Thymidine and leucine incorporation in soil bacteria with different cell size

Universal microbial reworking of dissolved organic matter along environmental gradients

Soils are losing increasing amounts of carbon annually to freshwaters as dissolved organic matter (DOM), which, if degraded, can offset their carbon sink capacity. However, the processes underlying DOM degradation across environments are poorly understood. Here we show DOM changes similarly along soil-aquatic gradients irrespective of environmental differences. Using ultrahigh-resolution mass spectrometry, we track DOM along soil depths and hillslope positions in forest catchments and relate its composition to soil microbiomes and physico-chemical conditions. Along depths and hillslopes, we find carbohydrate-like and unsaturated hydrocarbon-like compounds increase in abundance-weighted mass, and the expression of genes essential for degrading plant-derived carbohydrates explains >50% of the variation in abundance of these compounds. These results suggest that microbes transform plant-derived compounds, leaving DOM to become increasingly dominated by the same (i.e., universal), difficult-to-degrade compounds as degradation proceeds. By synthesising data from the land-to-ocean continuum, we suggest these processes generalise across ecosystems and spatiotemporal scales. Such general degradation patterns can help predict DOM composition and reactivity along environmental gradients to inform management of soil-to-stream carbon losses.

Hydrogen stable isotope probing of lipids demonstrates slow rates of microbial growth in soil

The rate at which microorganisms grow and reproduce is fundamental to our understanding of microbial physiology and ecology. While soil microbiologists routinely quantify soil microbial biomass levels and the growth rates of individual taxa in culture, there is a limited understanding of how quickly microbes actually grow in soil. For this work, we posed the simple question: what are the growth rates of soil microorganisms? In this study, we measure these rates in three distinct soil environments using hydrogen-stable isotope probing of lipids with 2H-enriched water. This technique provides a taxa-agnostic quantification of in situ microbial growth from the degree of 2H enrichment of intact polar lipid compounds ascribed to bacteria and fungi. We find that growth rates in soil are quite slow and correspond to average generation times of 14 to 45 d but are also highly variable at the compound-specific level (4 to 402 d), suggesting differential growth rates among community subsets. We observe that low-biomass microbial communities exhibit more rapid growth rates than high-biomass communities, highlighting that biomass quantity alone does not predict microbial productivity in soil. Furthermore, within a given soil, the rates at which specific lipids are being synthesized do not relate to their quantity, suggesting a general decoupling of microbial abundance and growth in soil microbiomes. More generally, we demonstrate the utility of lipid-stable isotope probing for measuring microbial growth rates in soil and highlight the importance of measuring growth rates to complement more standard analyses of soil microbial communities.

Direct toxicity of six antibiotics on soil bacterial communities affected by the addition of bio-adsorbents

Reducing the toxicity caused by antibiotics on bacterial communities in the soil is one of the great challenges of this century. For this, the effectiveness of amending the soil with different bioadsorbents such as crushed mussel shell (CMS), pine bark (PB) and biomass ash (BA), as well as combinations of them (CMS + PB and PB + BA) was studied at different doses (0 g kg^-1 to 48 g kg^-1). Soil samples were spiked, separately, with increasing doses (0-2000 mg kg^-1) of cefuroxime (CMX), amoxicillin (AMX), clarithromycin (CLA), azithromycin (AZI), ciprofloxacin (CIP) and trimethoprim (TMP). Their toxicity on bacterial growth was estimated using the tritium-labeled leucine (³H) incorporation method. Toxicity was observed to behave differently depending on the antibiotic family and bioadsorbent, although in different magnitude and at different doses. The toxicity of β-lactams (AMX and CXM) was reduced by up to 54% when the highest doses of bio-adsorbents were added due to the increase in pH (CMS and BA) and carbon (PB) contribution. Macrolides (CLA and AZI) showed slight toxicity in un-amended soil samples, which increased by up to 65% with the addition of the bio-adsorbents. The toxicity of CIP (a fluoroquinolone) increased with the dose of the bio-adsorbents, reaching up to 20% compared with the control. Finally, the toxicity of TMP (a diaminopyrimidine) slightly increased with the dose of bio-adsorbents. The by-products that increase soil pH are those that showed the highest increases of CLA, AZI, CIP and TMP toxicities. These results could help to prevent/reduce environmental pollution caused by different kinds of antibiotics, selecting the most appropriated bio-adsorbents and doses.

