Methane uptake in soils from Pinus radiata plantations, a reverting shrubland and adjacent pastures: Effects of land-use change, and soil texture, water and mineral nitrogen

Afforestation and reforestation of pastures are key land-use changes in New Zealand that help sequester carbon (C) to offset its carbon dioxide (CO₂) emissions under the Kyoto Protocol. However, relatively little attention has been given so far to associated changes in trace gas fluxes. Here, we measure methane (CH₄) fluxes and CO₂ production, as well as microbial C, nitrogen (N) and mineral-N, in intact, gradually dried (ca. 2 months at 20 °C) cores of a volcanic soil and a heavier textured, non-volcanic soil collected within plantations of Pinus radiata D. Don (pine) and adjacent permanent pastures. CH₄ fluxes and CO₂ production were also measured in cores of another volcanic soil under reverting shrubland (mainly Kunzea var. ericoides (A. Rich) J. Thompson) and an adjacent pasture. CH₄ uptake in the pine and shrubland cores of the volcanic soils at field capacity averaged about 35 and 14 μg CH₄-C m⁻² h⁻¹, respectively, and was significantly higher than in the pasture cores (about 21 and 6 μg CH₄-C m⁻² h⁻¹, respectively). In the non-volcanic soil, however, CH₄-C uptake was similar in most cores of the pine and pasture soils, averaging about 7-9 μg m⁻² h⁻¹, except in very wet samples. In contrast, rates of CO₂ production and microbial C and N concentrations were significantly lower under pine than under pasture. In the air-dry cores, microbial C and N had declined in the volcanic soil, but not in the non-volcanic soil; ammonium-N, and especially nitrate-N, had increased significantly in all samples. CH₄ uptake was, with few exceptions, not significantly influenced by initial concentrations of ammonium-N or nitrate-N, nor by their changes on air-drying. A combination of phospholipid fatty acid (PLFA) and stable isotope probing (SIP) analyses of only the pine and pasture soils showed that different methanotrophic communities were probably active in soils under the different vegetations. The C18 PLFAs (type II methanotrophs) predominated under pine and C16 PLFAs (type I methanotrophs) predominated under pasture. Overall, vegetation, soil texture, and water-filled pore space influenced CH₄-C uptake more than did soil mineral-N concentrations.     

The differential effects of ammonium and nitrate on methanotrophs in rice field soil

It has been known that nitrogenous fertilizers can either stimulate or inhibit methane oxidation in soils. The mechanism, however, remains unclear. Here we conducted laboratory incubation experiments to evaluate the effects of ammonium versus nitrate amendment on CH₄ oxidation in a rice field soil. The results showed that both N forms stimulated CH₄ oxidation. But nitrate stimulated CH₄ oxidation to a greater extent than ammonium per unit N base. The 16S rRNA genes and the pmoA genes were analyzed to determine the dynamics of total bacterial and methanotrophic populations, respectively. The methanotrophic community consisted of type I and type II methanotrophs and was dominated by type I group after two weeks of incubation. Nitrate promoted both types of methanotrophs, but ammonium promoted only type I. DNA-based stable isotope probing confirmed that ammonium stimulated the incorporation of ¹³CH₄ into type I methanotrophs but not type II, while nitrate caused almost homogenous distribution of ¹³CH₄ in type I and type II methanotrophs. Our study suggests that nitrate can promote CH₄ oxidation more significantly than ammonium and is probably a better N source for both types of methanotrophs in rice field soil. More investigations, e.g. using ¹⁵N labeling, are necessary to elucidate this possibility.     

Methane concentrations and methanotrophic community structure influence the response of soil methane oxidation to nitrogen content in a temperate forest

