Changes in microbial community characteristics and soil organic matter with nitrogen additions in two tropical forests

Microbial communities and their associated enzyme activities affect the amount and chemical quality of carbon (C) in soils. Increasing nitrogen (N) deposition, particularly in N-rich tropical forests, is likely to change the composition and behavior of microbial communities and feed back on ecosystem structure and function. This study presents a novel assessment of mechanistic links between microbial responses to N deposition and shifts in soil organic matter (SOM) quality and quantity. We used phospholipid fatty acid (PLFA) analysis and microbial enzyme assays in soils to assess microbial community responses to long-term N additions in two distinct tropical rain forests. We used soil density fractionation and 13C nuclear magnetic resonance (NMR) spectroscopy to measure related changes in SOM pool sizes and chemical quality. Microbial biomass increased in response to N fertilization in both tropical forests and corresponded to declines in pools of low-density SOM. The chemical quality of this soil C pool reflected ecosystem-specific changes in microbial community composition. In the lower-elevation forest, there was an increase in gram-negative bacteria PLFA biomass, and there were significant losses of labile C chemical groups (O-alkyls). In contrast, the upper-elevation tropical forest had an increase in fungal PLFAs with N additions and declines in C groups associated with increased soil C storage (alkyls). The dynamics of microbial enzymatic activities with N addition provided a functional link between changes in microbial community structure and SOM chemistry. Ecosystem-specific changes in microbial community composition are likely to have far-reaching effects on soil carbon storage and cycling. This study indicates that microbial communities in N-rich tropical forests can be sensitive to added N, but we can expect significant variability in how ecosystem structure and function respond to N deposition among tropical forest types.     

Environmental and Biological Assessment of Exposure to Benzene in Petroleum Workers

Occupational exposure to benzene was measured in two gasoline marketing terminals and five major refineries in Singapore. A total of 280 workers were monitored over two years. This assessment was carried out with two primary objectives: (1) To find out the extent of occupational exposure to benzene in the petroleum industry in Singapore, (2) To identify suitable biomarkers for monitoring of low levels of benzene exposure. The exposure was measured in five different categories of petroleum and petrochemical workers, i.e., truck drivers, despatch assistant, process operators, oil movements operators and laboratory technicians. The results revealed wide variations in exposure, from 0.01 to 13.6 ppm for personal time weighted average (TWA) exposure over the whole workshift. The exposure of truck drivers appeared to be the highest, with geometric mean (GM) of 1.98 ppm (ranged from 0.25 to 13.6 ppm). The average benzene exposure for process operators was relative low with a GM of 0.04 ppm. Lowest benzene exposure was found in the laboratory technicians, with a GM of 0.02 ppm. As cigarette smoking is known to affect metabolism of benzene, data analyses on the relationships with environmental exposure were conducted only on the 190 nonsmokers. The results showed that urinary trans, trans-muconic acid (ttMA), unmetabolized benzene in urine (UBZ) and benzene in blood (BBZ) were better biomarkers for low level benzene exposure as compared to urinary phenolic metabolites in urine, such as hydroquinone, phenol and catechol.     

Microbial and environmental effects on avian egg viability: do tropical mechanisms act in a temperate environment?

The viability of freshly laid avian eggs declines after several days of exposure to ambient temperatures above physiological zero, and declines occur faster in tropical than temperate ecosystems. Microbial infection during preincubation exposure has recently been shown as a second cause of egg viability decline in the tropics, but whether microbial processes influence the viability of wild bird eggs in temperate ecosystems is unknown. We determined the microbial load on eggshells, the incidence of microbial penetration of egg contents, and changes in the viability of wild bird eggs (Sialia mexicana, Tachycineta bicolor, Tachycineta thalassina) experimentally exposed to temperate-zone ambient conditions in situ in a mediterranean climate in northern California. Initial microbial loads on eggshells were generally low, although they were significantly higher on eggs laid in old boxes than in new boxes. Eggshell microbial loads did not increase with exposure to ambient conditions, were not reduced by twice-daily disinfection with alcohol, and were unaffected by parental incubation. The rate of microbial penetration into egg contents was low and unaffected by the duration of exposure. Nevertheless, egg viability declined very gradually and significantly with exposure duration, and the rate of decline differed among species. In contrast to studies performed in the tropics, we found little evidence that temperature or microbial mechanisms of egg viability decline were important at our temperate-zone site; neither temperatures above physiological zero nor alcohol disinfection was significantly related to hatching success. Delaying the onset of incubation until the penultimate or last egg of a clutch at our study site may maintain hatching synchrony without a large trade-off in egg viability. These results provide insight into the environmental mechanisms that may be responsible for large-scale latitudinal patterns in avian clutch size and hatching asynchrony.     

