Rice roots select for type I methanotrophs in rice field soil

Resistance mechanisms of cereal plants and rhizosphere soil microbial communities to chromium stress

Agricultural soils contaminated with heavy metals poison crops and disturb the normal functioning of rhizosphere microbial communities. Different crops and rhizosphere microbial communities exhibit different heavy metal resistance mechanisms. Here, indoor pot studies were used to assess the mechanisms of grain and soil rhizosphere microbial communities on chromium (Cr) stress. Millet grain variety 'Jingu 21' (Setaria italica) and soil samples were collected prior to control (CK), 6 hours after (Cr_6h), and 6 days following (Cr_6d) Cr stress. Transcriptomic analysis, high-throughput sequencing and quantitative polymerase chain reaction (qPCR) were used for sample determination and data analysis. Cr stress inhibited the expression of genes related to cell division, and photosynthesis in grain plants while stimulating the expression of genes related to DNA replication and repair, in addition to plant defense systems resist Cr stress. In response to chromium stress, rhizosphere soil bacterial and fungal community compositions and diversity changed significantly (p < 0.05). Both bacterial and fungal co-occurrence networks primarily comprised positively correlated edges that would serve to increase community stability. However, bacterial community networks were larger than fungal community networks and were more tightly connected and less modular than fungal networks. The abundances of C/N functional genes exhibited increasing trends with increased Cr exposure. Overall, these results suggest that Cr stress primarily prevented cereal seedlings from completing photosynthesis, cell division, and proliferation while simultaneously triggering plant defense mechanisms to resist the toxic effects of Cr. Soil bacterial and fungal populations exhibited diverse response traits, community-assembly mechanisms, and increased expression of functional genes related to carbon and nitrogen cycling, all of which are likely related to microbial survival during Cr stress. This study provides new insights into resistance mechanisms, microbial community structures, and mechanisms of C/N functional genes responses in cereal plants to heavy metal contaminated agricultural soils. Portions of this text were previously published as part of a preprint (https://www.researchsquare.com/article/rs-2891904/v1).

Harnessing biological nitrogen fixation in plant leaves

The importance of biological nitrogen fixation (BNF) in securing food production for the growing world population with minimal environmental cost has been increasingly acknowledged. Leaf surfaces are one of the biggest microbial habitats on Earth, harboring diverse free-living N2-fixers. These microbes inhabit the epiphytic and endophytic phyllosphere and contribute significantly to plant N supply and growth. Here, we summarize the contribution of phyllosphere-BNF to global N cycling, evaluate the diversity of leaf-associated N2-fixers across plant hosts and ecosystems, illustrate the ecological adaptation of N2-fixers to the phyllosphere, and identify the environmental factors driving BNF. Finally, we discuss potential BNF engineering strategies to improve the nitrogen uptake in plant leaves and thus sustainable food production.

Aerobic and denitrifying methanotrophs: Dual wheels driving soil methane emission reduction

The greenhouse gas methane in soils has been considered to be consumed mainly by aerobic methane-oxidizing bacteria for a long time. In the last decades, the discovery of anaerobic methanotrophs greatly complemented the methane cycle, but their contribution rates and ecological significance in soils remain undescribed. In this work, the soil samples from forest, grassland and cropland in four different climatic regions were collected to investigate these conventional and novel methanotrophs. A dual-core microbial methane sink, responsible for over 80 % of soil methane emission reduction, was unveiled. The aerobic core was performed by aerobic methanotrophic bacteria in topsoil, who played important roles in stabilizing bacterial communities. The anaerobic core was denitrifying methanotrophs in anoxic soils, including denitrifying methanotrophic bacteria from NC10 phylum and denitrifying methanotrophic archaea from ANME-2d clade. They were ubiquitous in terrestrial soils and potentially led to around 50 % of the total methane removal. Human activities such as livestock farming and rice cultivation further promoted the contribution rates of these denitrifying methanotrophs. This work elucidated the emission reduction contribution of different methanotrophs in the continental setting, which would help to reduce uncertainties in the estimations of the soil methane emission.

