively excluded at 26 and 28 degrees C. This indicated that resource partitioning was insufficient to maintain coexistence at these temperatures. 4. Here we show that in both red and white environments in which temperature varied between 22 and 32 degrees C, Paramecium coexisted with Colpidium. Consistent with the differential effects of temperature on their intrinsic growth rates, Paramecium population dynamics were largely unaffected by temperature regimes, and Colpidium showed more variable population dynamics in the red environments. 5. Temperature-dependent competitive effects of Colpidium on Paramecium, together with resource partitioning, appeared to be responsible for the coexistence in the white environments; resource partitioning and the storage effect appeared to account for the coexistence in the red environments. 6. These results suggest that temperature fluctuation may play important roles in regulating species coexistence and diversity in ecological communities.     

On maintenance and metabolisms in soil microbial communities

Plant and Soil - Biochemistry is an essential yet undervalued aspect of soil ecology, especially when analyzing soil C cycling. We assume, based on tradition, intuition or hope, that the complexity...     

Biodiversity of soil microbial communities in agricultural systems

The productivity and health of agricultural systems depend greatly upon the functional processes carried out by soil microorganisms and soil microbial communities. The biodiversity of the soil microbial communities and the effect of diversity on the stability of the agricultural system, is unknown. Taxonomic approaches to estimating biodiversity of soil microbial communities are limited by difficulties in defining suitable taxonomic units and the apparent non-culturability of the majority of the microbial species present in the soil. Analysis of functional diversity may be a more meaningful approach but is also limited by the need to culture organisms. Approaches which do not rely on culturing organisms such as fatty acid analysis and 16S/18S rRNA analysis have provided an insight into the extent of genetic diversity within communities and may be useful in the analysis of community structure. Scale effects, including successional processes associated with organic matter decomposition, local effects associated with abiotic soil factors, and regional effects including the effect of agricultural management practices, on the diversity of microbial communities are considered. Their impact is important in relation to the minimum biodiversity required to maintain system function.     

Plant phylodiversity enhances soil microbial productivity in facilitation-driven communities

The classical relationship between biodiversity and ecosystem functioning can be better understood when the phylogenetic component of biodiversity is considered. We linked plant phylodiversity and ecosystem functioning in a water-limited gypsum ecosystem driven by plant facilitation. We tested whether (1) plant facilitation relaxes the abiotic filter imposed by gypsum, allowing the establishment of non-gypsophyte plant species, and consequently increasing plant phylodiversity, and (2) plant phylodiversity influences soil microbial productivity. Our data revealed that the gypsophyte Ononis tridentata spatially determines a macrophytic mosaic, ameliorates the microenvironment, and maximizes plant richness and phylodiversity through facilitating non-gypsophyte species. Beyond the direct effect of the nurse plant on soil microbial biomass, activity, and respiration, the analyses suggest a direct effect of plant phylodiversity (MPD) on these general indicators of soil microbial productivity. Plant diversity (Shannon index) neither correlated with the mentioned parameters nor with specific indicators of C, N and P cycling. This is the first report of a relationship between producer phylodiversity and decomposer productivity, which supports phylogenetic diversity as a relevant player of the ecosystem functioning.     

Temporal variability in soil microbial communities across land-use types

Although numerous studies have investigated changes in soil microbial communities across space, questions about the temporal variability in these communities and how this variability compares across soils have received far less attention. We collected soils on a monthly basis (May to November) from replicated plots representing three land-use types (conventional and reduced-input row crop agricultural plots and early successional grasslands) maintained at a research site in Michigan, USA. Using barcoded pyrosequencing of the 16S rRNA gene, we found that the agricultural and early successional land uses harbored unique soil bacterial communities that exhibited distinct temporal patterns. α-Diversity, the numbers of taxa or lineages, was significantly influenced by the sampling month with the temporal variability in α-diversity exceeding the variability between land-use types. In contrast, differences in community composition across land-use types were reasonably constant across the 7-month period, suggesting that the time of sampling is less important when assessing β-diversity patterns. Communities in the agricultural soils were most variable over time and the changes were significantly correlated with soil moisture and temperature. Temporal shifts in bacterial community composition within the successional grassland plots were less predictable and are likely a product of complex interactions between the soil environment and the more diverse plant community. Temporal variability needs to be carefully assessed when comparing microbial diversity across soil types and the temporal patterns in microbial community structure can not necessarily be generalized across land uses, even if those soils are exposed to the same climatic conditions.     

