[Show abstract][Hide abstract] ABSTRACT: In anoxic environments, degradation of organic matter (OM) results in strong fractionation of carbon isotopes, with formation of 13C-depleted CH4. Propionate and acetate are important products of OM fermentation. Propionate is further fermented to acetate. Acetate is a direct precursor of CH4, the remainder usually being produced from H2-mediated CO2 reduction. There is a paucity of data for the turnover of acetate and, even more so, propionate. We therefore analyzed the δ13C values of organic carbon, propionate, acetate and the methyl (Me) group of acetate (acetate-Me) during the production of CH4 in anoxic incubations of various flooded and non-flooded soils and various lake sediments. Incubation in the presence of methylfluoride (CH3F), which inhibits CH4 production from acetate, allowed exclusion of isotope effects during aceticlastic methanogenesis. Despite the variation inherent in the wide diversity of sample type and origin, the data collectively showed that the δ13C value of acetate was only marginally different (-2 ± 5‰) from that of OM, while propionate was depleted in 13C relative to total acetate (-6 ± 5‰). Acetate-Me was generally depleted in 13C relative to total acetate (-8 ± 5‰). Thus, isotopic enrichment factors during the degradation of OM to total propionate and acetate were much smaller than those during hydrogenotrophic and aceticlastic methanogenesis or the intramolecular difference in δ13C between the carboxyl (CO2H) and Me of acetate, so that the δ13C value of OM may be used as a proxy when data for acetate are not available.
[Show abstract][Hide abstract] ABSTRACT: Accumulating evidence suggests that thaumarchaeota may control nitrification in acidic soils. However, the composition of the thaumarchaeotal communities and their functioning is not well known. Therefore, we studied nitrification activity in relation to abundance and composition of thaumarchaeota in an acidic red soil from China, using microcosms incubated with and without cellulose amendment. Cellulose was selected to simulate the input of crop residues used to increase soil fertility by local farming. Accumulation of NO3--N was correlated with the growth of thaumarchaeota as determined by qPCR of 16S rRNA and ammonia monooxygenase (amoA) genes. Both nitrification activity and thaumarchaeotal growth were inhibited by acetylene. They were also inhibited by cellulose amendment, possibly due to the depletion of ammonium by enhanced heterotrophic assimilation. These results indicated that growth of thaumarchaeota was dependent on ammonia oxidation. The thaumarchaeotal 16S rRNA gene sequences in the red soil were dominated by a clade related to soil fosmid clone 29i4 within the group I.1b, which is widely distributed but so far uncultured. The archaeal amoA sequences were mainly related to the Nitrososphaera sister cluster. These observations suggest that fosmid clone 29i4 and Nitrososphaera sister cluster represent the same group of thaumarchaeota, and dominate ammonia oxidation in acidic red soil.This article is protected by copyright. All rights reserved.
[Show abstract][Hide abstract] ABSTRACT: Ammonia oxidation, performed by specialized microorganisms belonging to the Bacteria and Archaea, is the first and most limiting step of soil nitrification. Nitrification has not yet been examined in young volcanic soils. The aim of the present work was to evaluate the abundance and diversity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in acidic volcanic soils (andisols) of different defined ages to determine their relative contribution to nitrification and soil colonization. Soil was collected from three vegetated sites on Llaima Volcano (Chile) recolonized after lava eruptions in 1640, 1751 and 1957. Quantitative polymerase chain reaction, terminal restriction fragment length polymorphism and clone sequence analyses of the amoA gene were performed for the AOA and AOB communities. All soils showed high nitrification potentials, but they were highest in the younger soils. Archaeal amoA genes outnumbered bacterial amoA genes at all sites, and AOA abundances were found to be proportional to the nitrification potentials. Sequencing indicated the presence of AOA related to Nitrososphaera and Nitrosotalea, and AOB related primarily to Nitrosospira and sporadically to Nitrosomonas. The study showed that both AOA and AOB are early colonizers of andisols, but that AOA outnumber AOB and play an important role in nitrification.