An Archaic Approach to a Modern Issue: Endophytic Archaea for Sustainable Agriculture

Archaea have existed for over 3.5 billion years, yet they were detected in the plant endosphere only in the recent past and still, not much is known about them. Archaeal endophytes may be important microorganisms for sustainable agriculture, particularly in the face of climate change and increasing food demand due to population growth. Recent advances in culture-independent methods of research have revealed a diverse abundance of archaea from the phyla Euryarchaeota, Crenarchaeaota, and Thaumarchaeota globally that are associated with significant crops such as maize, rice, coffee, and olive. Novel insights into the plant microbiome have revealed specific genes in archaea that may be involved in numerous plant metabolic functions including amino acid production and phytohormone modulation. This is the first review article to address what is known about archaea as endophytes, including their patterns of colonization and abundance in various parts of different crop plants grown under diverse environmental conditions. This review aims to facilitate mainstream discussions and encourage future research regarding the occurrence and role of endophytic archaea in plants, particularly in relation to agricultural applications.

Experimental analysis and modeling of the methane degradation in a three stage biofilter using composted sawdust as packing media

Methane gas is a very effective greenhouse gas and the second-largest contributor to global warming. Biofiltration is an effective technology that uses microorganisms to degrade the pollutant by oxidizing it. In this work, the performance of a biofilter with supporting filter media, consisting of composted sawdust, is evaluated at three different sampling ports. Furthermore, a transient model is developed to predict methane concentration at various heights and times. The developed model is validated with the experimental data and shows good agreement with the experimental data. The highest removal efficiency and elimination capacity was found to be 72% and 0.108 g m^-3 h^-1 respectively. The effect of parameters such as specific surface area, the reaction rate constant, biofilm thickness and airflow rate were studied on the outlet methane concentration. Under similar conditions, the simulations showed that the removal efficiency of 95% might be achieved for the height of 2 m.

Comparison of wild rice (Oryza longistaminata) tissues identifies rhizome-specific bacterial and archaeal endophytic microbiomes communities and network structures

Compared with root-associated habitats, little is known about the role of microbiota inside other rice organs, especially the rhizome of perennial wild rice, and this information may be of importance for agriculture. Oryza longistaminata is perennial wild rice with various agronomically valuable traits, including large biomass on poor soils, high nitrogen use efficiency, and resistance to insect pests and disease. Here, we compared the endophytic bacterial and archaeal communities and network structures of the rhizome to other compartments of O. longistaminata using 16S rRNA gene sequencing. Diverse microbiota and significant variation in community structure were identified among different compartments of O. longistaminata. The rhizome microbial community showed low taxonomic and phylogenetic diversity as well as the lowest network complexity among four compartments. Rhizomes exhibited less phylogenetic clustering than roots and leaves, but similar phylogenetic clustering with stems. Streptococcus, Bacillus, and Methylobacteriaceae were the major genera in the rhizome. ASVs belonging to the Enhydrobacter, YS2, and Roseburia are specifically present in the rhizome. The relative abundance of Methylobacteriaceae in the rhizome and stem was significantly higher than that in leaf and root. Noteworthy type II methanotrophs were observed across all compartments, including the dominant Methylobacteriaceae, which potentially benefits the host by facilitating CH4-dependent N2 fixation under nitrogen nutrient-poor conditions. Our data offers a robust knowledge of host and microbiome interactions across various compartments and lends guidelines to the investigation of adaptation mechanisms of O. longistaminata in nutrient-poor environments for biofertilizer development in agriculture.

Myriophyllum elatinoides growth and rhizosphere bacterial community structure under different nitrogen concentrations in swine wastewater

In this study, Myriophyllum elatinoides growth under different nitrogen (N) concentrations (2, 250, 300, 350 and 400 mg L^-1) and changes in rhizosphere bacterial community structure were investigated. High N (>300 mg L^-1) concentrations caused reduction in M. elatinoides biomass. Growth tended to stabilize at 49 days. N concentration in roots were higher than that in stems and leaves under high N conditions. TN and NH₄⁺ removal efficiencies reached 84.0% and 87.2%, respectively, in M. elatinoides surface flow constructed wetlands (SFCWs). Rhizosphere bacterial diversity increased over time. Proteobacteria, Firmicutes, Cyanobacteria, and Bacteroidetes dominated at the phylum level. Genera Turicibacter, Allochromatium, and Methylocystis increased at low N (<300 mg L^-1) concentrations, while Pseudomonas increased at high N concentrations over the experimental period. Redundancy analysis showed that pH was strongly correlated with changes in rhizosphere bacterial community structure. These findings helped to insight into N removal mechanism in M. elatinoides.