Multivariate drug resistance and microbial risk assessment in tropical coastal communities

Multivariate water quality parameters and statistical analysis were used to evaluate the factors controlling coastal drinking water quality and associated health risks among fisherfolks. Multidrug-resistant strains noticed in 400 isolates show 62% Salmonella; 53% Shigella sp.; 48% E. coli; and 36% Vibrio sp. in groundwater sample. In component analysis seawater intrusion, redox reaction, anthropogenic pollution, and weather factors were responsible for more than 93.3% in postmonsoon and 89.4% in summer season, respectively, for Cumulative %. In epidemiology study, 66% and 76% of municipally supplied drinking water were used in Pondicherry and Rameshwaram, respectively, compared to the amount of groundwater (34% and 20%) used in the study area. Similarly, Pondicherry and Rameshwaram areas recorded open defecation instances of 94% and 82%, respectively where less than 5% of the population used hygienic sanitation as part of the Clean India Mission in rural areas.     

Impact of fumigants on soil microbial communities.

Agricultural soils are typically fumigated to provide effective control of nematodes, soilborne pathogens, and weeds in preparation for planting of high-value cash crops. The ability of soil microbial communities to recover after treatment with fumigants was examined using culture-dependent (Biolog) and culture-independent (phospholipid fatty acid [PLFA] analysis and denaturing gradient gel electrophoresis [DGGE] of 16S ribosomal DNA [rDNA] fragments amplified directly from soil DNA) approaches. Changes in soil microbial community structure were examined in a microcosm experiment following the application of methyl bromide (MeBr), methyl isothiocyanate, 1,3-dichloropropene (1,3-D), and chloropicrin. Variations among Biolog fingerprints showed that the effect of MeBr on heterotrophic microbial activities was most severe in the first week and that thereafter the effects of MeBr and the other fumigants were expressed at much lower levels. The results of PLFA analysis demonstrated a community shift in all treatments to a community dominated by gram-positive bacterial biomass. Different 16S rDNA profiles from fumigated soils were quantified by analyzing the DGGE band patterns. The Shannon-Weaver index of diversity, H, was calculated for each fumigated soil sample. High diversity indices were maintained between the control soil and the fumigant-treated soils, except for MeBr (H decreased from 1.14 to 0.13). After 12 weeks of incubation, H increased to 0.73 in the MeBr-treated samples. Sequence analysis of clones generated from unique bands showed the presence of taxonomically unique clones that had emerged from the MeBr-treated samples and were dominated by clones closely related to Bacillus spp. and Heliothrix oregonensis. Variations in the data were much higher in the Biolog assay than in the PLFA and DGGE assays, suggesting a high sensitivity of PLFA analysis and DGGE in monitoring the effects of fumigants on soil community composition and structure. Our results indicate that MeBr has the greatest impact on soil microbial communities and that 1,3-D has the least impact.     

Substantial labile carbon stocks and microbial activity in deeply weathered soils below a tropical wet forest

Contrary to large areas in Amazonia of tropical moist forests with a pronounced dry season, tropical wet forests in Costa Rica do not depend on deep roots to maintain an evergreen forest canopy through the year. At our Costa Rican tropical wet forest sites, we found a large carbon stock in the subsoil of deeply weathered Oxisols, even though only 0.04–0.2% of the measured root biomass (>2 mm diameter) to 3 m depth was below 2 m. In addition, we demonstrate that 20% or more of this deep soil carbon (depending on soil type) can be mobilized after forest clearing for pasture establishment. Microbial activity between 0.3 and 3 m depth contributed about 50% to the microbial activity in these soils, confirming the importance of the subsoil in C cycling. Depending on soil type, forest clearing for pasture establishment led from no change to a slight addition of carbon in the topsoil (0–0.3 m depth). However, this effect was countered by a substantial loss of C stocks in the subsoil (1–3 m depth). Our results show that large stocks of relatively labile carbon are not limited to areas with a prolonged dry season, but can also be found in deeply weathered soils below tropical wet forests. Forest clearing in such areas may produce unexpectedly high C losses from the subsoil.     

Management of soil microbial communities to enhance populations of Fusarium graminearum-antagonists in soil

Fusarium head blight (FHB), incited by Fusarium graminearum Schwabe is one of the most devastating diseases of wheat. Primary inoculum generated on crop residue is the driving force of FHB epidemics. Fusarium survival on crop residues is affected by soil microbial antagonists. The incorporation of green manures has been shown to increase the density and diversity of microbes in soils, particularly the density and the pathogen-inhibitory activity of specific bacteria and fungi. Evidence of increased streptomycete populations in soil as a response to green manure incorporation, and their negative effect on the survival of Fusarium oxysporum Schlechtendahl in soil, suggests their potential use to reduce the survival of related pathogens. There is, however, no precedent for the use of green manures to promote indigenous streptomycete populations to control FHB. This study investigated the use of green manures (sorghum–sudangrass hybrid [Sorghum bicolor (L.) Moench–S. bicolor (L.) Moench var. sudanense (Piper)] and common buckwheat [Fagopyrum esculentum (Moench)]) for reducing F. graminearum survival in association with wheat residues. Soil bacterial density, streptomycete density and the density and inhibitory activity of F. graminearum-antagonists were monitored from planting until 3 and 6 months following the incorporation of green manures in greenhouse and field experiments, respectively. The decomposition of wheat residues and survival of Fusarium in residues was also assessed. The use of green manures did not statistically impact the survival of F. graminearum in wheat residue. However, green manures promoted the development of higher densities and antagonistic abilities of F. graminearum-antagonists in soils. Additionally, streptomycete densities and F. graminearum-antagonist densities were significantly and positively correlated with reduced survival of Fusarium. The results of our study suggest that the use of green manures can enhance populations of indigenous soil microorganisms antagonistic to the survival of F. graminearum in wheat residue.     