Methane oxidation in forest soils removes atmospheric CH₄. Many studies have determined methane uptake rates and their controlling variables, yet the microorganisms involved have rarely been assessed simultaneously over the longer term. We measured methane uptake rates and the community structure of methanotrophic bacteria in temperate forest soil (sandy clay loam) on a monthly basis for two years in South Korea. Methane uptake rates at the field site did not show any seasonal patterns, and net uptake occurred throughout both years. In situ uptake rates and uptake potentials determined in the laboratory were 2.92 ± 4.07 mg CH₄ m⁻² day⁻¹ and 51.6 ± 45.8 ng CH₄ g⁻¹ soil day⁻¹, respectively. Contrary to results from other studies, in situ oxidation rates were positively correlated with soil nitrate concentrations. Short-term experimental nitrate addition (0.20-1.95 μg N g⁻¹ soil) significantly stimulated oxidation rates under low methane concentrations (1.7-2.0 ppmv CH₄), but significantly inhibited oxidation under high methane concentrations (300 ppmv CH₄). We analyzed the community structures of methanotrophic bacteria using a DNA-based fingerprinting method (T-RFLP). Type II methanotrophs dominated under low methane concentrations while Type I methanotrophs dominated under high methane concentrations. Nitrogen addition selectively inhibited Type I methanotrophic bacteria. Overall, the results of this study indicate that the effects of inorganic N on methane uptake depend on methane concentrations and that such a response is related to the dissimilar activation or inhibition of different types of methanotrophic bacteria.     

Immediate effects of nitrogen, phosphorus, and potassium amendments on the methanotrophic activity and abundance in a Chinese paddy soil under short-term incubation experiment

Purpose

Methane-oxidizing bacteria (methanotrophs) biologically consume and consequently affect the concentration of atmospheric methane (CH₄), the second most prominent greenhouse gas, and therefore play critical roles in the mitigation of global warming effect. Long-term fertilization often affects the methanotrophic community and CH₄ oxidation in various soils. Here, the immediate effects of nitrogen (N), phosphorus (P), and potassium (K) amendments on the CH₄ oxidation activity and methanotrophic community structure were evaluated.

Materials and methods

Paddy soil samples were collected from the Taoyuan Experimental Station of the Chinese Academy of Sciences in central Hunan Province of China. A laboratory-based incubation experiment was conducted to investigate the immediate effects of N, P, and K amendments on the methanotrophs in soil. The CH₄ oxidation rates and methanotrophic activities were determined by measuring the dynamic changes of CH₄ concentration in the incubation system. The methanotrophic abundance and community changes in all of the seven treatments with and without nutrients addition were studied using real-time PCR and denaturing gradient gel electrophoresis, respectively.

Results and discussion

All of the N, P, and K treatments significantly decreased the CH₄ oxidation activities. Compared with the control, the P and K amendments significantly increased the methanotrophic population size, but the N treatments have no effect on the methanotrophic abundance. A negative correlation was found between methanotrophic activity and methanotrophic abundance. We suggested that methanotrophic activity may not be inferred through the pmoA gene copies, especially in the short-term simulation experiments. Investigation of the methanotrophic population size and diversity is not enough to evaluate the soil CH₄ sink accurately.

Conclusions

We concluded that the additions of N, P, and K reduce the activity but enhance the abundance of methanotrophs in a Chinese paddy soil through a short-term incubation experiment. Additionally, we found that the CH₄ oxidation activity could be completely inhibited by Cl^? toxicity. Our results implied that caution should be exercised in the types and amounts of fertilizers, especially KCl in agricultural systems to control the instantaneous increase in CH₄ emission from the field.     

Varying atmospheric methane concentrations affect soil methane oxidation rates and methanotroph populations in pasture,an adjacent pine forest,and a landfill

We describe experiments to better understand how CH₄ oxidation rates by different methanotroph communities respond to changing CH₄ concentrations. We used a novel system of automatically monitored chambers to investigate the response of CH₄ oxidation rates in a New Zealand pasture and adjacent pine forest soil exposed to varying atmospheric CH₄ concentrations.Type II methanotrophs that dominate CH₄ oxidation in the forest soil became progressively saturated as CH₄ concentrations rose from ambient (1.8 ppmv) to 570 ppmv, as shown by a decrease in uptake efficiency from 20% to 2% removal. By contrast, CH₄ oxidation in the pasture soil where Type I methanotrophs dominate increased in proportion to the increase in CH₄ inlet concentration, oxidising about 2% of the inlet CH₄ flux throughout. Modelling based on Michaelis-Menten kinetics revealed that low-affinity (Type I) methanotrophs were solely responsible for CH₄ oxidation in pasture soils, whereas high affinity (Type II) methanotrophs only contributed about 10% of the CH₄ oxidation in the forest soil. Increased aeration status using a soil–perlite (1:1) mixture doubled CH₄ oxidation rates at both ambient (1.8 ppmv) and 40 ppmv atmospheric CH₄. A similar volcanic soil previously exposed for 8 y to high CH₄ fluxes from a landfill had removal efficiencies consistently above 95% for atmospheric CH₄ concentrations up to 7500 ppmv when the CH₄ oxidation rate was7000 μg CH₄ kg⁻¹soil h⁻¹.     