A novel method to remove nitrogen from reject water in wastewater treatment plants using a methane- and methanol-dependent bacterial consortium

This study proposes a novel method to directly treat reject water with a high ammonium content, without relying on dilution. The originality of this method resides in leveraging the coordinated action of a methane- and methanol-dependent bacterial consortium and the biogas generated from wastewater treatment facilities. Specifically, ammonium is removed through autotrophic assimilation in the glutamate cycle of methanotrophs and Methylophilus while, simultaneously, methanol generated by methanotrophs is treated through formaldehyde assimilation as Methylophilus undergo the same ribulose monophosphate cycle as methanotrophs. Using this method, the backflow of high-concentration ammonium into the wastewater treatment process was reduced to 59% in a single operation using a sequencing batch reactor at a mean influent concentration of 877.3 mg L^-1. However, the removal rate temporarily declined to an average of 37.6% at a concentration of 800 mg L^-1 or above, which was imputed to the influence of toxic intermediates.

Enrichment of Type I Methanotrophs with nirS Genes of Three Emergent Macrophytes in a Eutrophic Wetland in China

The pmoA gene, encoding particulate methane monooxygenase in methanotrophs, and nirS and nirK genes, encoding bacterial nitrite reductases, were examined in the root and rhizosphere sediment of three common emergent macrophytes (Phragmites australis, Typha angustifolia, and Scirpus triqueter) and unvegetated sediment from eutrophic Wuliangsuhai Lake in China. Sequencing analyses indicated that 334 out of 351 cloned pmoA sequences were phylogenetically the most closely related to type I methanotrophs (Gammaproteobacteria), and Methylomonas denitrificans-like organisms accounted for 44.4% of the total community. In addition, 244 out of 250 cloned nirS gene sequences belonged to type I methanotrophs, and 31.2% of nirS genes were the most closely related to paddy rice soil clone SP-2-12 in Methylomonas of the total community. Three genera of type I methanotrophs, Methylomonas, Methylobacter, and Methylovulum, were common in both pmoA and nirS clone libraries in each sample. A quantitative PCR (qPCR) analysis demonstrated that the copy numbers of the nirS and nirK genes were significantly higher in rhizosphere sediments than in unvegetated sediments in P. australis and T. angustifolia plants. In the same sample, the nirS gene copy number was significantly higher than that of nirK. Furthermore, type I methanotrophs were localized in the root tissues according to catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Thus, nirS-carrying type I methanotrophs were enriched in macrophyte root and rhizosphere sediment and are expected to play important roles in carbon/nitrogen cycles in a eutrophic wetland.

New molecular method to detect denitrifying anaerobic methane oxidation bacteria from different environmental niches

The denitrifying anaerobic methane oxidation is an ecologically important process for reducing the potential methane emission into the atmosphere. The responsible bacterium for this process was Candidatus Methylomirabilis oxyfera belonging to the bacterial phylum of NC10. In this study, a new pair of primers targeting all the five groups of NC10 bacteria was designed to amplify NC10 bacteria from different environmental niches. The results showed that the group A was the dominant NC10 phylum bacteria from the sludges and food waste digestate while in paddy soil samples, group A and group B had nearly the same proportion. Our results also indicated that NC10 bacteria could exist in a high pH environment (pH9.24) from the food waste treatment facility. The Pearson relationship analysis showed that the pH had a significant positive relationship with the NC10 bacterial diversity (p<0.05). The redundancy analysis further revealed that the pH, volatile solid and nitrite nitrogen were the most important factors in shaping the NC10 bacterial structure (p=0.01) based on the variation inflation factors selection and Monte Carlo test (999 times). Results of this study extended the existing molecular tools for studying the NC10 bacterial community structures and provided new information on the ecological distributions of NC10 bacteria.