[Show abstract][Hide abstract] ABSTRACT: Temperature is the major driving force for many biological as well as chemical reactions and may impact the fractionation of stable carbon isotopes. Thus, a good correlation between temperature and fractionation is observed in many chemical systems that are controlled by an equilibrium isotope effect. In contrast, biological systems that are usually controlled by a kinetic isotope effect are less well studied with respect to temperature effects and have shown contrasting results. We studied three different biological pathways (methylotrophic methanogenesis, hydrogenotrophic methanogenesis, acetogenesis by the acetyl-CoA pathway) which are characterized by very strong carbon isotope enrichment factors (−50‰ to −83‰). The microorganisms (Methanosarcina barkeri, Methanosarcina acetivorans, Methanolobus zinderi, Methanothermobacter marburgensis, Methanothermobacter thermoautotrophicus, Thermoanaerobacter kivui) exhibiting these pathways were grown at different temperatures ranging between 25 and 68 °C, and the fractionation factors were determined from 13C/12C isotope discrimination during substrate depletion and product formation.
Our experiments showed that the fractionation factors were different for the different metabolic pathways but were not much affected by the different growth temperatures. Slight variations were well within the standard errors of replication and regression analysis. Our results showed that temperature had no significant effect on the fractionation of stable carbon isotopes during anaerobic microbial metabolism with relatively strong isotope fractionation.
Geochimica et Cosmochimica Acta 01/2014; 140:95–105. · 3.88 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Methanogenic microbial communities in soil and sediment function only when the environment is inundated and anoxic. In contrast to submerged soils, desiccation of lake sediments happens only rarely. However, some predictions suggest that extreme events of drying will become more common in the Amazon region, and this will promote an increase in sediments drying and exposure. We asked whether and how such methanogenic communities can withstand desiccation stress. Therefore, we determined the rates and pathways of CH4 production (analysis of CH4 and δ(13) C of CH4 , CO2 and acetate), the copy numbers of bacterial and archaeal 16S rRNA genes and mcrA genes (quantitative PCR), and the community composition of Archaea and Bacteria (T-RFLP and pyrosequencing) in oxbow lake sediments of rivers in the Brazilian Amazon region. The rivers were of white water, black water and clear water type. The measurements were done with sediment in fresh state and after drying and rewetting. After desiccation and rewetting the composition of both, the archaeal and bacterial community changed. Since lake sediments from white water rivers exhibited only negligible methanogenic activity, probably because of relatively high iron and low organic matter content, they were not further analysed. The other sediments produced CH4 , with hydrogenotrophic methanogenesis usually accounting for > 50% of total activity. After desiccation and rewetting, archaeal and bacterial gene copy numbers decreased. The bacterial community showed a remarkable increase of Clostridiales from about 10% to > 30% of all Bacteria, partially caused by proliferation of specific taxa as the numbers of OTU shared with fresh sediment decreased from about 9% to 3%. Among the Archaea, desiccation specifically enhanced the relative abundance of either Methanocellales (black water) and/or Methanosarcinaceae (clear water). Despite the changes in gene copy numbers and composition of the microbial community, rates of CH4 production even increased after desiccation-rewetting, demonstrating that the function of the methanogenic microbial community had not been impaired. This result indicates that the increase in extreme events of drying may increase methane production in flooded sediments.
[Show abstract][Hide abstract] ABSTRACT: Archaea in rice fields play an important role in carbon and nitrogen cycling. They comprise methane-producing Euryarchaeota as well as ammonia-oxidizing Thaumarchaeota, but their community structures and population dynamics have not yet been studied in the same system. Different soil compartments (surface, bulk, rhizospheric soil) and ages of roots (young and old roots) at two N fertilization levels and at three time points (the panicle initiation, heading and maturity periods) of the season were assayed by determining the abundance (using qPCR) and composition (using T-RFLP and cloning/sequencing) of archaeal genes (mcrA, amoA, 16S rRNA). The community of total Archaea in soil and root samples mainly consisted of the methanogens and the Thaumarchaeota and their abundance increased over the season. Methanogens proliferated everywhere, but Thaumarchaeota only on the roots and in response to nitrogen fertilization. The community structures of Archaea, methanogens and Thaumarchaeota, were different in soil and root samples indicating niche differentiation. While Methanobacteriales were generally present, Methanosarcinaceae and Methanocellales were the dominant methanogens in soil and root samples, respectively. The results emphasize the specific colonization of roots by two ecophysiologically different groups of archaea which may belong to the core root biome. This article is protected by copyright. All rights reserved.