Influence of soil properties on the development of bacterial community tolerance to Cu, Ni, Pb and Zn

Pollution-Induced Community Tolerance (PICT) is a helpful and sensitive methodology to evaluate the effect of metal pollution in soils using microorganisms as indicators. PICT was used to determine the increase of bacterial community tolerance to Cu, Ni, Pb and Zn (Δlog IC₅₀), and to assess the influence of soil properties on the development of bacterial community tolerance to Cu, Ni, Pb, and Zn. Soil samples showed a wide range of properties, such as pH (3.96-7.47), texture (13.8-31.7% clay) or organic matter (9.7-30.7%). Bacterial growth measured by the [³H]-leucine incorporation method was used as the PICT endpoint. Bacterial communities generally developed tolerance in response to Cu, Ni and Zn additions to soils. However, bacterial communities showed no tolerance to Pb, probably due to high Pb sorption in studied soils. Soil properties influenced the development of bacterial community tolerance to Cu, Ni and Zn. Effective cation exchange and a soil sorption parameter (Freundlich's linearity index) were the selected variables to estimate Δlog IC₅₀ to Cu (R² = 0.65). Clay content and Ni-soluble are the main factors to estimate Δlog IC₅₀ to Ni (R² = 0.63). Organic matter content and a sorption parameter (maximum sorption capacity of the soil from Langmuir equation) are the soil properties to estimate Δlog IC₅₀ to Zn (R² = 0.45). Most of the variables exerted their effect in soil, i.e. PICT selection phase. However, clay content affected bacterial community tolerance determination (PICT detection phase), leading to overestimated measurements of bacterial community tolerance.

Effects of ciprofloxacin, trimethoprim, and amoxicillin on microbial structure and growth as emerging pollutants reaching crop soils

The presence of emerging pollutants, and specifically antibiotics, in agricultural soils has increased notably in recent decades, causing growing concern as regards potential environmental and health issues. With this in mind, the current study focuses on evaluating the toxicity exerted by three antibiotics (amoxicillin, trimethoprim, and ciprofloxacin) on the growth of soil bacterial communities, when these pollutants are present at different doses, and considered in the short, medium, and long terms (1, 8 and 42 days of incubation). Specifically, the research was carried out in 12 agricultural soils having different physicochemical characteristics and was performed by means of the leucine (³H) incorporation method. In addition, changes in the structure of soil microbial communities at 8 and 42 days were studied in four of these soils, using the phospholipids of fatty acids method for this. The main results indicate that the most toxic antibiotic was amoxicillin, followed by trimethoprim and ciprofloxacin. The results also show that the toxicity of amoxicillin decreases with time, with values of Log IC₅₀ ranging from 0.07 ± 0.05 to 3.43 ± 0.08 for day 1, from 0.95 ± 0.07 to 3.97 ± 0.15 for day 8, and from 2.05 ± 0.03 to 3.18 ± 0.04 for day 42, during the incubation period. Regarding trimethoprim, 3 different behaviors were observed: for some soils the growth of soil bacterial communities was not affected, for a second group of soils trimethoprim toxicity showed dose-response effects that remained persistent over time, and, finally, for a third group of soils the toxicity of trimethoprim increased over time, being greater for longer incubation times (42 days). As regards ciprofloxacin, this antibiotic did not show a toxicity effect on the growth of soil bacterial communities for any of the soils or incubation times studied. Furthermore, the principal component analysis performed with the phospholipids of fatty acids results demonstrated that the microbial community structure of these agricultural soils, which persisted after 42 days of incubation, depended mainly on soil characteristics and, to a lesser extent, on the dose and type of antibiotic (amoxicillin, trimethoprim or ciprofloxacin). In addition, it was found that, in this research, the application of the three antibiotics to soils usually favored the presence of fungi and Gram-positive bacteria.