Ecology of aerobic methanotrophs in controlling methane fluxes from wetlands

Methane (CH₄) is a critical greenhouse gas, with wetlands and flooded rice soils contributing >38% of the global emissions of CH₄. A key process that offsets CH₄ production is biological oxidation by methanotrophs that can consume as much as 90% of the CH₄ produced in aerobic soils. The objective was to review the literature on the biochemical pathways, ecology of methanotrophs, research methods, and environmental and management controls on CH₄ oxidation in wetlands. Methanotrophs have been extensively studied using phospholipid fatty acids (PLFA) but much less so using nucleic acid analysis or with the powerful stable-isotope probing technique of ¹³C-PLFA analysis. Of the environmental factors that affect CH₄ oxidation, temperature, water content and redox potential are the most important whereas a wide range of soil pH enables oxidation. Methane oxidation varies with season as functions of temperature and plant community shifts (changes with growth stage of C input chemistry and oxygenation from aquatic rhizospheres). Indirect evidence suggests there is greater CH₄ oxidation in pulsing than permanently flooded soils based on observations that static wetlands have greater emissions than pulsing wetlands. Basic research is needed on: the role of inorganic N species in controlling CH₄ oxidation pathways; phylogenetic analysis of methanotrophs; and environmental and edaphic effects on methanotroph growth and activity. Research is needed to develop wetland systems that optimize CH₄ oxidation relative to wetland type and environments and hydrology while maintaining and/or promoting other ecosystem services (e.g. C sequestration, pollution remediation, wildlife habitat, flood control).     

Diversity, abundance and vertical distribution of methane-oxidizing bacteria (methanotrophs) in the sediments of the Xianghai wetland, Songnen Plain, northeast China

Purpose

Methanotrophs in wetlands are of great importance because up to 90 % of the methane (CH₄) produced in such wetlands could be oxidized by methanotrophs before reaching the atmosphere. The Xianghai wetland of Songnen Plain represents an important ecosystem in northeast China. However, methanotrophic characteristics in this ecosystem have not been studied in detail. The aim of this study is to give an overview of methanotrophic diversity and vertical distribution in the sediments of this important wetland.

Materials and methods

Sediment cores were collected from three freshwater marshes, each dominated by a particular vegetation type: Carex alata, Phragmites australis and Typha orientalis. The diversity of methanotrophs was studied by phylogenetic analysis of both the 16S rRNA gene and the particulate methane monooxygenase (pmoA) gene. Methanotroph abundance was determined by quantitative PCR (qPCR) targeting the pmoA gene; group-specific pmoA gene quantification was also used to estimate the abundance of each methanotrophic group.

Results and discussion

16S rRNA and pmoA gene homological analysis revealed the presence of type Ia, Ib and II methanotrophs. Novel pmoA sequences distantly affiliated to cultured Methylococcus sp. were detected, implying the existence of novel methanotrophs in the wetland. Most obtained representatives of Methylobacter genus (both 16S rRNA and pmoA genes) were closely clustered in relation to sequences acquired from the Zoige wetland, Tibet and Siberia permafrost soils, therefore suggesting methanotrophs belonging to Methylobacter genus shared characteristics with methanotrophs in cold areas. The dominance of type I methanotrophs (especially the Methylobacter genus) was detected by both clone library analysis and group-specific qPCR assay. The relatively high methanotroph diversity and pmoA copy numbers measured in the T. orientalis marsh sediments indicated that vegetation type played an important role during CH₄ oxidation in the wetland.

Conclusions

We present the first data set on methanotroph diversity and vertical distribution in the sediments of the Xianghai wetland. DNA sequences information of Methylococcus-like methanotrophs in the wetland will facilitate the isolating of novel methanotrophs from the wetland. In a worldwide context, our study has enriched the database of genotypic diversity of methanotrophs, which will help in the understanding of the geographical distribution of methanotrophic communities.     