Responses of Methanogenic and Methanotrophic Communities to Elevated Atmospheric CO2 and Temperature in a Paddy Field

Although climate change is predicted to affect methane (CH₄) emissions in paddy soil, the dynamics of methanogens and methanotrophs in paddy fields under climate change have not yet been fully investigated. To address this issue, a multifactor climate change experiment was conducted in a Chinese paddy field using the following experimental treatments: (1) enrichment of atmospheric CO₂ concentrations (500 ppm, CE), (2) canopy air warming (2°C above the ambient, WA), (3) combined CO₂ enrichment and warming (CW), and (4) ambient conditions (CK). We analyzed the abundance of methanogens and methanotrophs, community structures, CH₄ production and oxidation potentials, in situ CH₄ emissions using real-time PCR, T-RFLP, and clone library techniques, as well as biochemical assays. Compared to the control under CE and CW treatments, CH₄ production potential, methanogenic gene abundance and soil microbial biomass carbon significantly increased; the methanogenic community, however, remained stable. The canopy air warming treatment only had an effect on CH₄ oxidation potential at the ripening stage. Phylogenic analysis indicated that methanogens in the rhizosphere were dominated by Methanosarcina, Methanocellales, Methanobacteriales, and Methanomicrobiales, while methanotrophic sequences were classified as Methylococcus, Methylocaldum, Methylomonas, Methylosarcina (Type I) and Methylocystis (Type II). However, the relative abundance of Methylococcus (Type I) decreased under CE and CW treatments and the relative abundance of Methylocystis (Type II) increased. The in situ CH₄ fluxes indicated similar seasonal patterns between treatments; both CE and CW increased CH₄ emissions. In conclusion results suggest that methanogens and methanotrophs respond differently to elevated atmospheric CO₂ concentrations and warming, thus adding insights into the effects of simulated global climate change on CH₄ emissions in paddy fields.

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.

Interactions of Methylotrophs with Plants and Other Heterotrophic Bacteria

Methylotrophs, which can utilize methane and/or methanol as sole carbon and energy sources, are key players in the carbon cycle between methane and CO₂, the two most important greenhouse gases. This review describes the relationships between methylotrophs and plants, and between methanotrophs (methane-utilizers, a subset of methylotrophs) and heterotrophic bacteria. Some plants emit methane and methanol from their leaves, and provide methylotrophs with habitats. Methanol-utilizing methylotrophs in the genus Methylobacterium are abundant in the phyllosphere and have the ability to promote the growth of some plants. Methanotrophs also inhabit the phyllosphere, and methanotrophs with high methane oxidation activities have been found on aquatic plants. Both plant and environmental factors are involved in shaping the methylotroph community on plants. Methanotrophic activity can be enhanced by heterotrophic bacteria that provide growth factors (e.g., cobalamin). Information regarding the biological interaction of methylotrophs with other organisms will facilitate a better understanding of the carbon cycle that is driven by methylotrophs.

Molecular diversity of the methanotrophic bacteria communities associated with disused tin-mining ponds in Kampar, Perak, Malaysia

In a previous study, notable differences of several physicochemical properties, as well as the community structure of ammonia oxidizing bacteria as judged by 16S rRNA gene analysis, were observed among several disused tin-mining ponds located in the town of Kampar, Malaysia. These variations were associated with the presence of aquatic vegetation as well as past secondary activities that occurred at the ponds. Here, methane oxidizing bacteria (MOB), which are direct participants in the nutrient cycles of aquatic environments and biological indicators of environmental variations, have been characterised via analysis of pmoA functional genes in the same environments. The MOB communities associated with disused tin-mining ponds that were exposed to varying secondary activities were examined in comparison to those in ponds that were left to nature. Comparing the sequence and phylogenetic analysis of the pmoA clone libraries at the different ponds (idle, lotus-cultivated and post-aquaculture), we found pmoA genes indicating the presence of type I and type II MOB at all study sites, but type Ib sequences affiliated with the Methylococcus/Methylocaldum lineage were most ubiquitous (46.7 % of clones). Based on rarefaction analysis and diversity indices, the disused mining pond with lotus culture was observed to harbor the highest richness of MOB. However, varying secondary activity or sample type did not show a strong variation in community patterns as compared to the ammonia oxidizers in our previous study.