Organic matter inputs shift soil enzyme activity and allocation patterns in a wet tropical forest

Soil extracellular enzymes mediate organic matter turnover and nutrient cycling yet remain little studied in one of Earth’s most rapidly changing, productive biomes: tropical forests. Using a long-term leaf litter and throughfall manipulation, we explored relationships between organic matter (OM) inputs, soil chemical properties and enzyme activities in a lowland tropical forest. We assayed six hydrolytic soil enzymes responsible for liberating carbon (C), nitrogen (N) and phosphorus (P), calculated enzyme activities and ratios in control plots versus treatments, and related these to soil biogeochemical variables. While leaf litter addition and removal tended to increase and decrease enzyme activities per gram soil, respectively, shifts in enzyme allocation patterns implied changes in relative nutrient constraints with altered OM inputs. Enzyme activity ratios in control plots suggested strong belowground P constraints; this was exacerbated when litter inputs were curtailed. Conversely, with double litter inputs, increased enzymatic investment in N acquisition indicated elevated N demand. Across all treatments, total soil C correlated more strongly with enzyme activities than soluble C fluxes, and enzyme ratios were sensitive to resource stoichiometry (soil C:N) and N availability (net N mineralization). Despite high annual precipitation in this site (MAP ~5 m), soil moisture positively correlated with five of six enzymes. Our results suggest resource availability regulates tropical soil enzyme activities, soil moisture plays an additional role even in very wet forests, and relative investment in C, N and P degrading enzymes in tropical soils will often be distinct from higher latitude ecosystems yet is sensitive to OM inputs.     

Composition of soil microbial communities enriched on a mixture of aromatic hydrocarbons

Soil contaminated with C5+, which contained benzene (45%, wt/wt), dicyclopentadiene (DCPD) plus cyclopentadiene (together 20%), toluene (6%), styrene (3%), xylenes (2%), naphthalene (2%), and smaller quantities of other compounds, served as the source for isolation of 55 genomically distinct bacteria (standards). Use of benzene as a substrate by these bacteria was most widespread (31 of 44 standards tested), followed by toluene (23 of 44), xylenes (14 of 44), styrene (10 of 44), and naphthalene (10 of 44). Master filters containing denatured genomic DNAs of all 55 standards were used to analyze the community compositions of C5+ enrichment cultures by reverse sample genome probing (RSGP). The communities enriched from three contaminated soils were similar to those enriched from three uncontaminated soils from the same site. The compositions of these communities were time dependent and showed a succession of Pseudomonas and Rhodococcus spp. before convergence on a composition dominated by Alcaligenes spp. The dominant community members detected by RSGP were capable of benzene degradation at all stages of succession. The enrichments effectively degraded all C5+ components except DCPD. Overall, degradation of individual C5+ hydrocarbons followed first-order kinetics, with the highest rates of removal for benzene.     

Variations in soil N cycling and trace gas emissions in wet tropical forests

We used a previously described precipitation gradient in a tropical montane ecosystem of Hawai’i to evaluate how changes in mean annual precipitation (MAP) affect the processes resulting in the loss of N via trace gases. We evaluated three Hawaiian forests ranging from 2200 to 4050 mm year⁻¹ MAP with constant temperature, parent material, ecosystem age, and vegetation. In situ fluxes of N₂O and NO, soil inorganic nitrogen pools (NH₄⁺ and NO₃⁻), net nitrification, and net mineralization were quantified four times over 2 years. In addition, we performed ¹⁵N-labeling experiments to partition sources of N₂O between nitrification and denitrification, along with assays of nitrification potential and denitrification enzyme activity (DEA). Mean NO and N₂O emissions were highest at the mesic end of the gradient (8.7±4.6 and 1.1±0.3 ng N cm⁻² h⁻¹, respectively) and total oxidized N emitted decreased with increased MAP. At the wettest site, mean trace gas fluxes were at or below detection limit (≤0.2 ng N cm⁻² h⁻¹). Isotopic labeling showed that with increasing MAP, the source of N₂O changed from predominately nitrification to predominately denitrification. There was an increase in extractible NH₄⁺ and decline in NO₃⁻, while mean net mineralization and nitrification did not change from the mesic to intermediate sites but decreased dramatically at the wettest site. Nitrification potential and DEA were highest at the mesic site and lowest at the wet site. MAP exerts strong control N cycling processes and the magnitude and source of N trace gas flux from soil through soil redox conditions and the supply of electron donors and acceptors.     