Methanotrophic communities in a landfill cover soil as revealed by [13C] PLFAs and respiratory quinones: Impact of high methane addition and landfill leachate irrigation

The soil microbial communities of a landfill cover substrate, which was treated with landfill gas (100 l CH₄ m^?2 d^?1) and landfill leachate for 1.5 years, were investigated by phospholipid fatty acid (PLFA), ergosterol and respiratory quinone analyses. The natural ¹³C depletion of methane was used to assess the activity of methanotrophs and carbon turnover in the soil system. Under methane addition, the soil microbial community was dominated by PLFAs (14:0 and 16:1 isomers) and quinones (ubiquinone-8 and 18-methylene-ubiquinone-8) related to type I methanotrophs, and 18:1 PLFAs contained in type II methanotrophs. While type I methanotrophic PLFAs were ¹³C depleted, i.e. type I methanotrophs were actively oxidising and assimilating methane, ¹³C depletion of 18:1 PLFAs was low and inconsistent with their abundance. This, possibly reflects isotopic discrimination, assimilation of carbon derived from type I methanotrophs and a high contribution of non-methanotrophic bacteria to the 18:1 isomers. Landfill leachate irrigation caused the methanotrophic community to shift closer to the soil surface. It also decreased 18:1 PLFAs, while type I methanotrophs were probably stimulated. Gram positive bacteria, but not fungi, were also ¹³C depleted and consequently involved in the secondary turnover of carbon originating from methanotrophic bacteria. Cy17:0 PLFA was ¹³C depleted in deep soil layers, indicating anaerobic methane oxidation.     

Induction of enhanced CH4 oxidation in soils: NH4 inhibition patterns

The influence of NH₄⁺ on microbial CH₄ oxidation is still poorly understood. Therefore, the influence of NH₄Cl and (NH₄)₂SO₄ on CH₄ oxidation was studied in soils at the different stages of the induction of enhanced methanotrophic activity. After a brief peak in the methanotrophic activity, a steady state was observed in which NH₄⁺ inhibited CH₄ oxidation at low CH₄ concentrations, and stimulated CH₄ oxidation at high concentrations. Chloride did not strongly inhibit CH₄ oxidation during this phase. During a second phase methanotrophic activity increased again. Ammonium no longer stimulated CH₄ oxidation, and Cl⁻ became an important source of uncompetitive inhibition. It was hypothesized that type I methanotrophs dominated during the first, soil-N-dependent phase while N₂-fixing type II methanotrophs dominated the second, soil-N-independent phase.     

Response of CH<Subscript>4</Subscript> oxidation and methanotrophic diversity to NH<Subscript>4</Subscript><Superscript>+</Superscript> and CH<Subscript>4</Subscript> mixing ratios

Methane oxidising activity and community structure of 11, specifically targeted, methanotrophic species have been examined in an arable soil. Soils were sampled from three different field plots, receiving no fertilisation (C), compost (G) and mineral fertiliser (M), respectively. Incubation experiments were carried out with and without pre-incubation at elevated CH₄ mixing ratios (100 ml CH₄ l⁻¹) and with and without ammonium (100 mg N kg⁻¹) pre-incubation. Four months after fertilisation, plots C, G and M did not show significant differences in physicochemical properties and CH₄ oxidising activity. The total number of methanotrophs (determined as the sum the 11 specifically targeted methanotrophs) in the fresh soils was 17.0×10⁶, 13.7×10⁶ and 15.5×10⁶ cells g⁻¹ for treatment C, G and M, respectively. This corresponded to 0.11 to 0.32% of the total bacterial number. The CH₄ oxidising activity increased 10⁵-fold (20–26 mg CH₄ g⁻¹ h⁻¹), the total number of methanotrophs doubled (28–76×10⁶ cells g⁻¹) and the methanotrophic diversity markedly increased in treatments with a pre-incubation at elevated CH₄ concentrations. In all soils and treatments, type II methanotrophs (62–91%) outnumbered type I methanotrophs (9–38%). Methylocystis and Methylosinus species were always most abundant. After pre-incubation with ammonium, CH₄ oxidation was completely inhibited; however, no change in the methanotrophic community structure could be detected.     