Linking Bacterial Growth Responses to Soil Salinity with Cd Availability

This study investigated the effects of different types of saline stress on the availability of cadmium (Cd) and bacterial growth. Changes in soil physicochemical properties and DTPA-Cd content as well as microbial responses after the addition of salts were measured. The addition of 18 g kg^-1 of salts with NaCl and Na₂SO₄ increased the available Cd content by up to 17.80%-29.79%. Respiration rate, biomass, and relative bacterial growth decreased with increasing salt concentrations. Estimated salinity tolerance of bacterial communities based on pollution-induced community tolerance. The salinity tolerance index EC₅₀ of the bacterial community was estimated by logistic equation and ranged from 4.32-12.63 g kg^-1. Structural equation modeling showed that soil salinity stress significantly affected Cd availability and bacterial community, while bacterial growth characteristics also contributed to reducing available Cd. We conclude that saline stress can alter soil Cd availability in soils by affecting the growth characteristics of soil bacterial communities.

Time-course evolution of bacterial community tolerance to tetracycline antibiotics in agricultural soils: A laboratory experiment

The presence of antibiotics in soils may increase the selection pressure on soil bacterial communities and cause tolerance to these pollutants. The temporal evolution of bacterial community tolerance to different concentrations of tetracycline (TC), oxytetracycline (OTC) and chlortetracycline (CTC) was evaluated in two soils. The results showed an increase of soil bacterial community tolerance to TC, CTC and OTC only in samples polluted with the highest antibiotic concentrations tested (2000 mg kg^-1). The magnitude of those increases was higher in the soil with the lower organic carbon content (1.6%) than in the soil with an organic carbon content reaching 3.4%. In the soil with low organic carbon content, the time-course evolution showed a maximum increase in the tolerance of bacterial communities to tetracycline antibiotics between 45 and 100 incubation days, while for longer incubation times (360 days) the tolerance decreased. In the soil with high organic carbon content, a similar behavior was found for OTC. However, for CTC and TC, slightly increases and decreases (respectively) were found in the bacterial community tolerance at intermediate incubation times, followed by values close to zero for TC after 360 days of incubation, while for CTC they remained higher than in the control. In conclusion, soil pollution due to tetracyclines may cause bacterial community tolerance to these antibiotics when present at high concentrations. In addition, the risk is higher in soils with low organic matter content, and it decreases with time.

The Effect of Clarithromycin Toxicity on the Growth of Bacterial Communities in Agricultural Soils

The presence of antibiotics in different environmental matrices is a growing concern. The introduction of antibiotics into the soil is mainly due to sewage treatment plants. Once in the soil, antibiotics may become toxic to microbial communities and, as a consequence, can pose a risk to the environment and human health. This study evaluates the potential toxicity of the antibiotic clarithromycin (CLA) in relation to the bacterial community of 12 soils with different characteristics. Bacterial community growth was evaluated in soils spiked in the laboratory with different concentrations of CLA after 1, 8, and 42 incubation days. The results indicated that the addition of clarithromycin to the soil may cause toxicity in the bacterial communities of the soil. In addition, it was observed that toxicity decreases between 1 and 8 incubation days, while the bacterial community recovers completely in most soils after 42 incubation days. The results also show that soil pH and effective cation exchange capacity may influence CLA toxicity.

Use of waste materials to prevent tetracycline antibiotics toxicity on the growth of soil bacterial communities

The increase of concentrations of tetracycline antibiotics in agricultural soils worldwide is of special concern, due to its potential toxic effects on soil bacterial communities. In the present work, the reuse of two waste/by-product materials as soil amendments was tested as a preventive practice for reducing tetracycline antibiotics toxicity in soils. Pine bark (PB), with high percentage of organic carbon, and crushed mussel shell (CMS), a frequent natural liming material, were added to 4 soils in doses 0, 6, 12 and 48 g of by-product per kg^-1 of soil (dry weight) of each one (separately). The soils and soil-waste mixtures were then spiked with tetracycline (TC), oxytetracycline (OTC) and chlortetracycline (CTC). After one day of incubation, the bacterial growth was estimated in soils and soil-mixtures using the leucine incorporation technique. The addition of PB to the soils showed two different behaviors, depending on the antibiotics. The toxicity of TC and OTC decreased with the addition of PB (toxicities going from 6 to 25% and from 5 to 36%, respectively). However, CTC toxicity did not change, or even increased in response to the PB amendment. Regarding soil amendment with CMS, it was not effective to prevent the toxicity of any of the three antibiotics studied.