[Show abstract][Hide abstract] ABSTRACT: Flooded rice fields are an important source of the greenhouse gas
methane. Methane is produced from rice straw (RS), soil organic matter
(SOM), and rice root organic carbon (ROC). Addition of RS is widely used
for ameliorating soil fertility. However, this practice provides
additional substrate for CH4 production and results in
increased CH4 emission. Here, we found that decomposing RS is
not only a substrate of CH4 production, but in addition
stimulates CH4 production from SOM and ROC. Apart from
accelerating the creation of reduced conditions in the soil environment,
RS decomposition exerted a positive priming effect on SOM-derived
CH4 production. In particular, hydrogenotrophic
methanogenesis from SOM-derived CO2 was stimulated,
presumably by H2 released from RS decomposition. On the other
hand, the positive priming effect of RS on ROC-derived CH4
production was probably caused by the significant increase of the
abundance of methanogenic archaea in the RS treatment compared with the
untreated control. Our results show that traditional management of rice
residues exerts a positive feedback on CH4 production from
rice fields, thus exacerbating its effect on the global CH4
[Show abstract][Hide abstract] ABSTRACT: The methanotrophs in rice field soil are crucial in regulating the emission of methane. Drainage substantially reduces methane emission from rice fields. However, it is poorly understood how drainage affects microbial methane oxidation. Therefore, we analyzed the dynamics of methane oxidation rates, composition (T-RFLP) and abundance (qPCR) of methanotroph pmoA genes (encoding a subunit of particulate methane monooxygenase) and their transcripts over the season and in response to alternate dry/wet cycles in planted paddy field microcosms. In situ methane oxidation accounted for less than 15% of total methane production but was enhanced by intermittent drainage. The dry/wet alternations resulted in distinct effects on the methanotrophic communities in different soil compartments (bulk soil, rhizosphere soil, surface soil). The methanotrophic communities of the different soil compartments also showed distinct seasonal dynamics. In bulk soil, potential methanotrophic activity and transcription of pmoA was relatively low, but was significantly stimulated by drainage. However, in the rhizosphere and surface soils it was the opposite, as potential methanotrophic activity and pmoA transcription were relatively high but decreased after drainage events and resumed after reflooding. While type II methanotrophs dominated the communities in the bulk soil and rhizosphere soil compartments (to less extent also in the surface soil), it was the pmoA of type I methanotrophs that was mainly transcribed under flooded condition. Drainage affected the composition of methanotrophic community only little, but strongly affected metabolically active methanotrophs. Our study revealed dramatic dynamics in abundance, composition, and activity of the various type I and type II methanotrophs both on a seasonal and spatial scale and showed strong effects of dry/wet alternation cycles, which enhanced the attenuation of methane flux into the atmosphere.
Applied and Environmental Microbiology 06/2013; · 3.95 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The relationship between total and metabolically active soil microbial communities can change drastically with environment. In drylands, water availability is a key factor limiting cells' activity. We surveyed the diversity of total and active archaea and bacteria in soils ranging from arid desert to Mediterranean forests. Thirty composited soil samples were retrieved from five sites along a precipitation gradient, collected from patches located between and under the dominant perennial plant at each site. Molecular fingerprinting was used to site-sort the communities according of their 16S rRNA genes (total community) and their rRNA (active community) amplified by PCR or RT-PCR from directly extracted soil nucleic acids. The differences between soil samples were much higher in total rather than active microbial communities: differences in DNA fingerprints between sites were 1.2 and 2.5 times higher than RNA differences (for archaea and bacteria, respectively). Patch-type discrepancies between DNA fingerprints were on average 2.7 to 19.7 times greater than RNA differences. Moreover, RNA-based community patterns were highly correlated with soil moisture but did not necessarily follow spatial distribution pattern. Our results suggest that in water-limited environments, the spatial patterns obtained by analysis of active communities are not as robust as those drawn from total communities. This article is protected by copyright. All rights reserved.