Methanotroph abundance not affected by applications of animal urine and a nitrification inhibitor,dicyandiamide, in six grazed grassland soils

Purpose  

Methanotrophs are an important group of methane (CH₄)-oxidizing bacteria in the soil, which act as a major sink for the greenhouse gas, CH₄. In grazed grassland, one of the ecologically most sensitive areas is the animal urine patch soil, which is a major source of both nitrate (NO₃ ⁻) leaching and nitrous oxide (N₂O) emissions. Nitrification inhibitors, such as dicyandiamide (DCD), have been used to mitigate NO₃ ⁻ leaching and N₂O emissions in grazed pastures. However, it is not clear if the high nitrogen loading rate in the animal urine patch soil and the use of nitrification inhibitors would have an impact on the abundance of methanotrophs in grazed grassland soils. The purpose of this study was to determine the effect of animal urine and DCD on methanotroph abundance in grazed grassland soils.     

Methane turnover and temperature response of methane-oxidizing bacteria in permafrost-affected soils of northeast Siberia

The abundance, activity, and temperature response of aerobic methane-oxidizing bacteria were studied in permafrost-affected tundra soils of northeast Siberia. The soils were characterized by both a high accumulation of organic matter at the surface and high methane concentrations in the water-saturated soils. The methane oxidation rates of up to 835 nmol CH₄ h⁻¹ g⁻¹ in the surface soils were similar to the highest values reported so far for natural wetland soils worldwide. The temperature response of methane oxidation was measured during short incubations and revealed maximum rates between 22 °C and 28 °C. The active methanotrophic community was characterized by its phospholipid fatty acid (PLFA) concentrations and with stable isotope probing (SIP). Concentrations of 16:1ω8 and 18:1ω8 PLFAs, specific to methanotrophic bacteria, correlated significantly with the potential methane oxidation rates. In all soils, distinct 16:1 PLFAs were dominant, indicating a predominance of type I methanotrophs. However, long-term incubation of soil samples at 0 °C and 22 °C demonstrated a shift in the composition of the active community with rising temperatures. At 0 °C, only the concentrations of 16:1 PLFAs increased and those of 18:1 PLFAs decreased, whereas the opposite was true at 22 °C. Similarly, SIP with ¹³CH₄ showed a temperature-dependent pattern. When the soils were incubated at 0 °C, most of the incorporated label (83%) was found in 16:1 PLFAs and only 2% in 18:1 PLFAs. In soils incubated at 22 °C, almost equal amounts of ¹³C label were incorporated into 16:1 PLFAs and 18:1 PLFAs (33% and 36%, respectively). We concluded that the highly active methane-oxidizing community in cold permafrost-affected soils was dominated by type I methanotrophs under in situ conditions. However, rising temperatures, as predicted for the future, seem to increase the importance of type II methanotrophs, which may affect methane cycling in northern wetlands.     

Abundance and community composition of methanotrophs in a Chinese paddy soil under long-term fertilization practices

