Population dynamics of type I and II methanotrophic bacteria in rice soils

Grazing exclusion alters soil methane flux and methanotrophic and methanogenic communities in alpine meadows on the Qinghai-Tibet Plateau

Grazing exclusion (GE) is an effective measure for restoring degraded grassland ecosystems. However, the effect of GE on methane (CH4) uptake and production remains unclear in dominant bacterial taxa, main metabolic pathways, and drivers of these pathways. This study aimed to determine CH4 flux in alpine meadow soil using the chamber method. The in situ composition of soil aerobic CH4-oxidizing bacteria (MOB) and CH4-producing archaea (MPA) as well as the relative abundance of their functional genes were analyzed in grazed and nongrazed (6 years) alpine meadows using metagenomic methods. The results revealed that CH4 fluxes in grazed and nongrazed plots were -34.10 and -22.82 μg‧m-2‧h-1, respectively. Overall, 23 and 10 species of Types I and II MOB were identified, respectively. Type II MOB comprised the dominant bacteria involved in CH4 uptake, with Methylocystis constituting the dominant taxa. With regard to MPA, 12 species were identified in grazed meadows and 3 in nongrazed meadows, with Methanobrevibacter constituting the dominant taxa. GE decreased the diversity of MPA but increased the relative abundance of dominated species Methanobrevibacter millerae from 1.47 to 4.69%. The proportions of type I MOB, type II MOB, and MPA that were considerably affected by vegetation and soil factors were 68.42, 21.05, and 10.53%, respectively. Furthermore, the structural equation models revealed that soil factors (available phosphorus, bulk density, and moisture) significantly affected CH4 flux more than vegetation factors (grass species number, grass aboveground biomass, grass root biomass, and litter biomass). CH4 flux was mainly regulated by serine and acetate pathways. The serine pathway was driven by soil factors (0.84, p < 0.001), whereas the acetate pathway was mainly driven by vegetation (-0.39, p < 0.05) and soil factors (0.25, p < 0.05). In conclusion, our findings revealed that alpine meadow soil is a CH4 sink. However, GE reduces the CH4 sink potential by altering vegetation structure and soil properties, especially soil physical properties.

Water table level controls methanogenic and methanotrophic communities and methane emissions in a Sphagnum-dominated peatland

Peatlands are important sources of the greenhouse gas methane emissions equipoised by methanogens and methanotrophs. However, knowledge about how microbial functional groups associated with methane production and oxidation respond to water table fluctuations has been limited to date. Here, methane-related microbial communities and the potentials of methane production and oxidation were determined along sectioned peat layers in a subalpine peatland across four Sphagnum-dominated sites with different water table levels. Methane fluxes were also monitored at these sites. The results showed that mcrA gene copies for methanogens were the highest in the 10- to 15-cm peat layer, which was also characterized by the maximum potential methane production (24.53 ± 1.83 nmol/g/h). Copy numbers of the pmoA gene for type Ia and Ib methanotrophs were enriched in the 0-5 cm peat layer with the highest potential methane oxidation (43.09 ± 3.44 nmol/g/h). For the type II methanotrophs, the pmoA gene copies were higher in the 10- to 15-cm peat layer. Hydrogenotrophic methanogens and type II methanotrophs dominated the methane functional groups. Deterministic process contributed more to methanogenic and methanotrophic community assemblages in comparison with stochastic process. The level of water table significantly shaped methanogenic and methanotrophic community structures and regulated methane fluxes. Compared with vascular plants, Sphagnum mosses significantly reduced the methane emissions in peatlands. Collectively, these findings enhance a comprehensive understanding of the effect of the water table level on methane functional groups, with consequential implications for reducing methane emissions within peatland ecosystems.IMPORTANCEThe water table level is recognized as a critical factor in regulating methane emissions, which are largely dependent on the balance of methanogens and methanotrophs. Previous studies on peat methane emissions have been mostly focused on spatial-temporal variations and the relationship with meteorological conditions. However, the role of the water table level in methane emissions remains unknown. In this work, four representative microhabitats along a water table gradient in a Sphagnum-dominated peatland were sampled to gain an insight into methane functional communities and methane emissions as affected by the water table level. The changes in methane-related microbial community structure and assembly were used to characterize the response to the water table level. This study improves the understanding of the changes in methane-related microbial communities and methane emissions with water table levels in peatlands.

Methane-Oxidizing Activity Enhances Sulfamethoxazole Biotransformation in a Benthic Constructed Wetland Biomat

Ammonia monooxygenase and analogous oxygenase enzymes contribute to pharmaceutical biotransformation in activated sludge. In this study, we hypothesized that methane monooxygenase can enhance pharmaceutical biotransformation within the benthic, diffuse periphytic sediments (i.e., "biomat") of a shallow, open-water constructed wetland. To test this hypothesis, we combined field-scale metatranscriptomics, porewater geochemistry, and methane gas fluxes to inform microcosms targeting methane monooxygenase activity and its potential role in pharmaceutical biotransformation. In the field, sulfamethoxazole concentrations decreased within surficial biomat layers where genes encoding for the particulate methane monooxygenase (pMMO) were transcribed by a novel methanotroph classified as Methylotetracoccus. Inhibition microcosms provided independent confirmation that methane oxidation was mediated by the pMMO. In these same incubations, sulfamethoxazole biotransformation was stimulated proportional to aerobic methane-oxidizing activity and exhibited negligible removal in the absence of methane, in the presence of methane and pMMO inhibitors, and under anoxia. Nitrate reduction was similarly enhanced under aerobic methane-oxidizing conditions with rates several times faster than for canonical denitrification. Collectively, our results provide convergent in situ and laboratory evidence that methane-oxidizing activity can enhance sulfamethoxazole biotransformation, with possible implications for the combined removal of nitrogen and trace organic contaminants in wetland sediments.

Prospecting the significance of methane-utilizing bacteria in agriculture

Microorganisms act as both the source and sink of methane, a potent greenhouse gas, thus making a significant contribution to the environment as an important driver of climate change. The rhizosphere and phyllosphere of plants growing in natural (mangroves) and artificial wetlands (flooded agricultural ecosystems) harbor methane-utilizing bacteria that oxidize methane at the source and reduce its net flux. For several decades, microorganisms have been used as biofertilizers to promote plant growth. However, now their role in reducing net methane flux, especially from flooded agricultural ecosystems is gaining momentum globally. Research in this context has mainly focused on taxonomic aspects related to methanotrophy among diverse bacterial genera, and environmental factors that govern methane utilization in natural and artificial wetland ecosystems. In the last few decades, concerted efforts have been made to develop multifunctional microbial inoculants that can oxidize methane and alleviate greenhouse gas emissions, as well as promote plant growth. In this context, combinations of taxonomic groups commonly found in rice paddies and those used as biofertilizers are being explored. This review deals with methanotrophy among diverse bacterial domains, factors influencing methane-utilizing ability, and explores the potential of novel methane-utilizing microbial consortia with plant growth-promoting traits in flooded ecosystems.