[Show abstract][Hide abstract] ABSTRACT:  Lakes are a significant source of atmospheric CH4 and play an important role in the global carbon cycle. Little information on methane production in high-altitude lakes is available. We determined the methanogenic archaeal community composition, the methanogenic pathways, and carbon isotope fractionation in lake sediments and wetland soils on the Tibetan Plateau at about 4000 m above sea level (asl). We measured CH4 production rates and the δ13C of CO2, CH4, and acetate in the presence and absence of methyl fluoride, an inhibitor of acetotrophic methanogenesis, in sediments of five lakes (Awong Co, Bangong Co, Gongzhu Co, Daze Co, and Ranwu) and wetland soils adjacent to Bangong Co and Ranwu. Methane in Bangong Co sediment and in the wetland soil near Ranwu was mainly produced by acetotrophic methanogenesis, whereas methane in the sediments of the two saline lakes Awong Co and Gongzhu Co was mainly generated by hydrogenotrophic methanogensis; chemolithotrophic acetogenesis and methanol-dependent methanogenesis may also have played a role. The stable carbon isotope fractionation during CH4 production from CO2 was relatively large (average ε = −78‰). The methanogenic communities were similar to those found in lowland lake sediments, but those of saline and nonsaline Tibetan lakes differed. Hydrogenotrophic methanogens were dominant in lake sediments, while acetotrophic methanogens were dominant in wetland soils. Our results revealed diversity in the methanogenic communities and their methanogenic pathways and indicated that they are affected by sediment characteristics, such as salinity. However, the CH4 production rates ranging from 6 to 122 nmol day−1 g dry weight−1 showed no relationship to environmental characteristics and were not limited by microbial abundance.
[Show abstract][Hide abstract] ABSTRACT: Irrigated rice fields in Uruguay are temporarily established on soils used as cattle pastures. Typically, 4 years of cattle pasture are alternated with 2 years of irrigated rice cultivation. Thus, oxic upland conditions are rotated with seasonally anoxic wetland conditions. Only the latter conditions are suitable for the production of CH4 from anaerobic degradation of organic matter. We studied soil from a permanent pasture as well as soils from different years of the pasture-rice rotation hypothesizing that activity and structure of the bacterial and archaeal communities involved in production of CH4 change systematically with the duration of either oxic or anoxic conditions. Soil samples were taken from drained fields, air-dried and used for the experiments. Indeed, methanogenic archaeal gene copy numbers (16S rRNA, mcrA) were lower in soil from the permanent pasture than from the pasture-rice alternation fields, but within the latter, there was no significant difference. Methane production started to accumulate after 16 days and 7 days of anoxic incubation in soil from the permanent pasture and the pasture-rice alternation fields respectively. Then, CH4 production rates were slightly higher in the soils used for pasture than for rice production. Analysis of δ(13) C in CH4 , CO2 and acetate in the presence and absence of methyl fluoride, an inhibitor of aceticlastic methanogenesis, indicated that CH4 was mainly (58-75%) produced from acetate, except in the permanent pasture soil (42%). Terminal restriction fragment length polymorphism (T-RFLP) of archaeal 16S rRNA genes showed no difference among the soils from the pasture-rice alternation fields with Methanocellaceae and Methanosarcinaceae as the main groups of methanogens, but in the permanent pasture soil, Methanocellaceae were relatively less abundant. T-RFLP analysis of bacterial 16S rRNA genes allowed the distinction of permanent pasture and fields from the pasture-rice rotation, but nevertheless with a high similarity. Pyrosequencing of bacterial 16S rRNA genes generally revealed Firmicutes as the dominant bacterial phylum, followed by Proteobacteria, Acidobacteria and Actinobacteria. We conclude that a stable methanogenic microbial community established once pastures have been turned into management by pasture-rice alternation despite the fact that 2 years of wetland conditions were followed by 4 years of upland conditions that were not suitable for CH4 production.