Background, aim, and scope  As the second most important greenhouse gas, methane (CH₄) is produced from many sources such as paddy fields. Methane-oxidizing bacteria (methanotrophs) consume CH₄ in paddy soil and, therefore, reduce CH₄ emission to the atmosphere. In order to estimate the contribution of paddy fields as a source of CH₄, it is important to monitor the effects of fertilizer applications on the shifts of soil methanotrophs, which are targets in strategies to combat global climate change. In this study, real-time polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) based on 16S rRNA and pmoA genes, respectively, were used to analyze the soil methanotrophic abundance and community diversity under four fertilization treatments: urea (N), urea and potassium chloride (NK), urea, superphosphate, and potassium chloride (NPK), and urea, superphosphate, potassium chloride, and crop residues (NPK+C), compared to an untreated control (CON). The objective of this study was to examine whether soil methanotrophs responded to the long-term, different fertilizer regimes by using a combination of quantitative and qualitative molecular approaches. Materials and methods  Soil samples were collected from the Taoyuan Experimental Station of Agro-ecosystem Observation at Changde (28°55′ N, 111°26′ E), central Hunan Province of China, in July 2006. Soil DNAs were extracted from the samples, then the 16S rRNA genes were quantified by real-time PCR and the pmoA genes were amplified via general PCR followed by DGGE, cloning, sequencing, and phylogenetic analysis. The community diversity indices were assessed through the DGGE profile. Results  Except for NPK, other treatments of N, NK, and NPK+C showed significantly higher copy numbers of type I methanotrophs (7.0–9.6 × 10⁷) than CON (5.1 × 10⁷). The copy numbers of type II methanotrophs were significantly higher in NPK+C (2.8 × 10⁸) and NK (2.5 × 10⁸) treatments than in CON (1.4 × 10⁸). Moreover, the ratio of type II to type I methanotrophic copy numbers ranged from 1.88 to 3.32, indicating that the type II methanotrophs dominated in all treatments. Cluster analyses based on the DGGE profile showed that the methanotrophic community in NPK+C might respond more sensitively to the environmental variation. Phylogenetic analysis showed that 81% of the obtained pmoA sequences were classified as type I methanotrophs. Furthermore, the type I-affiliated sequences were related to Methylobacter, Methylomicrobium, Methylomonas, and some uncultured methanotrophic clones, and those type II-like sequences were affiliated with Methylocystis and Methylosinus genera. Discussion  There was an inhibitory effect on the methanotrophic abundance in the N and a stimulating effect in the NK and NPK+C treatments, respectively. During the rice-growing season, the type II methanotrophs might be more profited from such a coexistence of low O₂ and high CH₄ concentration environment than the type I methanotrophs. However, type I methanotrophs seemed to be more frequently detected. The relatively complex diversity pattern in the NPK+C treatment might result from the strong CH₄ production. Conclusions  Long-term fertilization regimes can both affect the abundance and the composition of the type I and type II methanotrophs. The inhibited effects on methanotrophic abundance were found in the N treatment, compared to the stimulated effects from the NK and NPK+C treatments. The fertilizers of nitrogen, potassium, and the crop residues could be important factors controlling the abundance and community composition of the methanotrophs in the paddy soil. Recommendations and perspectives  Methanotrophs are a fascinating group of microorganisms playing an important role in the biogeochemical carbon cycle and in the control of global climate change. However, it is still a challenge for the cultivation of the methanotrophs, although three isolates were obtained in the extreme environments very recently. Therefore, future studies will be undoubtedly conducted via molecular techniques just like the applications in this study.     

Structure and activity of soil-inhabiting methanotrophic communities in northern forest of Japan

In a Japanese forest, CH₄ uptake rate and methanotrophic community structure in the soil were investigated at four sites of different vegetation. At two of these sites, undergrowth was dominated by Sasa senanensis, and that of another was dominated by Sasa kurilensis. At the rest site, undergrowth had been removed artificially. The tree-layer composition differed between the two sites with S. senanensis, but tree layer of the other two sites were dominated by the same species. At the site lacking undergrowth, observed CH₄ uptake rate was twice as high as that at the other sites. Under laboratory conditions, soil sample from the site lacking undergrowth exhibited CH₄ consumption rate higher than that of the adjacent site with the same dominating tree species. The community structures of methanotrophs were investigated with denaturing gradient gel electrophoresis (DGGE) of the gene encoding particulate methane monooxygenase (pmoA). The banding patterns observed were different depending on the type of undergrowth vegetation. The sequences of the DGGE bands were closely related to each other and belonged to the “upland soil cluster alpha” (USCα). These results imply possible close relationship between the undergrowth vegetation and methanotrophic communities in forest soils.     

Changes in methanotrophic community composition after rice crop harvest in tropical soils

Four selected tropical field sites from India were studied to assess the diversity and community structure of methanotrophs in rice fields following crop harvest. The rate of methane oxidation ranged from 0.04 to 0.11 μmol L⁻¹ h⁻¹ g⁻¹ dry weight in soils. Methanotrophic population size was high for the agriculture farm of Banaras Hindu University (BHU) site followed by agriculture farm of the Indian Institute of Vegetable Research (IIVR), Ghazipur, and Barkachcha. The cloning, restriction fragment length polymorphism, and sequence analyses of the pmoA gene fragment amplified from soil DNA extracts revealed the presence of type I and type II methanotrophs. The phylogenetic affiliation and community analysis based on the presence or absence of sequences showed that methanotrophs community composition in Barkachcha and Ghazipur soils was similar. IIVR soils, however, were quite different, while BHU soils were intermediate among the sites with regard to methanotrophic community composition. Diversity index of the methanotrophic community was high at the IIVR site. The study revealed that the rice harvest led to a change in type I methanotrophs from all the sites while type II community composition was almost uniform.     