In Vivo Evidence of Single 13C and 15N Isotope-Labeled Methanotrophic Nitrogen-Fixing Bacterial Cells in Rice Roots

Methane-oxidizing bacteria (methanotrophs) play an ecological role in methane and nitrogen fluxes because they are capable of nitrogen fixation and methane oxidation, as indicated by genomic and cultivation-dependent studies. However, the chemical relationships between methanotrophy and diazotrophy and aerobic and anaerobic reactions, respectively, in methanotrophs remain unclear. No study has demonstrated the cooccurrence of both bioactivities in a single methanotroph bacterium in its natural environment. Here, we demonstrate that both bioactivities in type II methanotrophs occur at the single-cell level in the root tissues of paddy rice (Oryza sativa L. cv. Nipponbare). We first verified that difluoromethane, an inhibitor of methane monooxygenase, affected methane oxidation in rice roots. The results indicated that methane assimilation in the roots mostly occurred due to oxygen-dependent processes. Moreover, the results indicated that methane oxidation-dependent and methane oxidation-independent nitrogen fixation concurrently occurred in bulk root tissues. Subsequently, we performed fluorescence in situ hybridization and NanoSIMS analyses, which revealed that single cells of type II methanotrophs (involving six amplicon sequence variants) in paddy rice roots simultaneously and logarithmically fixed stable isotope gases ¹⁵N₂ and ¹³CH₄ during incubation periods of 0, 23, and 42 h, providing in vivo functional evidence of nitrogen fixation in methanotrophic cells. Furthermore, ¹⁵N enrichment in type II methanotrophs at 42 h varied among cells with an increase in ¹³C accumulation, suggesting that either the release of fixed nitrogen into root systems or methanotroph metabolic specialization is dependent on different microenvironmental niches in the root.

The synergy of environmental and microbial variations caused by hydrologic management affects the carbon emission in the Three Gorges Reservoir

The synergy of environmental and microbiological changes caused by hydrologic management on carbon emissions of river reservoirs remains unknown. Here, we investigated physiochemistry parameters, compositions of dissolved organic matter (DOM), carbon fluxes (CH₄ and CO₂), and microbial communities in the surface waters of the Three Gorges Reservoir (TGR) within one whole hydrological year. The results showed that hydrologic management significantly changed physiochemistry and DOM composition of the TGR water, and further influenced microbial community composition and functions. DOM content during the drainage period was much lower than during the impoundment period. During the impoundment period, humification extent of DOM became decreasing, while biotransformation extent became increasing compared with the drainage period. DOM composition and water pH exhibited significant correlation with the fluxes of CH₄ and CO₂, respectively. Microbial community composition and function significantly differed between the drainage and impoundment periods. Most of the differential microbial taxa were affiliated with functional groups involved in carbon cycle such as methanotrophy and phototrophy, which showed significant correlation with carbon fluxes. CH₄ and CO₂ fluxes can be mostly explained by synergy of microbial function with DOM composition and water pH, respectively. Such synergistic effect may account for the observed temporal variations of CH₄ fluxes and spatial variations of CO₂, and for the relatively low annual carbon emissions in the TGR. In summary, the synergy of environmental and microbial variations caused by hydrologic management affects carbon emissions from river reservoirs.

Unique high Arctic methane metabolizing community revealed through in situ 13CH4-DNA-SIP enrichment in concert with genome binning

Greenhouse gas (GHG) emissions from Arctic permafrost soils create a positive feedback loop of climate warming and further GHG emissions. Active methane uptake in these soils can reduce the impact of GHG on future Arctic warming potential. Aerobic methane oxidizers are thought to be responsible for this apparent methane sink, though Arctic representatives of these organisms have resisted culturing efforts. Here, we first used in situ gas flux measurements and qPCR to identify relative methane sink hotspots at a high Arctic cytosol site, we then labeled the active microbiome in situ using DNA Stable Isotope Probing (SIP) with heavy 13CH4 (at 100 ppm and 1000 ppm). This was followed by amplicon and metagenome sequencing to identify active organisms involved in CH4 metabolism in these high Arctic cryosols. Sequencing of 13C-labeled pmoA genes demonstrated that type II methanotrophs (Methylocapsa) were overall the dominant active methane oxidizers in these mineral cryosols, while type I methanotrophs (Methylomarinovum) were only detected in the 100 ppm SIP treatment. From the SIP-13C-labeled DNA, we retrieved nine high to intermediate quality metagenome-assembled genomes (MAGs) belonging to the Proteobacteria, Gemmatimonadetes, and Chloroflexi, with three of these MAGs containing genes associated with methanotrophy. A novel Chloroflexi MAG contained a mmoX gene along with other methane oxidation pathway genes, identifying it as a potential uncultured methane oxidizer. This MAG also contained genes for copper import, synthesis of biopolymers, mercury detoxification, and ammonia uptake, indicating that this bacterium is strongly adapted to conditions in active layer permafrost and providing new insights into methane biogeochemical cycling. In addition, Betaproteobacterial MAGs were also identified as potential cross-feeders with methanotrophs in these Arctic cryosols. Overall, in situ SIP labeling combined with metagenomics and genome binning demonstrated to be a useful tool for discovering and characterizing novel organisms related to specific microbial functions or biogeochemical cycles of interest. Our findings reveal a unique and active Arctic cryosol microbial community potentially involved in CH4 cycling.

Methane emissions may be driven by hydrogenotrophic methanogens inhabiting the stem tissues of poplar

Living trees in forests emit methane (CH₄ ) from their stems. However, the magnitudes, patterns, drivers, origins, and biogeochemical pathways of these emissions remain poorly understood. We measured in situ CH₄ fluxes in poplar stems and soils using static chambers and investigated the microbial communities of heartwood and sapwood by sequencing bacterial 16S, archaeal 16S, and fungal ITS rRNA genes. Methane emissions from poplar stems occurred throughout the sampling period. The mean CH₄ emission rate was 2.7 mg m^-2  stem d^-1 . Stem CH₄ emission rate increased significantly with air temperature, humidity, soil water content, and soil CH₄ fluxes, but decreased with increasing sampling height. The CO₂ reduction and methylotrophic methanogenesis were the major methanogenic pathways in wood tissues. The dominant methanogen groups detected in stem tissues were Methanobacterium, Methanobrevibacter, Rice Cluster I, Methanosarcina, Methanomassiliicoccus, Methanoculleus, and Methanomethylophilaceae. In addition, three methanotrophic genera were identified in the heartwood and sapwood - Methylocystis, Methylobacterium, and Paracoccus. Overall, stem CH₄ emissions can originate directly from the internal tissues or co-occur from soils and stems. The co-existence of methanogens and methanotrophs within heartwood and sapwood highlights a need for future research in the microbial mechanisms underlying stem CH₄ exchange with the atmosphere.

