Marco Luna-Guido

Methanogenesis and Methanotrophy in Soil: A Review

Abstract Global warming, as a result of an increase in the mean temperature of the planet, might lead to catastrophic events for humanity. This temperature increase is mainly the result of an increase in the atmospheric greenhouse gases (GHG) concentration. Water vapor, carbon dioxide (CO 2 ), methane (CH 4 ) and nitrous oxide (N 2 O) are the most important GHG, and human activities, such as industry, livestock and agriculture, contribute to the production of these gases. Methane, at an atmospheric concentration of 1.7 μmol mol −1 currently, is responsible for 16% of the global warming due to its relatively high global warming potential. Soils play an important role in the CH 4 cycle as methanotrophy (oxidation of CH 4 ) and methanogenesis (production of CH 4 ) take place in them. Understanding methanogenesis and methanotrophy is essential to establish new agriculture techniques and industrial processes that contribute to a better balance of GHG. The current knowledge of methanogenesis and methanotrophy in soils, anaerobic CH 4 oxidation and methanotrophy in extreme environments is also discussed.

Chemical and biological characteristics of alkaline saline soils from the former Lake Texcoco as affected by artificial drainage

Abstract Soils from the former Lake Texcoco are alkaline saline and were artificially drained and irrigated with sewage effluents since the late 1980s. Undrained soil and soil drained for 1, 5 and 8 years were sampled, characterized and incubated aerobically for 90 days at 22±1  °C while production of CO2, available P and concentrations of NH4+, NO2– and NO3– were monitored. Artificial drainage decreased pHH2O, water holding capacity, organic C, total N, and Na+, K+, Mg2+, B, Cl– and SO42– concentrations, increased inorganic C and Ca2+ concentrations more than 5-fold while total P was not affected. Microbial biomass C decreased with increased length of drainage but bacteria, actinomycetes, denitrifiers and cellulose-utilizing bacteria tended to show opposite trends. CO2 production was less in soils drained ≥5 years compared to undrained soil but more than in soils drained for 1 year. Emission of NH3 was negligible and concentrations of NH4+ remained constant over time in each soil. Nitrification, as witnessed by increases in NO3– concentrations, occurred in soil drained for 8 years. NO2– concentrations decreased in soils drained ≤1 year in the first 7 days of the incubation and remained constant thereafter. It was found that artificial drainage of soils from the former Lake Texcoco profoundly affected soil characteristics. Decreases in pH and Na+, K+, Cl– and SO42– concentrations made conditions more favourable for plant growth, although low concentrations of inorganic N and available P might be limiting factors.

Remediation of PAHs in a saline-alkaline soil amended with wastewater sludge and the effect on dynamics of C and N

Contamination of soil with hydrocarbons occurs frequently and organic material, such as sludge, is often applied to accelerate their dissipation. Little is known, however, how sludge characteristics affect removal of polycyclic aromatic hydrocarbons (PAHs) from alkaline-saline soil. Soil of the former lake Texcoco with pH 9 and electrolytic conductivity 7 dS m(-1) was contaminated with phenanthrene and anthracene and amended with sludge, sterilized sludge, sludge adjusted to maintain pH in contaminated soil or glucose plus an inorganic N and P source while emission of CO2 and concentrations of NH4+, NO3-, NO2-, extractable P, phenanthrene and anthracene were monitored in an aerobic incubation experiment of 112 days. An agricultural soil from Acolman treated in the same way served as control. Contaminating the Texcoco soil increased emission of CO2 significantly, but not in the Acolman soil. After 112 days, the largest concentration of anthracene and phenanthrene was found in the Acolman soil added with glucose and the lowest in the sludge-amended soil. The largest concentration of anthracene in the Texcoco soil was found in soil added with sterile sludge and the lowest in the sludge-amended soil. The largest concentration of phenanthrene in the Texcoco soil was found in the glucose-amended soil and the lowest in the sludge-amended soil. It was found that addition of sludge removed more phenanthrene, but not anthracene from soil compared to the unamended contaminated soil, glucose inhibited dissipation of PAHs while microorganisms in the sludge contributed to their removal, and adjustment of soil pH had no effect. Organic material can be used to accelerate removal of hydrocarbons from soil, but the effect is controlled by soil type, contaminant and organic material characteristics.