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.

Methanogenic pathway and fraction of CH(4) oxidized in paddy fields: seasonal variation and effect of water management in winter fallow season

A 2-year field and incubation experiment was conducted to investigate δ¹³C during the processes of CH₄ emission from the fields subjected to two water managements (flooding and drainage) in the winter fallow season, and further to estimate relative contribution of acetate to total methanogenesis (F_ac) and fraction of CH₄ oxidized (F_ox) based on the isotopic data. Compared with flooding, drainage generally caused CH₄, either anaerobically or aerobically produced, depleted in ¹³C. There was no obvious difference between the two in transport fractionation factor (ε_transport) and δ¹³C-value of emitted CH₄. CH₄ emission was negatively related to its δ¹³C-value in seasonal variation (P<0.01). Acetate-dependent methanogenesis in soil was dominant (60–70%) in the late season, while drainage decreased F_ac-value by 5–10%. On roots however, CH₄ was mostly produced through H₂/CO₂ reduction (60–100%) over the season. CH₄ oxidation mainly occurred in the first half of the season and roughly 10–90% of the CH₄ was oxidized in the rhizosphere. Drainage increased F_ox-value by 5–15%, which is possibly attributed to a significant decrease in production while no simultaneous decrease in oxidation. Around 30–70% of the CH₄ was oxidized at the soil-water interface when CH₄ in pore water was released into floodwater, although the amount of CH₄ oxidized therein might be negligible relative to that in the rhizosphere. CH₄ oxidation was also more important in the first half of the season in lab conditions and about 5–50% of the CH₄ was oxidized in soil while almost 100% on roots. Drainage decreased F_ox-value on roots by 15% as their CH₄ oxidation potential was highly reduced. The findings suggest that water management in the winter fallow season substantially affects F_ac in the soil and F_ox in the rhizosphere and roots rather than F_ac on roots and F_ox at the soil-water interface.

Dry/Wet cycles change the activity and population dynamics of methanotrophs in rice field soil

The methanotrophs in rice field soil are crucial in regulating the emission of methane. Drainage substantially reduces methane emission from rice fields. However, it is poorly understood how drainage affects microbial methane oxidation. Therefore, we analyzed the dynamics of methane oxidation rates, composition (using terminal restriction fragment length polymorphism [T-RFLP]), and abundance (using quantitative PCR [qPCR]) of methanotroph pmoA genes (encoding a subunit of particulate methane monooxygenase) and their transcripts over the season and in response to alternate dry/wet cycles in planted paddy field microcosms. In situ methane oxidation accounted for less than 15% of total methane production but was enhanced by intermittent drainage. The dry/wet alternations resulted in distinct effects on the methanotrophic communities in different soil compartments (bulk soil, rhizosphere soil, surface soil). The methanotrophic communities of the different soil compartments also showed distinct seasonal dynamics. In bulk soil, potential methanotrophic activity and transcription of pmoA were relatively low but were significantly stimulated by drainage. In contrast, however, in the rhizosphere and surface soils, potential methanotrophic activity and pmoA transcription were relatively high but decreased after drainage events and resumed after reflooding. While type II methanotrophs dominated the communities in the bulk soil and rhizosphere soil compartments (and to a lesser extent also in the surface soil), it was the pmoA of type I methanotrophs that was mainly transcribed under flooded conditions. Drainage affected the composition of the methanotrophic community only minimally but strongly affected metabolically active methanotrophs. Our study revealed dramatic dynamics in the abundance, composition, and activity of the various type I and type II methanotrophs on both a seasonal and a spatial scale and showed strong effects of dry/wet alternation cycles, which enhanced the attenuation of methane flux into the atmosphere.