Succession of bacterial community and methanotrophy during lake shrinkage

Purpose

The shrinkage of vast inland lakes affects microbially mediated soil biogeochemical processes, which are critical for maintaining ecosystem sustainability, such as microbial diversity and a balanced CH₄ budget. Here we aimed to elucidate shifts in the bacterial community and methanotrophy during the shrinkage of a saline lake.

Materials and methods

Sediments and soils along a gradient transecting a saline lake, saline riparian land, and grassland were collected. The succession of microbial communities was characterized by high-throughput sequencing of the V4-V5 region of 16S rRNA genes coupled to non-metric multidimensional scaling (NMDS), linear discriminant effect size (LEfSe), community assembly, and co-occurrence network analyses. We further incubated these samples under a 10% CH₄ (v/v) atmospheric condition to determine the response of methane oxidation potentials and of methanotrophs to lake shrinkage by using pmoA-based qPCR and amplicon sequencing.

Results and discussion

LEfSe and NMDS analyses showed significant differences in bacterial communities among 3 stages of lake shrinkage. The microbial taxa with the highest increase were phylogenetically affiliated with unclassified Rhizobiales, Panacagrimonas, and Pseudomonas in saline and grassland soils when compared with sediments. Microbial community assembly was largely determined by deterministic rather than stochastic processes (NTI?>?2). The drastic increase of Methylocystis-like (type II) methanotrophs was observed during lake shrinkage, while type I methanotrophs showed a decreasing trend. However, upon consuming high-concentration methane of about 10%, type I methanotrophs dominated methane-oxidizing communities in lake sediment (Methylomonas), riparian saline soil (Methylomicrobium), and grassland soil (Methylobacter). Structural equation model identified soil pH, C/N ratio, and soil texture as key factors affecting methane oxidation rates and the methanotrophic community.

Conclusions

Lake shrinkage showed profound impacts on the overall bacterial communities and methane oxidizers. Soil physico-chemical properties likely shaped the bacterial community and phylogenetically distinct methanotrophs during lake shrinkage.

     

Methane oxidation activity and bacterial community composition in a simulated landfill cover soil is influenced by the growth of Chenopodium album L.

Oxygen availability in landfill cover soil is a major limitation to the growth and activity of methanotrophs as methane oxidation is an aerobic microbial process. Plants tolerant to high concentrations of landfill gas (LFG) may play an important role in improving methane oxidation within landfill cover soil and reducing emission of methane, a greenhouse gas, from it. In this study, the effect of an LFG tolerant plant Chenopodium album L. on methane oxidation activity (MOA) and bacterial community composition in landfill cover soil was investigated. Soil samples from four simulated lysimeters with and without LFG and plant vegetation were taken at 4 stages during the plant's development cycle. Results showed that the total number of culturable bacteria in soil could be significantly increased (P < 0.05) by the growth of C. album. The total number of methanotrophs and MOA in soils with LFG was significantly higher (P < 0.05) than in soils without LFG on sampling days 90, 150 and 210. The total number of methanotrophs and MOA in lysimeters with LFG added increased in the presence of C. album when the plant entered the seed setting stage. Polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) gel patterns of 16S rDNA gene fragment and band sequencing analyses showed apparent differences in soil bacterial communities in the presence of LFG and plant vegetation. Members of the genus Methylosarcina were found to be the active and dominant methanotrophs in rhizosphere soil of C. album with LFG, while Methylococcus, Methylocystis, and Methylosinus were the primary methanotroph genera in LFG soil without C. album. Thus, C. album appears to select for specific methanotrophic bacteria in the presence of LFG. Soil MOA and microbial diversity can also be significantly affected by the presence of this plant.     

Conversion of cropland to forest increases soil CH4 oxidation and abundance of CH4 oxidizing bacteria with stand age