[Show abstract][Hide abstract] ABSTRACT: Biological soil crusts (biocrusts) are photosynthetic mats formed through an association of prokaryotic and eukaryotic microorganisms with soil particles. Biocrusts are found in virtually any terrestrial ecosystem where vascular plant coverage is abiotically limited, with drylands comprising the primary habitat for them. We studied the dynamics of the active bacterial community in two biocrusts from an arid and a hyperarid region in the Negev Desert, Israel, under light-oxic and dark-anoxic incubation conditions after simulated rainfall. We used H2 (18) O for hydrating the crusts and analysed the bacterial community in the upper and lower parts of the biocrust using an RNA-stable isotope probing approach coupled with 454-pyrosequencing. In both biocrusts, two distinct bacterial communities developed under each incubation condition. The active anaerobic communities were initially dominated by members of the order Bacillales which were later replaced by Clostridiales. The aerobic communities on the other hand were dominated by Sphingobacteriales and several Alphaproteobacteria (Rhizobiales, Rhodobacterales, Rhodospirillales and Rubrobacteriales). Actinomycetales were the dominant bacterial order in the dry crusts but quickly collapsed and accounted for < 1% of the community by the end of the incubation. Our study shows that biocrusts host a diverse community whose members display complex interactions as they resuscitate from dormancy.
[Show abstract][Hide abstract] ABSTRACT: Both bacteria and archaea potentially contribute to ammonia oxidation, but their roles in freshwater sediment are still poorly understood. Seasonal differences in the relative activity of these groups might exist since cultivated archaeal ammonia oxidizers have higher temperature optima than their bacterial counterparts. In this study, sediment collected from the eutrophic freshwater Lake Taihu (China) was incubated at different temperatures (4°C, 15°C, 25°C and 37°C) for up to 8 weeks. We examined the active bacterial and archaeal ammonia oxidizers in these sediment microcosms by combined stable isotope probing (SIP) and molecular community analysis. The results showed that accumulation of nitrate in microcosms correlated negatively with temperature although ammonium depletion was the same, which might be related to an enhanced activity of other nitrogen transformation processes. Incubation at different temperatures significantly changed the microbial community composition as revealed by 454 pyrosequencing targeting bacterial 16S rRNA genes. After 8-weeks incubation, 13C-bicarbonate labeling of bacterial amoA genes, which encode the ammonia monooxygenase subunit A, and an observed increase in copy numbers indicated the activity of ammonia-oxidizing bacteria in all microcosms. Nitrosomonas sp. Is79A3 and Nitrosomonas communis lineages dominated the heavy fraction of CsCl gradients at low and high temperatures, respectively, indicating a niche differentiation of active bacterial ammonia oxidizers along the temperature gradient. The 13C-labelling of ammonia-oxidizing archaea in microcosms incubated at 4-25°C was minor. In contrast, significant 13C-labelling of Nitrososphaera-like archaea and changes in the abundance and composition of archaeal amoA genes were observed at 37°C, implicating autotrophic growth of ammonia oxidizing archaea in warmer conditions.
Applied and Environmental Microbiology 03/2013; · 3.95 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The dynamics of populations and activities of ammonia-oxidizing and nitrite-oxidizing microorganisms were investigated in rice microcosms treated with two levels of nitrogen. Different soil compartments (surface, bulk, rhizospheric soil) and roots (young and old roots) were collected at three time points (the panicle initiation, heading and maturity periods) of the season. The population dynamics of bacterial (AOB) and archaeal (AOA) ammonia oxidizers was assayed by determining the abundance (using qPCR) and composition (using T-RFLP and cloning/sequencing) of their amoA genes (coding for a subunit of ammonia monooxygenase), that of nitrite oxidizers (NOB) by quantifying the nxrA gene (coding for a subunit of nitrite oxidase of Nitrobacter spp.) and the 16S rRNA gene of Nitrospira spp. The activity of the nitrifiers was determined by measuring the rates of potential ammonia oxidation and nitrite oxidation and by quantifying the copy numbers of amoA and nxrA transcripts. Potential nitrite oxidation activity was much higher than potential ammonia oxidation activity and was not directly affected by nitrogen amendment demonstrating the importance of ammonia oxidizers as pace makers for nitrite oxidizer populations. Marked differences in the distribution of bacterial and archaeal ammonia oxidizers, and of Nitrobacter-like and Nitrospira-like nitrite oxidizers were found in the different compartments of planted paddy soil indicating niche differentiation. In bulk soil, ammonia-oxidizing bacteria (Nitrosospira and Nitrosomonas) were at low abundance and displayed no activity, but in surface soil their activity and abundance was high. Nitrite oxidation in surface soil was dominated by Nitrospira spp. By contrast, ammonia-oxidizing Thaumarchaeota and Nitrobacter spp. seemed to dominate nitrification in rhizospheric soil and on rice roots. In contrast to soil compartment, the level of N fertilization and the time point of sampling had only little effect on the abundance, composition and activity of the nitrifying communities. The results of our study show that in rice fields population dynamics and activity of nitrifiers is mainly differentiated by the soil compartments rather than by nitrogen amendment or season.