Response of nitrite-dependent anaerobic methanotrophs to elevated atmospheric CO2 concentration in paddy fields

Nitrite-dependent anaerobic methane oxidation (n-damo) catalyzed by Candidatus Methylomirabilis oxyfera (M. oxyfera)-like bacteria is a new pathway for the regulation of methane emissions from paddy fields. Elevated atmospheric CO₂ concentrations (e[CO₂]) can indirectly affect the structure and function of microbial communities. However, the response of M. oxyfera-like bacteria to e[CO₂] is currently unknown. Here, we investigated the effect of e[CO₂] (ambient CO₂ + 200 ppm) on community composition, abundance, and activity of M. oxyfera-like bacteria at different depths (0-5, 5-10, and 10-20 cm) in paddy fields across multiple rice growth stages (tillering, jointing, and flowering). High-throughput sequencing showed that e[CO₂] had no significant effect on the community composition of M. oxyfera-like bacteria. However, quantitative PCR suggested that the 16S rRNA gene abundance of M. oxyfera-like bacteria increased significantly in soil under e[CO₂], particularly at the tillering stage. Furthermore, ¹³CH₄ tracer experiments showed potential n-damo activity of 0.31-8.91 nmol CO₂ g^-1 (dry soil) d^-1. E[CO₂] significantly stimulated n-damo activity, especially at the jointing and flowering stages. The n-damo activity and abundance of M. oxyfera-like bacteria increased by an average of 90.9% and 50.0%, respectively, under e[CO₂]. Correlation analysis showed that the increase in soil dissolved organic carbon content caused by e[CO₂] had significant effects on the activity and abundance of M. oxyfera-like bacteria. Overall, this study provides the first evidence for a positive response of M. oxyfera-like bacteria to e[CO₂], which may help reduce methane emissions from paddy fields under future climate change conditions.

Revealing the community and metabolic potential of active methanotrophs by targeted metagenomics in the Zoige wetland of the Tibetan Plateau

The Zoige wetland of the Tibetan Plateau is one of the largest alpine wetlands in the world and a major emission source of methane. Methane oxidation by methanotrophs can counteract the global warming effect of methane released in the wetlands. Understanding methanotroph activity, diversity and metabolism at the molecular level can guide the isolation of the uncultured microorganisms and inform strategy-making decisions and policies to counteract global warming in this unique ecosystem. Here we applied DNA stable isotope probing using ¹³ C-labelled methane to label the genomes of active methanotrophs, examine the methane oxidation potential and recover metagenome-assembled genomes (MAGs) of active methanotrophs. We found that gammaproteobacteria of type I methanotrophs are responsible for methane oxidation in the wetland. We recovered two phylogenetically novel methanotroph MAGs distantly related to extant Methylobacter and Methylovulum. They belong to type I methanotrophs of gammaproteobacteria, contain both mxaF and xoxF types of methanol dehydrogenase coding genes, and participate in methane oxidation via H₄ MPT and RuMP pathways. Overall, the community structure of active methanotrophs and their methanotrophic pathways revealed by DNA-SIP metagenomics and retrieved methanotroph MAGs highlight the importance of methanotrophs in suppressing methane emission in the wetland under the scenario of global warming.

The response of methanotrophs to additions of either ammonium, nitrate or urea in alpine swamp meadow soil as revealed by stable isotope probing

Different forms of nitrogen (N) are deposited on the Qinghai-Tibetan plateau (QTP), while their differential effects on soil methanotrophs and their activity remain elusive. We constructed microcosms amended with different N fertilizers (ammonia, nitrate and urea) using the soils sampled from a swamp meadow on the QTP. The responses of active methanotrophs to different forms of nitrogen were determined by stable isotope probing with 5% 13C-methane. At the early stage of incubation, all N fertilizers, especially urea, suppressed methane oxidation compared with the control. The methane oxidation rate increased during the incubation, suggesting an adaptation and stimulation of some methanotrophs to elevated methane. At the onset of the incubation, the type II methanotrophs Methylocystis were most abundant, but decreased during the incubation and were replaced by the type Ia methanotrophs Methylomonas. Ammonia and urea had similar effects on the methanotroph communities, both characterized by an elevation in the proportion of Methylobacter and more diverse methanotroph communities. Nitrate had less effect on the methanotroph community. Our results uncovered the active methanotrophs responding to different nitrogen forms, and suggested that urea-N might have large effects on methanotroph diversity and activity in swamp meadow soils on the QTP.

Methane-based denitrification kinetics and syntrophy in a membrane biofilm reactor at low methane pressure

A methane-based membrane biofilm reactor (MBfR) was assessed for a tertiary nitrogen removal process in domestic wastewater treatment. To mitigate effluent dissolved methane concentrations, the MBfR was operated with a 20% methane mixing ratio and a low pressure of 0.003 atm. The nitrate concentration was reduced from 20 to 4 mg/L with a low methane concentration of 3.3 mg/L in the effluent at 4 h hydraulic retention time (HRT). An in situ dissolved oxygen sensor showed a concentration of 0.045 mg/L in the MBfR, demonstrating methane oxidation under hypoxic conditions. Both 16S rRNA gene sequencing and metagenomic analysis identified bacteria capable of oxidation of methane coupled to denitrification (Methylocystis), whereas other bacteria were implicated in either methane oxidation (Methylococcus) or nitrate reduction (Escherichia). Reduced genetic potential for nitrate reduction to nitrite at a shorter HRT coincided with a decreased efficiency of denitrification, suggesting rate limitation by this initial step of denitrification. Genes encoding nitrite reduction to dinitrogen were at similar relative abundance under both HRT conditions. Our results provide mechanistic evidence for microbial syntrophy between aerobic methanotrophs and denitrifiers in methane-fed MBfRs operated under varying HRTs, with important implications for novel biological nitrogen removal to dilute wastewater.

Differentiated Mechanisms of Biochar Mitigating Straw-Induced Greenhouse Gas Emissions in Two Contrasting Paddy Soils

Straw returns to the soil is an effective way to improve soil organic carbon and reduce air pollution by straw burning, but this may increase CH₄ and N₂O emissions risks in paddy soils. Biochar has been used as a soil amendment to improve soil fertility and mitigate CH₄ and N₂O emissions. However, little is known about their interactive effect on CH₄ and N₂O emissions and the underlying microbial mechanisms. In this study, a 2-year pot experiment was conducted on two paddy soil types (an acidic Utisol, TY, and an alkaline Inceptisol, BH) to evaluate the influence of straw and biochar applications on CH₄ and N₂O emissions, and on related microbial functional genes. Results showed that straw addition markedly increased the cumulative CH₄ emissions in both soils by 4.7- to 9.1-fold and 23.8- to 72.4-fold at low (S1) and high (S2) straw input rate, respectively, and significantly increased mcrA gene abundance. Biochar amendment under the high straw input (BS2) significantly decreased CH₄ emissions by more than 50% in both soils, and increased both mcrA gene and pmoA gene abundances, with greatly enhanced pmoA gene and a decreased mcrA/pmoA gene ratio. Moreover, methanotrophs community changed distinctly in response to straw and biochar amendment in the alkaline BH soil, but showed slight change in the acidic TY soil. Straw had little effect on N₂O emissions at low input rate (S1) but significantly increased N₂O emissions at the high input rate (S2). Biochar amendment showed inconsistent effect on N₂O emissions, with a decreasing trend in the BH soil but an increasing trend in the TY soil in which high ammonia existed. Correspondingly, increased nirS and nosZ gene abundances and obvious community changes in nosZ gene containing denitrifiers in response to biochar amendment were observed in the BH soil but not in the TY soil. Overall, our results suggested that biochar amendment could markedly mitigate the CH₄ and N₂O emissions risks under a straw return practice via regulating functional microbes and soil physicochemical properties, while the performance of this practice will vary depending on soil parent material characteristics.