Use of biomass ash to reduce toxicity affecting soil bacterial community growth due to tetracycline antibiotics

Tetracycline antibiotics (TA) used in veterinary medicine reach terrestrial ecosystems mostly via the repeated applications of animal manures and slurries on agricultural soils, where they may cause toxic effects on bacterial communities. In the current work, we studied the efficacy of adding doses of 0, 6, 24 and 48 g kg^-1 of biomass ash (BA) to four different soils to reduce potential negative effects of tetracycline antibiotics. Specifically, soil samples were polluted with different concentrations of tetracycline, oxytetracycline or chlortetracycline, and the bacterial community growth was estimated using the ³H leucine incorporation technique. Soil amendment with BA increased soil pH (1.3-4.8 units), total carbon (0.7-5.8 g kg^-1) and Fe and Al oxides concentrations (0.25-3.98 g kg^-1), as well as bacterial activity (1-9 times compared to the control). In addition, BA amendment at high doses (24 or 48 g kg^-1) resulted in a similar toxicity decrease for the three antibiotics, but with variations among soils. The reductions in antibiotics toxicity were very variable, ranging between 5% and 100% (total recovery). In view of that, the spreading of BA could be interesting as management practice to reduce risks of soil pollution and subsequent toxicity on bacterial communities due to tetracycline antibiotics.

Effect of Oxytetracycline and Chlortetracycline on Bacterial Community Growth in Agricultural Soils

Toxicity on soil bacterial community growth caused by the antibiotics oxytetracycline (OTC) and chlortetracycline (CTC) was studied in 22 agricultural soils after 1, 8 and 42 incubation days. The leucine incorporation method was used with this aim, estimating the concentration of each antibiotic which caused an inhibition of 50% in bacterial community growth (log IC50). For OTC, the mean log IC50 was 2.70, 2.81, 2.84 for each of the three incubation times, while the values were 2.05, 2.22 and 2.47 for CTC, meaning that the magnitude of OTC toxicity was similar over time, whereas it decreased significantly for CTC with incubation time. In addition, results showed that the toxicity on bacterial community growth due to CTC is significantly higher than when due to OTC. Moreover, the toxicity on bacterial community growth due to both antibiotics is dependent on soil properties. Specifically, an increase in soil pH and silt content resulted in higher toxicity of both antibiotics, while increases in total organic carbon and clay contents caused decreases in OTC and CTC toxicities. The results also show that OTC toxicity can be well predicted by means of specific equations, using the values of pH measured in KCl and those of effective cation exchange capacity as input variables. CTC toxicity may be predicted (but with low precision) using pH measured in KCl and total organic carbon. These equations may help to predict the negative effects caused by OTC and CTC on soil bacteria using easily measurable soil parameters.

Linking Microbial Community Structure to Trait Distributions and Functions Using Salinity as an Environmental Filter