[Show abstract][Hide abstract] ABSTRACT: Methanogens typically occur in reduced anoxic environments. However, in recent studies it has been shown that many aerated upland soils, including desert soils also host active methanogens. Here we show that soil samples from high-altitude cold deserts in the western Himalayas (Ladakh, India) produce CH4 after incubation as slurry under anoxic conditions at rates comparable to those of hot desert soils. Samples of matured soil from three different vegetation belts (arid, steppe, and subnival) were compared with younger soils originating from frontal and lateral moraines of receding glaciers. While methanogenic rates were higher in the samples from matured soils, CH4 was also produced in the samples from the recently deglaciated moraines. In both young and matured soils, those covered by a biological soil crust (biocrust) were more active than their bare counterparts. Isotopic analysis showed that in both cases CH4 was initially produced from H2/CO2 but later mostly from acetate. Analysis of the archaeal community in the in situ soil samples revealed a clear dominance of sequences related to Thaumarchaeota, while the methanogenic community comprised only a minor fraction of the archaeal community. Similar to other aerated soils, the methanogenic community was comprised almost solely of the genera Methanosarcina and Methanocella, and possibly also Methanobacterium in some cases. Nevertheless, ~10(3) gdw(-1) soil methanogens were already present in the young moraine soil together with cyanobacteria. Our results demonstrate that Methanosarcina and Methanocella not only tolerate atmospheric oxygen but are also able to survive in these harsh cold environments. Their occurrence in newly deglaciated soils shows that they are early colonizers of desert soils, similar to cyanobacteria, and may play a role in the development of desert biocrusts.
Frontiers in Microbiology 01/2013; 4:359. · 3.90 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Acetogenic bacteria are able to grow autotrophically on hydrogen and carbon dioxide by using the acetyl-CoA pathway. Acetate is the end product of this reaction. In contrast to the fermentative route of acetate production, which shows almost no fractionation of carbon isotopes, the acetyl-CoA pathway has been reported to exhibit a preference for the light carbon. In Acetobacterium woodii the isotope fractionation factor (ε) for (13)C/(12)C has previously been reported to be ε = -58.6‰. To investigate whether such a strong fractionation is a general feature of acetogenic bacteria, we measured the stable carbon isotope fractionation factor of ten acetogenic strains grown on H(2)/CO(2). The average fractionation factor was ε(TIC)= -57.2‰ for utilization of total inorganic carbon (TIC) and ε(acetate)= -54.6‰ for production of acetate. The strongest fractionation was found for Sporomusa sphaeroides (ε(TIC)= -68.3‰), the lowest fractionation for Morella thermoacetica (ε(TIC)= -38.2‰). To investigate the reproducibility of our measurements, we determined the fractionation factor of 21 biological replicates of Thermoanaerobacter kivui. In general, our study confirmed the strong fractionation of stable carbon during chemolithotrophic acetate formation in acetogenic bacteria. However, specificities of the bacterial strain as well as cultural conditions may have a moderate influence on the overall fractionation.
Applied and Environmental Microbiology 12/2012; · 3.95 Impact Factor