Atmospheric CH4 oxidation by Arctic permafrost and mineral cryosols as a function of water saturation and temperature

The response of methanotrophic bacteria capable of oxidizing atmospheric CH₄ to climate warming is poorly understood, especially for those present in Arctic mineral cryosols. The atmospheric CH₄ oxidation rates were measured in microcosms incubated at 4 °C and 10 °C along a 1-m depth profile and over a range of water saturation conditions for mineral cryosols containing type I and type II methanotrophs from Axel Heiberg Island (AHI), Nunavut, Canada. The cryosols exhibited net consumption of ~2 ppmv CH₄ under all conditions, including during anaerobic incubations. Methane oxidation rates increased with temperature and decreased with increasing water saturation and depth, exhibiting the highest rates at 10 °C and 33% saturation at 5 cm depth (260 ± 60 pmol CH₄ gdw^-1 d^-1 ). Extrapolation of the CH₄ oxidation rates to the field yields net CH₄ uptake fluxes ranging from 11 to 73 μmol CH₄  m^-2 d^-1 , which are comparable to field measurements. Stable isotope mass balance indicates ~50% of the oxidized CH₄ is incorporated into the biomass regardless of temperature or saturation. Future atmospheric CH₄ uptake rates at AHI with increasing temperatures will be determined by the interplay of increasing CH₄ oxidation rates vs. water saturation and the depth to the water table during summer thaw.

Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker

Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing "unknown methanotrophic bacteria." This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities.

Uncultivated Methylocystis Species in Paddy Soil Include Facultative Methanotrophs that Utilize Acetate

Methanotrophs are crucial in regulating methane emission from rice field systems. Type II methanotrophs in particular are often observed in high abundance in paddy soil. Some cultivated species of Methylocystis are able to grow on acetate in the absence of methane. We hypothesize that the dominant type II methanotrophs in paddy soil might facultatively utilize acetate for growth, which we evaluate in the present study. The measurement of methane oxidation rates showed that the methanotrophic activity in paddy soil was inhibited by the addition of acetate compared to the continuous supplementation of methane, but the paddy soil maintained the methane oxidation capacity and recovered following methane supplementation. Terminal restriction fragment length polymorphism analysis (T-RFLP) combined with cloning and sequencing of pmoA genes showed that Methylocystis was enriched after incubation with added acetate, while the type I methanotrophs Methylocaldum/Methylococcus and Methylobacter were enriched by methane supplementation. A comparison of pmoA sequences obtained in this study with those in the public database indicated that they were globally widespread in paddy soils or in associated with rice roots. Furthermore, we performed stable isotope probing (SIP) of pmoA messenger RNA (mRNA) to investigate the assimilation of (13)C-acetate by paddy soil methanotrophs. RNA-SIP revealed that Methylocystis-related methanotrophs which shared the same genotype of the above enriched species were significantly labelled. It indicates that these methanotrophs actively assimilated the labelled acetate in paddy soil. Altogether, these results suggested that uncultivated Methylocystis species are facultative methanotrophs utilizing acetate as a secondary carbon source in paddy soil.

High resolution depth distribution of Bacteria, Archaea, methanotrophs, and methanogens in the bulk and rhizosphere soils of a flooded rice paddy

The communities and abundances of methanotrophs and methanogens, along with the oxygen, methane, and total organic carbon (TOC) concentrations, were investigated along a depth gradient in a flooded rice paddy. Broad patterns in vertical profiles of oxygen, methane, TOC, and microbial abundances were similar in the bulk and rhizosphere soils, though methane and TOC concentrations and 16S rRNA gene copies were clearly higher in the rhizosphere soil than in the bulk soil. Oxygen concentrations decreased sharply to below detection limits at 8 mm depth. Pyrosequencing of 16S rRNA genes showed that bacterial and archaeal communities varied according to the oxic, oxic-anoxic, and anoxic zones, indicating that oxygen is a determining factor for the distribution of bacterial and archaeal communities. Aerobic methanotrophs were maximally observed near the oxic-anoxic interface, while methane, TOC, and methanogens were highest in the rhizosphere soil at 30–200 mm depth, suggesting that methane is produced mainly from organic carbon derived from rice plants and is metabolized aerobically. The relative abundances of type I methanotrophs such as Methylococcus, Methylomonas, and Methylocaldum decreased more drastically than those of type II methanotrophs (such as Methylocystis and Methylosinus) with increasing depth. Methanosaeta and Methanoregula were predominant methanogens at all depths, and the relative abundances of Methanosaeta, Methanoregula, and Methanosphaerula, and GOM_Arc_I increased with increasing depth. Based on contrasts between absolute abundances of methanogens and methanotrophs at depths sampled across rhizosphere and bulk soils (especially millimeter-scale slices at the surface), we have identified populations of methanogens (Methanosaeta, Methanoregula, Methanocella, Methanobacterium, and Methanosphaerula), and methanotrophs (Methylosarcina, Methylococcus, Methylosinus, and unclassified Methylocystaceae) that are likely physiologically active in situ.

Metaproteomic identification of diazotrophic methanotrophs and their localization in root tissues of field-grown rice plants

In a previous study by our group, CH4 oxidation and N2 fixation were simultaneously activated in the roots of wild-type rice plants in a paddy field with no N input; both processes are likely controlled by a rice gene for microbial symbiosis. The present study examined which microorganisms in rice roots were responsible for CH4 oxidation and N2 fixation under the field conditions. Metaproteomic analysis of root-associated bacteria from field-grown rice (Oryza sativa Nipponbare) revealed that nitrogenase complex-containing nitrogenase reductase (NifH) and the alpha subunit (NifD) and beta subunit (NifK) of dinitrogenase were mainly derived from type II methanotrophic bacteria of the family Methylocystaceae, including Methylosinus spp. Minor nitrogenase proteins such as Methylocella, Bradyrhizobium, Rhodopseudomonas, and Anaeromyxobacter were also detected. Methane monooxygenase proteins (PmoCBA and MmoXYZCBG) were detected in the same bacterial group of the Methylocystaceae. Because these results indicated that Methylocystaceae members mediate both CH4 oxidation and N2 fixation, we examined their localization in rice tissues by using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). The methanotrophs were localized around the epidermal cells and vascular cylinder in the root tissues of the field-grown rice plants. Our metaproteomics and CARD-FISH results suggest that CH4 oxidation and N2 fixation are performed mainly by type II methanotrophs of the Methylocystaceae, including Methylosinus spp., inhabiting the vascular bundles and epidermal cells of rice roots.