The structure and function of microbial communities vary along environmental gradients; however, interlinking the two has been challenging. In this study, salinity was used as an environmental filter to study how it could shape trait distributions, community structures, and the resulting functions of soil microbes. The environmental filter was applied by salinizing nonsaline soil (0 to 22 mg NaCl g^-1). Our targeted community trait distribution (salt tolerance) was determined with dose-response relationships between bacterial growth and salinity. The bacterial community structure responses were resolved with Illumina 16S rRNA gene amplicon sequencing, and the microbial functions determined were respiration and bacterial and fungal growth. Salt exposure quickly resulted in filtered trait distributions, and stronger filters resulted in larger shifts. The filtered trait distributions correlated well with community composition differences, suggesting that trait distribution shifts were driven at least partly by species turnover. While salt exposure decreased respiration, microbial growth responses appeared to be characterized by competitive interactions. Fungal growth was highest when bacterial growth was inhibited by the highest salinity, and it was lowest when the bacterial growth rate peaked at intermediate salt levels. These findings corroborated a higher potential for fungal salt tolerance than bacterial salt tolerance for communities derived from a nonsaline soil. In conclusion, by using salt as an environmental filter, we could interlink the targeted trait distribution with both the community structure and resulting functions of soil microbes.IMPORTANCE Understanding the role of ecological communities in maintaining multiple ecosystem processes is a central challenge in ecology. Soil microbial communities perform vital ecosystem functions, such as the decomposition of organic matter to provide plant nutrition. However, despite the functional importance of soil microorganisms, attribution of ecosystem function to particular constituents of the microbial community has been impeded by a lack of information linking microbial processes to community composition and structure. Here, we apply a conceptual framework to determine how microbial communities influence ecosystem processes, by applying a "top-down" trait-based approach. By determining the dependence of microbial processes on environmental factors (e.g., the tolerance to salinity), we can define the aggregate response trait distribution of the community, which then can be linked to the community structure and the resulting function performed by the microbial community.

Linking bacterial community composition to soil salinity along environmental gradients

Salinization is recognized as a threat to soil fertility worldwide. A challenge in understanding the effects of salinity on soil microbial communities is the fact that it can be difficult to disentangle the effects of salinity from those of other variables that may co-vary with salinity. Here we use a trait-based approach to identify direct effects of salinity on soil bacterial communities across two salinity gradients. Through dose–response relationships between salinity and bacterial growth, we quantified distributions of the trait salt tolerance within the communities. Community salt tolerance was closely correlated with soil salinity, indicating a strong filtering effect of salinity on the bacterial communities. Accompanying the increases in salt tolerance were consistent shifts in bacterial community composition. We identified specific bacterial taxa that increased in relative abundances with community salt tolerance, which could be used as bioindicators for high community salt tolerance. A strong filtering effect was also observed for pH across the gradients, with pH tolerance of bacterial communities correlated to soil pH. We propose phenotypic trait distributions aggregated at the community level as a useful approach to study the role of environmental factors as filters of microbial community composition.

Biotic and abiotic dissipation of tetracyclines using simulated sunlight and in the dark

Veterinary antibiotics reaching soils and water bodies are considered emerging pollutants deserving special attention. In this work, dissipation of tetracycline (TC), oxytetracycline (OTC) and chlortetracycline (CTC) is investigated. Dissipation experiments in filtered water, using simulated sunlight, resulted in the following degradation sequence: TC < OTC ≈ CTC, with half-life values of 229, 101 and 104 min, respectively; however, no dissipation took place in the dark. Dissipation of the three tetracyclines in culture medium and with simulated sunlight was much higher, giving the sequence TC ≈ OTC < CTC, with half-lives of 9, 10 and 7 min, respectively; in the dark, TC and OTC did not suffer dissipation, but it was around 28% for CTC at the end of the experiment (480 min). The variable explaining a higher dissipation in culture medium and with light was pH, as this parameter caused changes in the distribution of species of tetracyclines, affecting degradation. Adding bacterial suspensions extracted from soil and poultry manure increased dissipation, giving the sequence: TC ≈ OTC < CTC, which is attributed to the presence of humic acids, which adsorb these antibiotics. These results could facilitate understanding the fate of antibiotics reaching environmental compartments and causing public health hazards.