Niche differentiation of ammonia oxidizers and nitrite oxidizers in rice paddy soil

The dynamics of populations and activities of ammonia-oxidizing and nitrite-oxidizing microorganisms were investigated in rice microcosms treated with two levels of nitrogen. Different soil compartments (surface, bulk, rhizospheric soil) and roots (young and old roots) were collected at three time points (the panicle initiation, heading and maturity periods) of the season. The population dynamics of bacterial (AOB) and archaeal (AOA) ammonia oxidizers was assayed by determining the abundance (using qPCR) and composition (using T-RFLP and cloning/sequencing) of their amoA genes (coding for a subunit of ammonia monooxygenase), that of nitrite oxidizers (NOB) by quantifying the nxrA gene (coding for a subunit of nitrite oxidase of Nitrobacter spp.) and the 16S rRNA gene of Nitrospira spp. The activity of the nitrifiers was determined by measuring the rates of potential ammonia oxidation and nitrite oxidation and by quantifying the copy numbers of amoA and nxrA transcripts. Potential nitrite oxidation activity was much higher than potential ammonia oxidation activity and was not directly affected by nitrogen amendment demonstrating the importance of ammonia oxidizers as pace makers for nitrite oxidizer populations. Marked differences in the distribution of bacterial and archaeal ammonia oxidizers, and of Nitrobacter-like and Nitrospira-like nitrite oxidizers were found in the different compartments of planted paddy soil indicating niche differentiation. In bulk soil, ammonia-oxidizing bacteria (Nitrosospira and Nitrosomonas) were at low abundance and displayed no activity, but in surface soil their activity and abundance was high. Nitrite oxidation in surface soil was dominated by Nitrospira spp. By contrast, ammonia-oxidizing Thaumarchaeota and Nitrobacter spp. seemed to dominate nitrification in rhizospheric soil and on rice roots. In contrast to soil compartment, the level of N fertilization and the time point of sampling had only little effect on the abundance, composition and activity of the nitrifying communities. The results of our study show that in rice fields population dynamics and activity of nitrifiers is mainly differentiated by the soil compartments rather than by nitrogen amendment or season.

Biofiltration of air polluted with methane at concentration levels similar to swine slurry emissions: influence of ammonium concentration

An evaluation of the effect of ammonium on the performance of two up-flow inorganic packed bed biofilters treating methane was conducted. The air flow rate was set to 3.0 L min(-1) for an empty bed residence time of 6.0 min. The biofilter was fed with a methane concentration of 0.30% (v/v). The ammonium concentration in the nutrient solution was increased by small increments (from 0.01 to 0.025 gN-NH(4) (+) L(-1)) for one biofilter and by large increments of 0.05 gN-NH(4) (+) L(-1) in the other biofilter. The total concentration of nitrogen was kept constant at 0.5 gN-NH(4) (+) L(-1) throughout the experiment by balancing ammonium with nitrate. For both biofilters, the methane elimination capacity, carbon dioxide production, nitrogen bed retention and biomass content decreased with the ammonium concentration in the nutrient solution. The biofilter with smaller ammonium increments featured a higher elimination capacity and carbon dioxide production rate, which varied from 4.9 to 14.3 g m(-3) h(-1) and from 11.5 to 30 g m(-3) h(-1), respectively. Denitrification was observed as some values of the nitrate production rate were negative for ammonium concentrations below 0.2 gN-NH(4) (+) L(-1). A Michalelis-Menten-type model fitted the ammonium elimination rate and the nitrate production rate.

Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice

The above- and below-ground parts of rice plants create specific habitats for various microorganisms. In this study, we characterized the phyllosphere and rhizosphere microbiota of rice cultivars using a metaproteogenomic approach to get insight into the physiology of the bacteria and archaea that live in association with rice. The metaproteomic datasets gave rise to a total of about 4600 identified proteins and indicated the presence of one-carbon conversion processes in the rhizosphere as well as in the phyllosphere. Proteins involved in methanogenesis and methanotrophy were found in the rhizosphere, whereas methanol-based methylotrophy linked to the genus Methylobacterium dominated within the protein repertoire of the phyllosphere microbiota. Further, physiological traits of differential importance in phyllosphere versus rhizosphere bacteria included transport processes and stress responses, which were more conspicuous in the phyllosphere samples. In contrast, dinitrogenase reductase was exclusively identified in the rhizosphere, despite the presence of nifH genes also in diverse phyllosphere bacteria.