A rice gene for microbial symbiosis, Oryza sativa CCaMK, reduces CH4 flux in a paddy field with low nitrogen input

Plants have mutualistic symbiotic relationships with rhizobia and fungi by the common symbiosis pathway, of which Ca(2+)/calmodulin-dependent protein kinase (encoded by CCaMK) is a central component. Although Oryza sativa CCaMK (OsCCaMK) is required for fungal accommodation in rice roots, little is known about the role of OsCCaMK in rice symbiosis with bacteria. Here, we report the effect of a Tos17-induced OsCCaMK mutant (NE1115) on CH4 flux in low-nitrogen (LN) and standard-nitrogen (SN) paddy fields compared with wild-type (WT) Nipponbare. The growth of NE1115 was significantly decreased compared with that of the WT, especially in the LN field. The CH4 flux of NE1115 in the LN field was significantly greater (156 to 407% in 2011 and 170 to 816% in 2012) than that of the WT, although no difference was observed in the SN field. The copy number of pmoA (encodes methane monooxygenase in methanotrophs) was significantly higher in the roots and rhizosphere soil of the WT than in those of NE1115. However, the mcrA (encodes methyl coenzyme M reductase in methanogens) copy number did not differ between the WT and NE1115. These results were supported by a (13)C-labeled CH4-feeding experiment. In addition, the natural abundance of (15)N in WT shoots (3.05‰) was significantly lower than in NE1115 shoots (3.45‰), suggesting greater N2 fixation in the WT because of dilution with atmospheric N2 (0.00‰). Thus, CH4 oxidation and N2 fixation were simultaneously activated in the root zone of WT rice in the LN field and both processes are likely controlled by OsCCaMK.

The microbial communities and potential greenhouse gas production in boreal acid sulphate, non-acid sulphate, and reedy sulphidic soils

Acid sulphate (AS) soils along the Baltic coasts contain significant amounts of organic carbon and nitrogen in their subsoils. The abundance, composition, and activity of microbial communities throughout the AS soil profile were analysed. The data from a drained AS soil were compared with those from a drained non-AS soil and a pristine wetland soil from the same region. Moreover, the potential production of methane, carbon dioxide, and nitrous oxide from the soils was determined under laboratory conditions. Direct microscopic counting, glucose-induced respiration (GIR), whole cell hybridisation, and extended phospholipid fatty acid (PLFA) analysis confirmed the presence of abundant microbial communities in the topsoil and also in the deepest Cg2 horizon of the AS soil. The patterns of microbial counts, biomass and activity in the profile of the AS soil and partly also in the non-AS soil therefore differed from the general tendency of gradual decreases in soil profiles. High respiration in the deepest Cg2 horizon of the AS soil (5.66 μg Cg(-1)h(-1), as compared to 2.71 μg Cg(-1)h(-1) in a top Ap horizon) is unusual but reasonable given the large amount of organic carbon in this horizon. Nitrous oxide production peaked in the BCgc horizon of the AS and in the BC horizon of the non-AS soil, but the peak value was ten-fold higher in the AS soil than in the non-AS soil (82.3 vs. 8.6 ng Ng(-1)d(-1)). The data suggest that boreal AS soils on the Baltic coast contain high microbial abundance and activity. This, together with the abundant carbon and total and mineral nitrogen in the deep layers of AS soils, may result in substantial gas production. Consequently, high GHG emissions could occur, for example, when the generally high water table is lowered because of arable farming.

Environmental impacts on the diversity of methane-cycling microbes and their resultant function

Methane is an important anthropogenic greenhouse gas that is produced and consumed in soils by microorganisms responding to micro-environmental conditions. Current estimates show that soil consumption accounts for 5–15% of methane removed from the atmosphere on an annual basis. Recent variability in atmospheric methane concentrations has called into question the reliability of estimates of methane consumption and calls for novel approaches in order to predict future atmospheric methane trends. This review synthesizes the environmental and climatic factors influencing the consumption of methane from the atmosphere by non-wetland, terrestrial soil microorganisms. In particular, we focus on published efforts to connect community composition and diversity of methane-cycling microbial communities to observed rates of methane flux. We find abundant evidence for direct connections between shifts in the methane-cycling microbial community, due to climate and environmental changes, and observed methane flux levels. These responses vary by ecosystem and associated vegetation type. This information will be useful in process-based models of ecosystem methane flux responses to shifts in environmental and climatic parameters.

The relative contribution of methanotrophs to microbial communities and carbon cycling in soil overlying a coal-bed methane seep

Seepage of coal-bed methane (CBM) through soils is a potential source of atmospheric CH4 and also a likely source of ancient (i.e. (14) C-dead) carbon to soil microbial communities. Natural abundance (13) C and (14) C compositions of bacterial membrane phospholipid fatty acids (PLFAs) and soil gas CO2 and CH4 were used to assess the incorporation of CBM-derived carbon into methanotrophs and other members of the soil microbial community. Concentrations of type I and type II methanotroph PLFA biomarkers (16:1ω8c and 18:1ω8c, respectively) were elevated in CBM-impacted soils compared with a control site. Comparison of PLFA and 16s rDNA data suggested type I and II methanotroph populations were well estimated and overestimated by their PLFA biomarkers, respectively. The δ(13) C values of PLFAs common in type I and II methanotrophs were as negative as -67‰ and consistent with the assimilation of CBM. PLFAs more indicative of nonmethanotrophic bacteria had δ(13) C values that were intermediate indicating assimilation of both plant- and CBM-derived carbon. Δ(14) C values of select PLFAs (-351 to -936‰) indicated similar patterns of CBM assimilation by methanotrophs and nonmethanotrophs and were used to estimate that 35-91% of carbon assimilated by nonmethanotrophs was derived from CBM depending on time of sampling and soil depth.

Diversity of cultivable methane-oxidizing bacteria in microsites of a rice paddy field: investigation by cultivation method and fluorescence in situ hybridization (FISH)

The diversity of cultivable methane-oxidizing bacteria (MOB) in the rice paddy field ecosystem was investigated by combined culture-dependent and fluorescence in situ hybridization (FISH) techniques. Seven microsites of a Japanese rice paddy field were the focus of the study: floodwater, surface soil, bulk soil, rhizosphere soil, root, basal stem of rice plant, and rice stumps of previous harvest. Based on pmoA gene analysis and transmission electron microscopy (TEM), four type I, and nine type II MOB isolates were obtained from the highest dilution series of enrichment cultures. The type I MOB isolates included a novel species in the genus Methylomonas from floodwater and this is the first type I MOB strain isolated from floodwater of a rice paddy field. In the type I MOB, two isolates from stumps were closely related to Methylomonas spp.; one isolate obtained from rhizosphere soil was most related to Methyloccocus-Methylocaldum-Methylogaea clade. Almost all the type II MOB isolates were related to Methylocystis methanotrophs. FISH confirmed the presence of both types I and II MOB in all the microsites and in the related enrichment cultures. The study reported, for the first time, the diversity of cultivable methanotrophs including a novel species of type I MOB in rice paddy field compartments. Refining growth media and culture conditions, in combination with molecular approaches, will allow us to broaden our knowledge on the MOB community in the rice paddy field ecosystem and consequently to implement strategies for mitigating CH₄ emission from this ecosystem.