Comparative Toxicities of Salts on Microbial Processes in Soil

Soil salinization is a growing threat to global agriculture and carbon sequestration, but to date it remains unclear how microbial processes will respond. We studied the acute response to salt exposure of a range of anabolic and catabolic microbial processes, including bacterial (leucine incorporation) and fungal (acetate incorporation into ergosterol) growth rates, respiration, and gross N mineralization and nitrification rates. To distinguish effects of specific ions from those of overall ionic strength, we compared the addition of four salts frequently associated with soil salinization (NaCl, KCl, Na2SO4, and K2SO4) to a nonsaline soil. To compare the tolerance of different microbial processes to salt and to interrelate the toxicity of different salts, concentration-response relationships were established. Growth-based measurements revealed that fungi were more resistant to salt exposure than bacteria. Effects by salt on C and N mineralization were indistinguishable, and in contrast to previous studies, nitrification was not found to be more sensitive to salt exposure than other microbial processes. The ion-specific toxicity of certain salts could be observed only for respiration, which was less inhibited by salts containing SO4(2-) than Cl(-) salts, in contrast to the microbial growth assessments. This suggested that the inhibition of microbial growth was explained solely by total ionic strength, while ion-specific toxicity also should be considered for effects on microbial decomposition. This difference resulted in an apparent reduction of microbial growth efficiency in response to exposure to SO4(2-) salts but not to Cl(-) salts; no evidence was found to distinguish K(+) and Na(+) salts.

Cell size distributions of soil bacterial and archaeal taxa

Cell size is a key ecological trait of soil microorganisms that determines a wide range of life history attributes, including the efficiency of nutrient acquisition. However, because of the methodological issues associated with determining cell sizes in situ, we have a limited understanding of how cell abundances vary across cell size fractions and whether certain microbial taxa have consistently smaller cells than other taxa. In this study, we extracted cells from three distinct soils and fractionated them into seven size ranges (5 μm to 0.2 μm) by filtration. Cell abundances in each size fraction were determined by direct microscopy, with the taxonomic composition of each size fraction determined by high-throughput sequencing of the 16S rRNA gene. Most of the cells were smaller than cells typically grown in culture, with 59 to 67% of cells <1.2 μm in diameter. Furthermore, each size fraction harbored distinct bacterial and archaeal communities in each of the three soils, and many of the taxa exhibited distinct size distribution patterns, with the smaller size fractions having higher relative abundances of taxa that are rare or poorly characterized (including Acidobacteria, Gemmatimonadetes, Crenarchaeota, Verrucomicrobia, and Elusimicrobia). In general, there was a direct relationship between average cell size and culturability, with those soil taxa that are poorly represented in culture collections tending to be smaller. Size fractionation not only provides important insight into the life history strategies of soil microbial taxa but also is a useful tool to enable more focused investigations into those taxa that remain poorly characterized.

Importance of inoculum properties on the structure and growth of bacterial communities during Recolonisation of humus soil with different pH

The relationship between community structure and growth and pH tolerance of a soil bacterial community was studied after liming in a reciprocal inoculum study. An unlimed (UL) humus soil with a pH of 4.0 was fumigated with chloroform for 4 h, after which < 1 % of the initial bacterial activity remained. Half of the fumigated soil was experimentally limed (EL) to a pH of 7.6. Both the UL and the EL soil were then reciprocally inoculated with UL soil or field limed (FL) soil with a pH of 6.2. The FL soil was from a 15-year-old experiment. The structural changes were measured on both bacteria in soil and on bacteria able to grow on agar plates using phospholipids fatty acid (PLFA) and denaturing gradient gel electrophoresis (DGGE) analysis. The developing community pH tolerance and bacterial growth were also monitored over time using thymidine incorporation. The inoculum source had a significant impact on both growth and pH tolerance of the bacterial community in the EL soil. These differences between the EL soil inoculated with UL soil and FL soil were correlated to structural changes, as evidenced by both PLFA and DGGE analyses on the soil. Similar correlations were seen to the fraction of the community growing on agar plates. There were, however, no differences between the soil bacterial communities in the unlimed soils with different inocula. This study showed the connection between the development of function (growth), community properties (pH tolerance) and the structure of the bacterial community. It also highlighted the importance of both the initial properties of the community and the selection pressure after environmental changes in shaping the resulting microbial community.

Stable isotope probing of amino sugars--a promising tool to assess microbial interactions in soils

RATIONALE

Bacteria and fungi are key protagonists of litter degradation in soils. Often they have to share common substrates, which has led to special interactions between both microbial groups. Due to the historical classification of bacteriology and mycology as two separate fields of microbial research, the understanding of their interactions in soils is scares, while it is crucial for a better understanding of nutrient recycling and carbon sequestration in soils. Therefore, a new approach to investigate fungal-bacterial interactions is proposed using stable isotope probing of their amino sugar biomarkers.