Reduction of perchlorate and nitrate by microbial communities in vadose soil

Perchlorate contamination is a concern because of the increasing frequency of its detection in soils and groundwater and its presumed inhibitory effect on human thyroid hormone production. Although significant perchlorate contamination occurs in the vadose (unsaturated) zone, little is known about perchlorate biodegradation potential by indigenous microorganisms in these soils. We measured the effects of electron donor (acetate and hydrogen) and nitrate addition on perchlorate reduction rates and microbial community composition in microcosm incubations of vadose soil. Acetate and hydrogen addition enhanced perchlorate reduction, and a longer lag period was observed for hydrogen (41 days) than for acetate (14 days). Initially, nitrate suppressed perchlorate reduction, but once perchlorate started to be degraded, the process was stimulated by nitrate. Changes in the bacterial community composition were observed in microcosms enriched with perchlorate and either acetate or hydrogen. Denaturing gradient gel electrophoresis analysis and partial sequencing of 16S rRNA genes recovered from these microcosms indicated that formerly reported perchlorate-reducing bacteria were present in the soil and that microbial community compositions were different between acetate- and hydrogen-amended microcosms. These results indicate that there is potential for perchlorate bioremediation by native microbial communities in vadose soil.     

Changes in soil microbial communities modulate interactions between maize and weeds

Plant and Soil - Despite the importance of the soil microbiota to plant growth, the role of soil microorganisms in crop-weed competition remains largely unexplored. Here, we investigated the...     

Principal methods for isolation and identification of soil microbial communities

Soil microbial populations play crucial role in soil properties and influence below-ground ecosystem processes. Microbial composition and functioning changes the soil quality through decomposition of organic matter, recycling of nutrients, and biological control of parasites of plants. Moreover, the discovery that soil microbes may translate into benefits for biotechnology, management of agricultural, forest, and natural ecosystems, biodegradation of pollutants, and waste treatment systems maximized the need of scientists for the isolation and their characterization. Operations such as the production of antibiotics and enzymic activities from microorganisms of soil constitute objectives of industry in her effort to cope with the increase of population of earth and disturbance of environment and may ameliorate the effects of global climate change. In the past decades, new biochemical and molecular techniques have been developed in our effort to identify and classify soil bacteria. The goal of measuring the soil microbial diversity is difficult because of the limited knowledge about bacteria species and classification through families and orders. Molecular techniques extend our knowledge about microbial diversity and help the taxonomy of species. Measuring and monitoring soil microbial communities can lead us to better understanding of their composition and function in many ecosystem processes.     

植被恢复对亚热带退化红壤区土壤化学性质与微生物群落的影响

利用1991年在江西省泰和县严重退化的丘陵红壤区建立的长期森林恢复实验基地,以自然恢复的荒草地为对照,分析了湿地松纯林、枫香纯林、湿地松-枫香混交林3种植被类型造林19年后土壤养分和微生物群落数量的变化.结果表明:枫香纯林和湿地松-枫香混交林的土壤有机碳含量(15.16±3.53和16.42±0.49 g·kg-1)显著高于荒草地(9.30±1.13g·kg-1);土壤全磷含量表现为荒草地(0.30±0.02 g·kg-1)＞湿地松-枫香混交林(0.22±0.04g·kg-1)＞枫香纯林(0.14±0.01 g·kg-1);土壤有效磷含量为枫香纯林(1.66±0.02mg·kg-1)、湿地松-枫香混交林(2.47 ±0.27 mg·kg-1)和湿地松纯林(1.15±0.71 mg·kg-1)显著高于荒草地(0.01±0.00 mg·kg-1);土壤的微生物总数、细菌数量及百分比、土壤无机解磷菌和有机解磷菌数量均为枫香纯林、湿地松-枫香混交林显著高于湿地松纯林和荒草地;真菌数量及百分比、放线菌百分比为枫香纯林、湿地松-枫香混交林显著低于荒草地;土壤有机碳含量与细菌百分比呈极显著正相关,与真菌和放线菌百分比呈显著负相关;土壤有效磷与有机解磷菌数量呈显著正相关,与无机解磷菌数量不相关.枫香纯林和湿地松-枫香混交林可以作为亚热带退化红壤区植被恢复的推荐模式.