Rapid immobilization of applied nitrogen in saline–alkaline soils

The dynamics of inorganic N are important in soil, and this applies particularly to the saline–alkaline soils of the former lake Texcoco in Mexico with high pH and salinity where a forestation program was started in the 1970s. In soils of lake Texcoco, in Mexico, more than 50% of applied N could not be accounted for one day after application of 200 mg kg−1 soil along with glucose amendment. It was not clear whether this was due to abiotic or biotic processes, the form of inorganic N applied or the result of applying an easily decomposable substrate. We investigated this by adding glucose and 200 mg kg−1 soil as (NH4)2SO4-N or KNO3-N to sterilized and unsterilized soil. The changes in inorganic and ninhydrin N, microbial biomass C and production of CO2 were then monitored. Between the time of applying N and extraction with 0.5 M K2SO4, i.e., after ca 2 h, approximately 110 mg NH4+-N kg−1 dry soil could not be accounted for in the unsterilized and sterilized soil and that remained so for the entire incubation in the sterilized soil. After 1 day this increased to 140 mg NH4+-N kg−1 dry soil in the unsterilized control and 170 mg NH4+-N kg−1 dry soil in C amended soil. Volatilization of NH3 accounted for 56 mg NH4+-N kg−1 so the rest appeared to be adsorbed on the soil matrix. The NH3 volatilization and NH4+ fixed in the soil matrix remained constant over time and no oxidation to NO2− or NO3− had occurred, so unaccounted N in unsterilized soil was probably incorporated into the microbial biomass in excess of what was required for metabolic activity. The unaccounted N was ca 70 mg NO3−–N in nitrate amended soil after 3 days and 138 NO3−–N when glucose was additionally added. Losses through abiotic processes were absent as inferred from changes in sterilized soil and the aerobic incubation inhibited possible losses through denitrification. It was inferred that NO3− that could not be accounted for was taken up by micro-organisms in excess of what was required for metabolic activity.

Emission of CO2 and N2O from soil cultivated with common bean (Phaseolus vulgaris L.) fertilized with different N sources.

Addition of different forms of nitrogen fertilizer to cultivated soil is known to affect carbon dioxide (CO(2)) and nitrous oxide (N(2)O) emissions. In this study, the effect of urea, wastewater sludge and vermicompost on emissions of CO(2) and N(2)O in soil cultivated with bean was investigated. Beans were cultivated in the greenhouse in three consecutive experiments, fertilized with or without wastewater sludge at two application rates (33 and 55 Mg fresh wastewater sludge ha(-1), i.e. 48 and 80 kg N ha(-1) considering a N mineralization rate of 40%), vermicompost derived from the wastewater sludge (212 Mg ha(-1), i.e. 80 kg N ha(-1)) or urea (170 kg ha(-1), i.e. 80 kg N ha(-1)), while pH, electrolytic conductivity (EC), inorganic nitrogen and CO(2) and N(2)O emissions were monitored. Vermicompost added to soil increased EC at onset of the experiment, but thereafter values were similar to the other treatments. Most of the NO(3)(-) was taken up by the plants, although some was leached from the upper to the lower soil layer. CO(2) emission was 375 C kg ha(-1) y(-1) in the unamended soil, 340 kg C ha(-1) y(-1) in the urea-amended soil and 839 kg ha(-1) y(-1) in the vermicompost-amended soil. N(2)O emission was 2.92 kg N ha(-1) y(-1) in soil amended with 55 Mg wastewater sludge ha(-1), but only 0.03 kg N ha(-1) y(-1) in the unamended soil. The emission of CO(2) was affected by the phenological stage of the plant while organic fertilizer increased the CO(2) and N(2)O emission, and the yield per plant. Environmental and economic implications must to be considered to decide how many, how often and what kind of organic fertilizer could be used to increase yields, while limiting soil deterioration and greenhouse gas emissions.

Mineralization of 14C-labelled maize in alkaline saline soils

The turnover of organic material determines the availability of plant nutrients in unfertilized soils, and this applies particularly to the alkaline saline soil of the former Lake Texcoco in Mexico. Uniformly labelled [14C] maize and its neutral detergent fibre (NDF) fraction, mainly containing cellulose and hemi-cellulose, were added to these soils to investigate dynamics of C and N and the importance of the NDF fraction. Soil with electrolytic conductivity (EC) of 1.2, 3.2, 24.6 and 32.7 dS m−1 was incubated aerobically, while CO2 and 14CO2 production, and inorganic N dynamics (NH4+, NO2−, NO3−) were monitored. The amount of 14C-labelled maize mineralized after 97 days was >500 mg C kg−1 dry soil (D.S.) of the 1000 mg C kg−1 D.S. added in soils with EC≤ 24.6 dS m−1, but only 257 mg C kg−1 D.S. in soil with EC 32.7 dS m−1. The decomposition of the NDF fraction showed a lag, greatest in the soil with the largest EC and the amount of 14C-labelled NDF fraction mineralized after 97 days was > 300 mg C kg−1 D.S. in soils with EC ≤ 3.2 dS m−1, but in the soil with EC 32.7 dS m−1 it was only 118 mg C kg−1D.S. Application of 14C-labelled maize and the NDF fraction induced a priming effect, most accentuated at the onset of the incubation. The ratio between the amount of CO2 produced due to the priming effect and the 14CO2 produced was 16-times larger when 250 mg maize-C kg−1 D.S. was added and only 3-times when 2000 mg maize-C kg−1 D.S. was added. Oxidation of NO2− occurred in soil with EC 32.7 dS m−1 as witnessed by decreases in concentration of NO2− and increases in concentration of NO3−. It was found that EC affected the decomposition of maize, the NDF fraction and the priming effect. Decomposition of cellulose and oxidation of NO2− occurred in soil with EC 32.7 dS m−1 although cellulolytic micro-organisms and autotrophic NO2− oxidizers could previously not be isolated from this soil.