METHODS

An agricultural soil, under different microbial inhibition treatments, was incubated for 21 days with (13)C-labeled plant residues. Residue respiration was determined by measuring the isotopic composition and concentration of the produced CO2, using an isotope ratio mass spectrometer coupled to a trace gas preparation unit. At several time points, amino sugars were extracted, after hydrolysis, from the incubated microcosms. Subsequently, (13)C-isotopic composition and concentration of the individual amino sugars was determined using liquid chromatography/isotope ratio mass spectrometry.

RESULTS

When the bacterial community was inhibited, fungi showed an increased capacity to metabolize added plant residues indicating an antagonistic effect of bacteria towards fungi. Furthermore, the fungal community was able to take benefit of a larger portion of the residue, which indicates that this antagonism was at least partially due to interference competition. On the other hand, the inhibition of the fungal community appeared to have a very negative effect on the capacity of bacteria to metabolize added plant residues. Therefore, the bacterial community could be considered as playing a parasitic type role towards fungi during litter degradation.

CONCLUSIONS

This newly developed methodology proved to be very useful for elucidating microbial interactions during plant residue degradation.

Influence of different abiotic and biotic factors on the metalaxyl and carbofuran dissipation

Metalaxyl and carbofuran dissipation was studied in response to different factors (soil bacterial communities, light irradiation, presence of an inorganic culture medium and presence of soil) and combinations of these factors in short-term experiments (48 h). The soil microbial communities have no effect on metalaxyl or carbofuran dissipation in the time scale employed. Light irradiation and soil promote metalaxyl and carbofuran dissipation by photodegradation and adsorption, respectively. However, photodegradation has a stronger effect on metalaxyl and carbofuran dissipation than the adsorption of the pesticides in the soil. The addition of the culture medium have no direct effect on pesticide dissipation, degradation by microbial communities or adsorption but its presence greatly increased photodegradation.

Contrasting soil pH effects on fungal and bacterial growth suggest functional redundancy in carbon mineralization

The influence of pH on the relative importance of the two principal decomposer groups in soil, fungi and bacteria, was investigated along a continuous soil pH gradient at Hoosfield acid strip at Rothamsted Research in the United Kingdom. This experimental location provides a uniform pH gradient, ranging from pH 8.3 to 4.0, within 180 m in a silty loam soil on which barley has been continuously grown for more than 100 years. We estimated the importance of fungi and bacteria directly by measuring acetate incorporation into ergosterol to measure fungal growth and leucine and thymidine incorporation to measure bacterial growth. The growth-based measurements revealed a fivefold decrease in bacterial growth and a fivefold increase in fungal growth with lower pH. This resulted in an approximately 30-fold increase in fungal importance, as indicated by the fungal growth/bacterial growth ratio, from pH 8.3 to pH 4.5. In contrast, corresponding effects on biomass markers for fungi (ergosterol and phospholipid fatty acid [PLFA] 18:2omega6,9) and bacteria (bacterial PLFAs) showed only a two- to threefold difference in fungal importance in the same pH interval. The shift in fungal and bacterial importance along the pH gradient decreased the total carbon mineralization, measured as basal respiration, by only about one-third, possibly suggesting functional redundancy. Below pH 4.5 there was universal inhibition of all microbial variables, probably derived from increased inhibitory effects due to release of free aluminum or decreasing plant productivity. To investigate decomposer group importance, growth measurements provided significantly increased sensitivity compared with biomass-based measurements.