Microbial community response to addition of polylactate compounds to stimulate hexavalent chromium reduction in groundwater

To evaluate the efficacy of bioimmobilization of Cr(VI) in groundwater at the Department of Energy Hanford site, we conducted a series of microcosm experiments using a range of commercial electron donors with varying degrees of lactate polymerization (polylactate). These experiments were conducted using Hanford Formation sediments (coarse sand and gravel) immersed in Hanford groundwater, which were amended with Cr(VI) and several types of lactate-based electron donors (Hydrogen Release Compound, HRC; primer-HRC, pHRC; extended release HRC) and the polylactate-cysteine form (Metal Remediation Compound, MRC). The results showed that polylactate compounds stimulated an increase in bacterial biomass and activity to a greater extent than sodium lactate when applied at equivalent carbon concentrations. At the same time, concentrations of headspace hydrogen and methane increased and correlated with changes in the microbial community structure. Enrichment of Pseudomonas spp. occurred with all lactate additions, and enrichment of sulfate-reducing Desulfosporosinus spp. occurred with almost complete sulfate reduction. The results of these experiments demonstrate that amendment with the pHRC and MRC forms result in effective removal of Cr(VI) from solution most likely by both direct (enzymatic) and indirect (microbially generated reductant) mechanisms.     

Tropical forest soil microbial communities couple iron and carbon biogeochemistry

We report that iron-reducing bacteria are primary mediators of anaerobic carbon oxidation in upland tropical soils spanning a rainfall gradient (3500-5000 mm/yr) in northeast Puerto Rico. The abundant rainfall and high net primary productivity of these tropical forests provide optimal soil habitat for iron-reducing and iron-oxidizing bacteria. Spatially and temporally dynamic redox conditions make iron-transforming microbial communities central to the belowground carbon cycle in these wet tropical forests. The exceedingly high abundance of iron-reducing bacteria (up to 1.2 x 10(9) cells per gram soil) indicated that they possess extensive metabolic capacity to catalyze the reduction of iron minerals. In soils from the higher rainfall sites, measured rates of ferric iron reduction could account for up to 44% of organic carbon oxidation. Iron reducers appeared to compete with methanogens when labile carbon availability was limited. We found large numbers of bacteria that oxidize reduced iron at sites with high rates of iron reduction and large numbers of iron reducers. The coexistence of large populations of iron-reducing and iron-oxidizing bacteria is evidence for rapid iron cycling between its reduced and oxidized states and suggests that mutualistic interactions among these bacteria ultimately fuel organic carbon oxidation and inhibit CH4 production in these upland tropical forests.     

In situ reduction of chromium(VI) in heavily contaminated soils through organic carbon amendment

Chromium has become an important soil contaminant at many sites, and facilitating in situ reduction of toxic Cr(VI) to nontoxic Cr(III) is becoming an attractive remediation strategy. Acceleration of Cr(VI) reduction in soils by addition of organic carbon was tested in columns pretreated with solutions containing 1000 and 10 000 mg L(-1) Cr(VI) to evaluate potential in situ remediation of highly contaminated soils. Solutions containing 0,800, or 4000 mg L(-1) organic carbon in the form of tryptic soy broth or lactate were diffused into the Cr(VI)-contaminated soils. Changes in Cr oxidation state were monitored through periodic micro-XANES analyses of soil columns. Effective first-order reduction rate constants ranged from 1.4 x 10(-8) to 1.5 x 10(-7) s(-1), with higher values obtained for lower levels of initial Cr(VI) and higher levels of organic carbon. Comparisons with sterile soils showed that microbially dependent processes were largely responsible for Cr(VI) reduction, except in the soils initially exposed to 10 000 mg L(-1) Cr(VI) solutions that receive little (800 mg L(-1)) or no organic carbon. However, the microbial populations (< or = 2.1 x 10(5) g(-1)) in the viable soils are probably too low for direct enzymatic Cr(VI) reduction to be important. Thus, synergistic effects sustained in whole soil systems may have accounted for most of the observed reduction. These results show that acceleration of in situ Cr(VI) reduction with addition of organic carbon is possible in even heavily contaminated soils and suggest that microbially dependent reduction pathways can be dominant.     