Soil processes as affected by replacement of natural mesquite ecosystem with maize crop

Abstract In the central highlands of Mexico, the vegetation is dominated by mesquite (Prosopis spp.), a leguminous tree or shrub. An experiment was carried out to investigate how cultivating the land and the disappearance of the natural ecosystem affected the biological functioning of the soil. Soil was sampled from under the canopy of isolated (MESQ treatment) and densely growing mesquite trees (DENS treatment), from the surrounding soil not covered by the canopies of the trees (BARE treatment) and from adjacent land cultivated with maize (ARABLE treatment). Soil was characterized and then incubated aerobically for 39 days at 22±1  °C and CO2, N2O production, microbial biomass C and inorganic N concentrations were monitored. The organic C content was 2.3 times and 1.1 times greater in the MESQ and the BARE treatments, respectively, than in the ARABLE treatment, while microbial biomass C was 3.5 times and 1.3 times greater. The microbial biomass activity as expressed by CO2 production was 5.9 times and 3.9 times greater in the MESQ and the BARE treatments, respectively, than in the ARABLE treatment, while N mineralization, as witnessed by the increase in NO3– concentrations, was 3.4 times and 1.7 times greater. No significant amounts of N2O were produced in any of the treatments. It was found that cultivating land characterized by the presence of mesquite changed its characteristics profoundly, and even soil not covered by tree canopies had higher microbial biomass C, and C and N mineralization than soil cultivated with maize and beans.

Flocculant in wastewater affects dynamics of inorganic N and accelerates removal of phenanthrene and anthracene in soil

Recycling of municipal wastewater requires treatment with flocculants, such as polyacrylamide. It is unknown how polyacrylamide in sludge affects removal of polycyclic aromatic hydrocarbons (PAH) from soil. An alkaline-saline soil and an agricultural soil were contaminated with phenanthrene and anthracene. Sludge with or without polyacrylamide was added while emission of CO(2) and concentrations of NH(4)(+), NO(3)(-), NO(2)(-), phenanthrene and anthracene were monitored in an aerobic incubation experiment. Polyacrylamide in the sludge had no effect on the production of CO(2), but it reduced the concentration of NH(4)(+), increased the concentration of NO(3)(-) in the Acolman soil and NO(2)(-) in the Texcoco soil, and increased N mineralization compared to the soil amended with sludge without polyacrylamide. After 112d, polyacrylamide accelerated the removal of anthracene from both soils and that of phenanthrene in the Acolman soil. It was found that polyacrylamide accelerated removal of phenanthrene and anthracene from soil.

454 pyrosequencing-based characterization of the bacterial consortia in a well established nitrifying reactor.

This present study aimed to characterize the bacterial community in a well-established nitrifying reactor by high-throughput sequencing of 16S rRNA amplicons. The laboratory-scale continuous stirred tank reactor has been supplied with ammonium (NH(4)(+)) as sole energy source for over 5 years, while no organic carbon has been added, assembling thus a unique planktonic community with a mean NH(4)(+) removal rate of 86 ± 1.4 mg NH(4)(+)-N/(L d). Results showed a nitrifying community composed of bacteria belonging to Nitrosomonas (relative abundance 11.0%) as the sole ammonia oxidizers (AOB) and Nitrobacter (9.3%) as the sole nitrite oxidizers (NOB). The Alphaproteobacteria (42.3% including Nitrobacter) were the most abundant class within the Proteobacteria (62.8%) followed by the Gammaproteobacteria (9.4%). However, the Betaproteobacteria (excluding AOB) contributed only 0.08%, confirming that Alpha- and Gammaproteobacteria thrived in low-organic-load environments while heterotrophic Betaproteobacteria are not well adapted to these conditions. Bacteroidetes, known to metabolize extracellular polymeric substances produced by nitrifying bacteria and secondary metabolites of the decayed biomass, was the second most abundant phylum (30.8%). It was found that Nitrosomonas and Nitrobacter sustained a broad population of heterotrophs in the reactor dominated by Alpha- and Gammaproteobacteria and Bacteroidetes, in a 1:4 ratio of total nitrifiers to all heterotrophs.

Bacterial Communities in Soil Under Moss and Lichen-Moss Crusts

Biological soil crusts are symbiotic microbial communities formed by green algae, mosses, fungi, lichens, cyanobacteria and bacteria in different proportions. Crusts contribute to soil fertility and favour water retention and infiltration. However, little is known about the bacterial community structure in soil under the crusts. Soil was sampled under a moss crust (considered the MOSS group), lichen plus moss (considered the LICHEN group) and bare soil (considered the BARE group) and the microbial communities determined using nearly full 16S rRNA gene libraries. Bacteria belonging to seven different phyla were found and the Acidobacteria and Alphaproteobacteria were the dominant in each group. The crusts affected negatively the abundance of the Burkholderiales. The phylogenetic diversity and bacterial community membership were different in the LICHEN group compared to the BARE and MOSS groups, but not species richness and community structure. The beta diversity analysis also revealed a different bacterial community structure beneath the LICHEN and MOSS crusts, suggesting species-specific influence. This is a first insight into the effect of a biological soil crust on the bacterial community structure in an organic matter rich soil of a high altitude mountain forest.