Methanotrophic bacteria associated to rice roots: the cultivar effect assessed by T-RFLP and microarray analysis

Rice plants play a key role in regulating methane emissions from paddy fields by affecting both underlying processes: methane production and oxidation. Specific differences were reported for methane oxidation rates; however, studies on the bacterial communities involved are rare. Here, we analysed the methanotrophic community on the roots of 18 different rice cultivars by pmoA-based terminal restriction fragment length polymorphism (T-RFLP) and microarray analysis. Both techniques showed comparable and consistent results revealing a high diversity dominated by type II and type Ib methanotrophs. pmoA microarrays have been successfully used to study methane-oxidizing bacteria in various environments. However, the microarray's full potential resolving community structure has not been exploited yet. Here, we provide an example on how to include this information into multivariate statistics. The analysis revealed a rice cultivar effect on the methanotroph community composition that could be affiliated to the plant genotype. This effect became only significant by including the specific phylogenetic resolution provided by the microarray into the statistical analysis.

Bacterial and archaeal communities involved in the in situ degradation of (13) C-labelled straw in the rice rhizosphere

Rice straw is a major substrate for the production of methane in flooded rice fields and results in increase of CH4 emission into the atmosphere. We investigated the bacteria and archaea involved in straw degradation by adding (13) C-labelled straw to the rhizosphere of planted rice microcosms in the greenhouse. The degradation of added straw resulted in the production of (13) C-labelled CH4 as end-product, which was detected in the pore water. The incorporation of (13) C into ribosomal RNA of Bacteria and Archaea present in the rhizospheric soil and on the roots was assessed by stable isotope probing (SIP) followed by terminal restriction fragment polymorphism (T-RFLP) fingerprinting and cloning/sequencing of RNA fractions with different buoyant densities. Members of the Clostridium cluster I, III and XIVa were actively involved in straw degradation both in rhizospheric soil and on roots. However, on roots, Proteobacteria, Bacilli, Actinobacteria, Bacteroidetes and Chlorobi were also involved in the straw degradation process. Mostly Methanosarcina and to a less degree also Methanobacteriaceae were the dominant Archaea that assimilated straw-derived carbon in the rhizospheric soil. Both Bacteria and Archaea together were most likely responsible for the conversion of rice straw to CH4 . In conclusion, this study tackled the important and interesting issue of linking active microorganisms responsible for the straw degradation process to CH4 emission into the atmosphere.

Methanotrophic community structure of aged refuse and its capability for methane bio-oxidation

Aged refuse from waste landfills closed for eight years was examined and found to contain rich methanotrophs capable of biooxidation for methane. Specially, community structure and methane oxidation capability of methanotrophs in the aged refuse were studied. The amount of methanotrophs ranged 61.97 x 10(3)-632.91 x 10(3) cells/g (in dry basis) in aged refuse from Shanghai Laogang Landfill. Type I and II methanotrophs were found in the aged refuse in the presence of sterilized sewage sludge and only Type I methanotrophs were detected in the presence of nitrate minimal salt medium (NMS). The clone sequences of the pmoA gene obtained from the aged refuse were similar to the pmoA gene of Methylobacter Methylocaldum, and Methylocystis, and two clones were distinct with known genera of Type I methanotrophs according to phylogenetic analysis. Aged refuse enriched with NMS was used for methane biological oxidation and over 93% conversions were obtained.

Effects of ammonium and nitrite on growth and competitive fitness of cultivated methanotrophic bacteria

The effects of nitrite and ammonium on cultivated methanotrophic bacteria were investigated. Methylomicrobium album ATCC 33003 outcompeted Methylocystis sp. strain ATCC 49242 in cultures with high nitrite levels, whereas cultures with high ammonium levels allowed Methylocystis sp. to compete more easily. M. album pure cultures and cocultures consumed nitrite and produced nitrous oxide, suggesting a connection between denitrification and nitrite tolerance.

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.