We investigated CH₄ oxidation in afforested soils over a 200-year chronosequence in Denmark including different tree species (Norway spruce, oak and larch) and ages. Samples of the top mineral soil (0–5 cm and 5–15 cm depth) were incubated and analyzed for the abundance of the soil methane-oxidizing bacteria (MOB) and ammonia-oxidizing bacteria (AOB) and archaea (AOA) based on quantitative PCR (qPCR) on pmoA and amoA genes. Our study showed that CH₄ oxidation rates and the abundance of MOB increased simultaneously with time since afforestation, suggesting that the methanotrophic activity is reflected in the abundance of this functional group.The development of forest soils resulted in increased soil organic carbon and reduced bulk density, and these were the two variables that most strongly related to CH₄ oxidation rates in the forest soils. For the top mineral soil layer (0–5 cm) CH₄ oxidation rates did not differ between even aged stands from oak and larch, and were significantly smaller under Norway spruce. Compared to the other tree species Norway spruce caused a decrease in the abundance of MOB over time that could explain the decreased oxidation rates. However, the cause for the lower abundance remains unclear. The abundance of ammonia-oxidizers along the chronosequence decreased over time, oppositely to the MOB. However, our study did not indicate a direct link between CH₄ oxidation rates and ammonia-oxidizers. Here, we provide evidence for a positive impact of afforestation of former cropland on CH₄ oxidation capacity in soils most likely caused by an increased population size and activity of MOB.     

Tree species affect atmospheric CH4 oxidation without altering community composition of soil methanotrophs

Plant species exert strong effects on ecosystem functions and one of the emerging, and difficult to test hypotheses, is that plants alter soil functions through changing the community structure of soil microorganisms. We tested the hypothesis for atmospheric CH₄ oxidation by using soil samples from a Siberian afforestation experiment and exposing them to ¹³C-CH₄. We determined the activity of the soil methanotrophs under different tree species at three levels of initial CH₄ concentration (30, 200 and 1000 ppm) thus distinguishing the activities of low- and high-affinity methanotrophs. Half of the samples were incubated with ¹³C-enriched CH₄ (99.9%) and half with ¹²C-CH₄. This allowed an estimation of the amount of ¹³C incorporated into individual PLFAs and determination of PLFAs of methanotrophs involved in CH₄ oxidation at the different CH₄ concentrations. Tree species strongly altered the activity of atmospheric CH₄ oxidation without appearing to change the composition of high-affinity methanotrophs as evidenced by PLFA ¹³C labeling. The low diversity of atmospheric CH₄ oxidizers, presumably belonging to the UCSα group, may explain the lack of tree species effects on the composition of soil methanotrophs. We submit that the observed tree species effects on atmospheric CH₄ oxidation indicate an effect on biomass or cell-specific activities rather than by a community change and this may be related to the impact of the tree species on soil N cycling.     

Physiological, biochemical and molecular responses of the soil microbial community after afforestation of pastures with Pinus radiata

Afforestation and deforestation are key land-use changes across the world, and are considered to be dominant factors controlling ecosystem functioning and biodiversity. However, the responses of soil microbial communities to these land-use changes are not well understood. Because changes in soil microbial abundance and community structure have consequences for nutrient cycling, C-sequestration and long-term sustainability, we investigated impacts of land-use change, age of stand and soil physico-chemical properties on fungal and bacterial communities and their metabolic activities. This study was carried out at four sites in two geographical locations that were afforested on long-established pastures with Pinus radiata D. Don (pine). Two of the sites were on volcanic soils and two on non-volcanic soils and stand age ranged from 5 to 20 y. Microbial communities were analysed by biochemical (phospho-lipid fatty acids; PLFA) and molecular (multiplex-terminal restriction fragment length polymorphism; M-TRFLP) approaches. Both site and stand age influenced microbial properties, with changes being least detectable in the 5-y-old stand. Land use was a key factor influencing soil metabolic activities as measured by physiological profiling using MicroResp. Pasture soils had higher microbial biomass (P < 0.001), and metabolic activities (P < 0.001), and basal respiration rates were up to 2.8-times higher than in the pine soils. Microbial abundance analysis by PLFA showed that the fungal to bacterial ratio was higher in the pine soils (P < 0.01). Community analysis suggested that soil bacterial communities were more responsive to site (principal component 1; P < 0.001) than to land use (principal component 5; P < 0.001). In contrast, the fungal community was more affected by land-use change (principal component 1; P < 0.001) than by site, although site still had some influence on fungal community structure (principal component 2; P < 0.001). Redundancy analysis also suggested that bacterial and fungal communities responded differently to various soil abiotic properties, land-use change and location of sites. Overall, our results indicate that the change in land use from pasture to P. radiata stands had a direct impact on soil fungal communities but an indirect effect, through its effects on soil abiotic properties, on bacterial communities. Most of the changes in bacterial communities could be explained by altered soil physico-chemical properties associated with afforestation of pastures.