Ageing well: methane oxidation and methane oxidizing bacteria along a chronosequence of 2000 years

Rice is the staple food for more than half of the world's growing population. While the area planted to wetland rice is expected to increase further, virtually nothing is known about the long-term development of the respective microbial communities, and how these might influence biogeochemistry. Focusing on methane oxidizing bacteria, we studied a chronosequence of paddy fields in China aged 50-2000 years. Potential methanotrophic activity increased substantially with age of soil. Community composition was relatively similar in all fields. However, growth and activity of one particular subgroup of methanotrophs correlated to soil age suggesting an intricate abiotic control on methanotrophs evolving with time. Our results demonstrate that continuous rice agriculture does not only shape the microbial community, but also modifies the micro-environment in a way enabling faster growth and higher activity of selected populations.

Seasonal change in methanotrophic diversity and populations in a rice field soil assessed by DNA-stable isotope probing and quantitative real-time PCR

The community structure of methane-oxidizing bacteria (methanotrophs) is affected by concentrations of methane and oxygen. In rice fields, concentrations of both gases differ significantly between the flooded and drained seasons. We investigated the active methanotrophic community structures in flooded and drained soils by DNA-based stable isotope probing. Active methanotrophic diversity was assessed with clone library-based analyses of the 16S rRNA gene and the particulate methane monooxygenase gene (pmoA). The active methanotrophic populations were also estimated by group-specific quantitative real-time PCR assays targeting the 16S rRNA gene and the pmoA gene in (13)C-labeled DNA. These molecular biological analyses showed that the flooded rice field soil was dominated by Type II methanotrophs closely related to the genera Methylocystis and Methylosinus, whereas the drained rice field soil was dominated by Type I methanotrophs closely related to the genera Methylomonas, Methylosarcina, and Methylomicrobium. The alternating conditions in a rice field select for methanotrophs adapted to each environment, resulting in a dramatic change in methanotrophic community structure from one season to another.

Activity and diversity of methanotrophic bacteria at methane seeps in eastern Lake Constance sediments

The activity and community structure of aerobic methanotrophic communities were investigated at methane seeps (pockmarks) in the littoral and profundal zones of an oligotrophic freshwater lake (Lake Constance, Germany). Measurements of potential methane oxidation rates showed that sediments inside littoral pockmarks are hot spots of methane oxidation. Potential methane oxidation rates at littoral pockmark sites exceeded the rates of the surrounding sediment by 2 orders of magnitude. Terminal restriction fragment length polymorphism (T-RFLP) analysis of the pmoA gene revealed major differences in the methanotrophic community composition between littoral pockmarks and the surrounding sediments. Clone library analysis confirmed that one distinct Methylobacter-related group dominates the community at littoral pockmarks. In profundal sediments, the differences between pockmarks and surrounding sediments were found to be less pronounced.

Methanotrophs and copper

Methanotrophs, cells that consume methane (CH(4)) as their sole source of carbon and energy, play key roles in the global carbon cycle, including controlling anthropogenic and natural emissions of CH(4), the second-most important greenhouse gas after carbon dioxide. These cells have also been widely used for bioremediation of chlorinated solvents, and help sustain diverse microbial communities as well as higher organisms through the conversion of CH(4) to complex organic compounds (e.g. in deep ocean and subterranean environments with substantial CH(4) fluxes). It has been well-known for over 30 years that copper (Cu) plays a key role in the physiology and activity of methanotrophs, but it is only recently that we have begun to understand how these cells collect Cu, the role Cu plays in CH(4) oxidation by the particulate CH(4) monooxygenase, the effect of Cu on the proteome, and how Cu affects the ability of methanotrophs to oxidize different substrates. Here we summarize the current state of knowledge of the phylogeny, environmental distribution, and potential applications of methanotrophs for regional and global issues, as well as the role of Cu in regulating gene expression and proteome in these cells, its effects on enzymatic and whole-cell activity, and the novel Cu uptake system used by methanotrophs.

Diversity of methanotrophs in Zoige wetland soils under both anaerobic and aerobic conditions

Zoige wetland is one of the most important methane emission centers in China. The oxidation of methane in the wetland affects global warming, soil ecology and atmospheric chemistry. Despite their global significance, microorganisms that consume methane in Zoige wetland remain poorly characterized. In this study, we investigated methanotrophs diversity in soil samples from both anaerobic site and aerobic site in Zoige wetland using pmoA gene as a molecular marker. The cloning library was constructed according to the pmoA sequences detected. Four clusters of methanotrophs were detected. The phylogenetic tree showed that all four clusters detected were affiliated to type I methanotrophs. Two novel clusters (cluster 1, cluster 2) were found to relate to none of the recognized genera of methanotrophs. These clusters have no cultured representatives and reveal an ecological adaptation of particular uncultured methanotrophs in Zoige wetland. Two clusters were belonging to Methylobacter and Methylococcus separately. Denaturing gradient gel electrophoresis gel bands pattern retrieved from these two samples revealed that the community compositions of anaerobic soil and aerobic soil were different from each other while anaerobic soil showed a higher metanotrophs diversity. Real-time PCR assays of the two samples demonstrated that aerobic soil sample in Zoige wetland was 1.5 times as much copy numbers as anaerobic soil. These data illustrated that methanotrophs are a group of microorganisms influence the methane consumption in Zoige wetland.

Cross-feeding of methane carbon among bacteria on rice roots revealed by DNA-stable isotope probing

Most of methane in flooded rice fields is emitted via transport through the plant gas vascular system. In the reverse direction, oxygen is diffusing to the living roots, and hence, the rhizosphere and roots of rice serve as an important habitat for CH4 oxidation which reduces CH4 emission from flooded rice fields. A laboratory incubation experiment was performed to determine the activity and composition of the methanotrophic Proteobacteria inhabiting the rice root system. Excised root material from young- and old-nodal roots was collected and used for aerobic incubation in the presence of (13) C-labelled CH4 . Prior to the incubation, the root material was treated with ammonium to test the effect of N availability on the activity of methanotrophs. Analyses of pmoA genes revealed that type II methanotrophs related to Methylocystaceae were predominant and remained relatively stable during the incubation regardless of root material and ammonium treatments. The abundance of type I methanotrophs was much smaller but their composition was relatively more variable. 16S rDNA-based stable isotope probing revealed that Sphingomonadales and methanotrophic Methylocystaceae were the most active bacteria assimilating CH4 -derived carbon on young-nodal roots, whereas methylotrophic Methylophilales were active on old-nodal roots. These observations indicate the existence on rice roots of a bacterial food web that is driven by CH4 -derived carbon.