Microbial biomass, community structure and metal tolerance of a naturally Pb-enriched forest soil

The effect of long-term elevated soil Pb levels on soil microbiota was studied at a forest site in Norway, where the soil has been severely contaminated with Pb since the last period of glaciation (several thousand years). Up to 10% Pb (total amount, w/w) has been found in the top layer. The microbial community was drastically affected, as judged from changes in the phospholipid fatty acid (PLFA) pattern. Specific PLFAs that were high in Pb-enriched soil were branched (especially br17:0 and br18:0), whereas PLFAs common in eukaryotic organisms such as fungi (18:2omega6,9 and 20:4) were low compared with levels at adjacent, uncontaminated sites. Congruent changes in the PLFA pattern were found upon analyzing the culturable part of the bacterial community. The high Pb concentrations in the soil resulted in increased tolerance to Pb of the bacterial community, measured using both thymidine incorporation and plate counts. Furthermore, changes in tolerance were correlated to changes in the community structure. The bacterial community of the most contaminated soils showed higher specific activity (thymidine and leucine incorporation rates) and higher culturability than that of control soils. Fungal colony forming units (CFUs) were 10 times lower in the most Pb-enriched soils, the species composition was widely different from that in control soils, and the isolated fungi had high Pb tolerance. The most commonly isolated fungus in Pb-enriched soils was Tolypocladium inflatum. Comparison of isolates from Pb-enriched soil and isolates from unpolluted soils showed that T. inflatum was intrinsically Pb-tolerant, and that the prolonged conditions with high Pb had not selected for any increased tolerance.

Counting and size classification of active soil bacteria by fluorescence in situ hybridization with an rRNA oligonucleotide probe

A fluorescence in situ hybridization (FISH) technique based on binding of a rhodamine-labelled oligonucleotide probe to 16S rRNA was used to estimate the numbers of ribosome-rich bacteria in soil samples. Such bacteria, which have high cellular rRNA contents, were assumed to be active (and growing) in the soil. Hybridization to an rRNA probe, EUB338, for the domain Bacteria was performed with a soil slurry, and this was followed by collection of the bacteria by membrane filtration (pore size, 0.2 micrometer). A nonsense probe, NONEUB338 (which has a nucleotide sequence complementary to the nucleotide sequence of probe EUB338), was used as a control for nonspecific staining. Counting and size classification into groups of small, medium, and large bacteria were performed by fluorescence microscopy. To compensate for a difference in the relative staining intensities of the probes and for binding by the rhodamine part of the probe, control experiments in which excess unlabelled probe was added were performed. This resulted in lower counts with EUB338 but not with NONEUB338, indicating that nonspecific staining was due to binding of rhodamine to the bacteria. A value of 4.8 x 10(8) active bacteria per g of dry soil was obtained for bulk soil incubated for 2 days with 0.3% glucose. In comparison, a value of 3.8 x 10(8) active bacteria per g of dry soil was obtained for soil which had been air dried and subsequently rewetted. In both soils, the majority (68 to 77%) of actively growing bacteria were members of the smallest size class (cell width, 0.25 to 0.5 micrometer), but the active (and growing) bacteria still represented only approximately 5% of the total bacterial population determined by DAPI (4', 6-diamidino-2-phenylindole) staining. The FISH technique in which slurry hybridization is used holds great promise for use with phylogenetic probes and for automatic counting of soil bacteria.

Thymidine incorporation of bacteria sequentially extracted from soil using repeated homogenization-centrifugation

Bacteria were sequentially extracted from soil into a water suspension after shaking soil with water or mixing it in a blender followed by a low-speed centrifugation. Bacteria, which were released only after several cycles of homogenization-centrifugation, had higher growth rates as judged from thymidine and leucine incorporation, whereas bacteria that were more readily released by a gentle shaking procedure had the lowest growth rate. This indicated that bacteria more tightly bound to soil particles were growing faster than those that were more easily released into the water suspension. The same pattern was found both in an agricultural and a forest soil, with contrasting pH and organic matter content, and irrespective of whether the bacteria were labeled before or after the centrifugation steps. The different growth rates of the bacteria could not be explained by different partitioning of label between different macromolecules, different cell size, different viability of the bacteria, or different dilution of the added radioactive substrate in the different homogenization-centrifugation fractions. The total amount of phospholipid fatty acids per bacterial cell was also similar in the different fractions. Different composition of the bacterial communities in the different homogenization-centrifugation fractions was indicated by a gradually altered phospholipid fatty acid pattern of the extracted bacteria, and an increased hydrophobicity of the bacteria released only after several homogenization-centrifugation treatments.