Distribution of chromium contamination and microbial activity in soil aggregates

Biogeochemical transformations of redox-sensitive chemicals in soils can be strongly transport-controlled and localized. This was tested through experiments on chromium diffusion and reduction in soil aggregates that were exposed to chromate solutions. Reduction of soluble Cr(VI) to insoluble Cr(II) occurred only within the surface layer of aggregates with higher available organic carbon and higher microbial respiration. Sharply terminated Cr diffusion fronts develop when the reduction rate increases rapidly with depth. The final state of such aggregates consists of a Cr-contaminated exterior, and an uncontaminated core, each having different microbial community compositions and activity. Microbial activity was significantly higher in the more reducing soils, while total microbial biomass was similar in all of the soils. The small fraction of Cr(VI) remaining unreduced resides along external surfaces of aggregates, leaving it potentially available to future transport down the soil profile. Using the Thiele modulus, Cr(VI) reduction in soil aggregates is shown to be diffusion rate- and reaction rate-limited in anaerobic and aerobic aggregates, respectively. Thus, spatially resolved chemical and microbiological measurements are necessary within anaerobic soil aggregates to characterize and predict the fate of Cr contamination. Typical methods of soil sampling and analyses that average over redox gradients within aggregates can erase important biogeochemical spatial relations necessary for understanding these environments.     

Methods for measuring denitrification: diverse approaches to a difficult problem.

Denitrification, the reduction of the nitrogen (N) oxides, nitrate (NO3-) and nitrite (NO2-), to the gases nitric oxide (NO), nitrous oxide (N2O), and dinitrogen (N2), is important to primary production, water quality, and the chemistry and physics of the atmosphere at ecosystem, landscape, regional, and global scales. Unfortunately, this process is very difficult to measure, and existing methods are problematic for different reasons in different places at different times. In this paper, we review the major approaches that have been taken to measure denitrification in terrestrial and aquatic environments and discuss the strengths, weaknesses, and future prospects for the different methods. Methodological approaches covered include (1) acetylene-based methods, (2) 15N tracers, (3) direct N2 quantification, (4) N2:Ar ratio quantification, (5) mass balance approaches, (6) stoichiometric approaches, (7) methods based on stable isotopes, (8) in situ gradients with atmospheric environmental tracers, and (9) molecular approaches. Our review makes it clear that the prospects for improved quantification of denitrification vary greatly in different environments and at different scales. While current methodology allows for the production of accurate estimates of denitrification at scales relevant to water and air quality and ecosystem fertility questions in some systems (e.g., aquatic sediments, well-defined aquifers), methodology for other systems, especially upland terrestrial areas, still needs development. Comparison of mass balance and stoichiometric approaches that constrain estimates of denitrification at large scales with point measurements (made using multiple methods), in multiple systems, is likely to propel more improvement in denitrification methods over the next few years.     

Environmental controls on denitrifying communities and denitrification rates: insights from molecular methods.

The advent of molecular techniques has improved our understanding of the microbial communities responsible for denitrification and is beginning to address their role in controlling denitrification processes. There is a large diversity of bacteria, archaea, and fungi capable of denitrification, and their community composition is structured by long-term environmental drivers. The range of temperature and moisture conditions, substrate availability, competition, and disturbances have long-lasting legacies on denitrifier community structure. These communities may differ in physiology, environmental tolerances to pH and O2, growth rate, and enzyme kinetics. Although factors such as O2, pH, C availability, and NO3- pools affect instantaneous rates, these drivers act through the biotic community. This review summarizes the results of molecular investigations of denitrifier communities in natural environments and provides a framework for developing future research for addressing connections between denitrifier community structure and function.