Preferential cultivation of type II methanotrophic bacteria from littoral sediments (Lake Constance)

Most widely used medium for cultivation of methanotrophic bacteria from various environments is that proposed in 1970 by Whittenbury. In order to adapt and optimize medium for culturing of methanotrophs from freshwater sediment, media with varying concentrations of substrates, phosphate, nitrate, and other mineral salts were used to enumerate methanotrophs by the most probable number method. High concentrations (>1 mM) of magnesium and sulfate, and high concentrations of nitrate (>500 microM) significantly reduced the number of cultured methanotrophs, whereas phosphate in the range of 15-1500 microM had no influence. Also oxygen and carbon dioxide influenced the culturing efficiency, with an optimal mixing ratio of 17% O(2) and 3% CO(2); the mixing ratio of methane (6-32%) had no effect. A clone library of pmoA genes amplified by PCR from DNA extracted from sediment revealed the presence of both type I and type II methanotrophs. Nonetheless, the cultivation of methanotrophs, also with the improved medium, clearly favored growth of type II methanotrophs of the Methylosinus/Methylocystis group. Although significantly more methanotrophs could be cultured with the modified medium, their diversity did not mirror the diversity of methanotrophs in the sediment sample detected by molecular biology method.

A reanalysis of phospholipid fatty acids as ecological biomarkers for methanotrophic bacteria

Aerobic methane-oxidizing bacteria (MB) are the primary terrestrial sinks for the greenhouse gas methane. A distinct characteristic of MB is the presence of specific phospholipid ester-linked fatty acids (PLFA) in their membranes that differentiate them from each other and also from all other organisms. These distinct PLFA patterns facilitate microbial ecology studies. For example, the assimilation of C from methane into PLFA can be traced in environmental samples using stable isotope ((13)C) probing (SIP), which links the activity of MB to their community composition in situ. However, the phylogenetic resolution of this method is low because of a lack of PLFA profiles from cultured MB species. In this study, PLFA profiles of 22 alphaproteobacterial (type II) MB were analysed after growth on methane, methanol or both substrates together. Growth on different substrates did not affect the PLFA profiles of the investigated strains. A number of Methylocystis strains contained novel C18:2 fatty acids (omega 7c,12c and omega 6c,12c) that can be used as diagnostic biomarkers. The detection of these novel PLFA, combined with the analyses of multiple type II strains, increased the phylogenetic resolution of PLFA analysis substantially. Multivariate analysis of the expanded MB PLFA database identified species groups that closely reflected phylogenies based on 16S rRNA and pmoA gene sequences. The PLFA database therefore provides a robust framework for linking identity to activity in MB communities with a higher resolution than was previously possible.

Diversity of aerobic methanotrophic bacteria in a permafrost active layer soil of the Lena Delta, Siberia

With this study, we present first data on the diversity of aerobic methanotrophic bacteria (MOB) in an Arctic permafrost active layer soil of the Lena Delta, Siberia. Applying denaturing gradient gel electrophoresis and cloning of 16S ribosomal ribonucleic acid (rRNA) and pmoA gene fragments of active layer samples, we found a general restriction of the methanotrophic diversity to sequences closely related to the genera Methylobacter and Methylosarcina, both type I MOB. In contrast, we revealed a distinct species-level diversity. Based on phylogenetic analysis of the 16S rRNA gene, two new clusters of MOB specific for the permafrost active layer soil of this study were found. In total, 8 out of 13 operational taxonomic units detected belong to these clusters. Members of these clusters were closely related to Methylobacter psychrophilus and Methylobacter tundripaludum, both isolated from Arctic environments. A dominance of MOB closely related to M. psychrophilus and M. tundripaludum was confirmed by an additional pmoA gene analysis. We used diversity indices such as the Shannon diversity index or the Chao1 richness estimator in order to compare the MOB community near the surface and near the permafrost table. We determined a similar diversity of the MOB community in both depths and suggest that it is not influenced by the extreme physical and geochemical gradients in the active layer.

Identity of active methanotrophs in landfill cover soil as revealed by DNA-stable isotope probing

A considerable amount of methane produced during decomposition of landfill waste can be oxidized in landfill cover soil by methane-oxidizing bacteria (methanotrophs) thus reducing greenhouse gas emissions to the atmosphere. The identity of active methanotrophs in Roscommon landfill cover soil, a slightly acidic peat soil, was assessed by DNA-stable isotope probing (SIP). Landfill cover soil slurries were incubated with (13)C-labelled methane and under either nutrient-rich nitrate mineral salt medium or water. The identity of active methanotrophs was revealed by analysis of (13)C-labelled DNA fractions. The diversity of functional genes (pmoA and mmoX) and 16S rRNA genes was analyzed using clone libraries, microarrays and denaturing gradient gel electrophoresis. 16S rRNA gene analysis revealed that the cover soil was mainly dominated by Type II methanotrophs closely related to the genera Methylocella and Methylocapsa and to Methylocystis species. These results were supported by analysis of mmoX genes in (13)C-DNA. Analysis of pmoA gene diversity indicated that a significant proportion of active bacteria were also closely related to the Type I methanotrophs, Methylobacter and Methylomonas species. Environmental conditions in the slightly acidic peat soil from Roscommon landfill cover allow establishment of both Type I and Type II methanotrophs.

Abundance, distribution and potential activity of methane oxidizing bacteria in permafrost soils from the Lena Delta, Siberia

The methane oxidation potential of active layer profiles of permafrost soils from the Lena Delta, Siberia, was studied with regard to its respond to temperature, and abundance and distribution of type I and type II methanotrophs. Our results indicate vertical shifts within the optimal methane oxidation temperature and within the distribution of type I and type II methanotrophs. In the upper active layer, maximum methane oxidation potentials were detected at 21 degrees C. Deep active layer zones that are constantly exposed to temperatures below 2 degrees C showed a maximum potential to oxidize methane at 4 degrees C. Our results indicate a dominance of psychrophilic methanotrophs close to the permafrost table. Type I methanotrophs dominated throughout the active layer profiles but their number strongly fluctuated with depth. In contrast, type II methanotrophs were constantly abundant through the whole active layer and displaced type I methanotrophs close to the permafrost table. No correlation between in situ temperatures and the distribution of type I and type II methanotrophs was found. However, the distribution of type I and type II methanotrophs correlated significantly with in situ methane concentrations. Beside vertical fluctuations, the abundance of methane oxidizers also fluctuated according to different geomorphic units. Similar methanotroph cell counts were detected in samples of a flood plain and a polygon rim, whereas cell counts in samples of a polygon centre were up to 100 times lower.

Cultivation of methanotrophic bacteria in opposing gradients of methane and oxygen

In sediments, methane-oxidizing bacteria live in opposing gradients of methane and oxygen. In such a gradient system, the fluxes of methane and oxygen are controlled by diffusion and consumption rates, and the rate-limiting substrate is maintained at a minimum concentration at the layer of consumption. Opposing gradients of methane and oxygen were mimicked in a specific cultivation set-up in which growth of methanotrophic bacteria occurred as a sharp band at either c. 5 or 20 mm below the air-exposed end. Two new strains of methanotrophic bacteria were isolated with this system. One isolate, strain LC 1, belonged to the Methylomonas genus (type I methantroph) and contained soluble methane mono-oxygenase. Another isolate, strain LC 2, was related to the Methylobacter group (type I methantroph), as determined by 16S rRNA gene and pmoA sequence similarities. However, the partial pmoA sequence was only 86% related to cultured Methylobacter species. This strain accumulated significant amounts of formaldehyde in conventional cultivation with methane and oxygen, which may explain why it is preferentially enriched in a gradient cultivation system.

Diversity, composition, and geographical distribution of microbial communities in California salt marsh sediments

The Pacific Estuarine Ecosystem Indicators Research Consortium seeks to develop bioindicators of toxicant-induced stress and bioavailability for wetland biota. Within this framework, the effects of environmental and pollutant variables on microbial communities were studied at different spatial scales over a 2-year period. Six salt marshes along the California coastline were characterized using phospholipid fatty acid (PLFA) analysis and terminal restriction fragment length polymorphism (TRFLP) analysis. Additionally, 27 metals, six currently used pesticides, total polychlorinated biphenyls and polycyclic aromatic hydrocarbons, chlordanes, nonachlors, dichlorodiphenyldichloroethane, and dichlorodiphenyldichloroethylene were analyzed. Sampling was performed over large (between salt marshes), medium (stations within a marsh), and small (different channel depths) spatial scales. Regression and ordination analysis suggested that the spatial variation in microbial communities exceeded the variation attributable to pollutants. PLFA analysis and TRFLP canonical correspondence analysis (CCA) explained 74 and 43% of the variation, respectively, and both methods attributed 34% of the variation to tidal cycles, marsh, year, and latitude. After accounting for spatial variation using partial CCA, we found that metals had a greater effect on microbial community composition than organic pollutants had. Organic carbon and nitrogen contents were positively correlated with PLFA biomass, whereas total metal concentrations were positively correlated with biomass and diversity. Higher concentrations of heavy metals were negatively correlated with branched PLFAs and positively correlated with methyl- and cyclo-substituted PLFAs. The strong relationships observed between pollutant concentrations and some of the microbial indicators indicated the potential for using microbial community analyses in assessments of the ecosystem health of salt marshes.

The active methanotrophic community in hydromorphic soils changes in response to changing methane concentration

Methanotrophic communities were studied in several periodically water-saturated gleyic soils. When sampled, each soil had an oxic upper layer and consumed methane from the atmosphere (at 1.75 ppmv). In most gleyic soils the K(m(app)) values for methane were between 70 and 800 ppmv. These are higher than most values observed in dry upland soils, but lower than those measured in wetlands. Based on cultivation-independent retrieval of the pmoA-gene and quantification of partial pmoA gene sequences, type II (Alphaproteobacteria) methanotrophs of the genus Methylocystis spp. were abundant (> 10(7) pmoA target molecules per gram of dry soil). Type I (Gammaproteobacteria) methanotrophs related to the genera Methylobacter and Methylocaldum/Methylococcus were detected in some soils. Six pmoA sequence types not closely related to sequences from cultivated methanotrophs were detected as well, indicating that diverse uncultivated methanotrophs were present. Three Gleysols were incubated under different mixing ratios of (13)C-labelled methane to examine (13)C incorporation into phospholipid fatty acids (PLFAs). Phospholipid fatty acids typical of type II methanotrophs, 16:0 and 18:1omega7c, were labelled with (13)C in all soils after incubation under an atmosphere containing 30 ppmv of methane. Incubation under 500 ppmv of methane resulted in labelling of additional PLFAs besides 16:0 and 18:1omega7c, suggesting that the composition of the active methanotrophic community changed in response to increased methane supply. In two soils, 16:1 PLFAs typical of type I methanotrophs were strongly labelled after incubation under the high methane mixing ratio only. Type II methanotrophs are most likely responsible for atmospheric methane uptake in these soils, while type I methanotrophs become active when methane is produced in the soil.

Field released transgenic papaya effect on soil microbial communities and enzyme activities

Soil properties, microbial communities and enzyme activities were studied in soil amended with replicase (RP)-transgenic or non-transgenic papaya under field conditions. Compared with non-transgenic papaya, significant differences (P<0.05) were observed in total nitrogen in soils grown with transgenic papaya. There were also significant differences (P<0.05) in the total number of colony forming units (CFUs) of bacteria, actinomycetes and fungi between soils amended with RP-transgenic plants and non-transgenic plants. Compared with non-transgenic papaya, the total CFUs of bacteria, actinomycetes and fungi in soil with transgenic papaya increased by 0.43-1.1, 0.21-0.80 and 0.46-0.73 times respectively. Significantly higher (P<0.05) CFUs of bacteria, actinomycetes and fungi resistant to kanamycin (Km) were obtained in soils with RP-transgenic papaya than those with non-transgenic papaya in all concentrations of Km. Higher resistance quotients for Kmr (kanamycin resistant) bacteria, actinomycetes and fungi were found in soil planted with RP-transgenic papaya, and the resistance quotients for Kmr bacteria, actinomycetes and fungi in soils with transgenic papaya increased 1.6-4.46, 0.63-2.5 and 0.75-2.30 times. RP-transgenic papaya and non-transgenic papaya produced significantly different enzyme activities in arylsulfatase (5.4-5.9x), polyphenol oxidase (0.7-1.4x), invertase (0.5-0.79x), cellulase (0.23-0.35x) and phosphodiesterase (0.16-0.2x). The former three soil enzymes appeared to be more sensitive to the transgenic papaya than the others, and could be useful parameters in assessing the effects of transgenic papaya. Transgenic papaya could alter soil chemical properties, enzyme activities and microbial communities.

Abundance, activity, and community structure of pelagic methane-oxidizing bacteria in temperate lakes

The abundance and activity of methane-oxidizing bacteria (MOB) in the water column were investigated in three lakes with different contents of nutrients and humic substances. The abundance of MOB was determined by analysis of group-specific phospholipid fatty acids from type I and type II MOB, and in situ activity was measured with a 14CH4 transformation method. The fatty acid analyses indicated that type I MOB most similar to species of Methylomonas, Methylomicrobium, and Methylosarcina made a substantial contribution (up to 41%) to the total bacterial biomass, whereas fatty acids from type II MOB generally had very low concentrations. The MOB biomass and oxidation activity were positively correlated and were highest in the hypo- and metalimnion during summer stratification, whereas under ice during winter, maxima occurred close to the sediments. The methanotroph biomass-specific oxidation rate (V) ranged from 0.001 to 2.77 mg CH4-C mg(-1) C day(-1) and was positively correlated with methane concentration, suggesting that methane supply largely determined the activity and biomass distribution of MOB. Our results demonstrate that type I MOB often are a large component of pelagic bacterial communities in temperate lakes. They represent a potentially important pathway for reentry of carbon and energy into pelagic food webs that would otherwise be lost as evasion of CH4.