Crop rotation of flooded rice with upland maize impacts the resident and active methanogenic microbial community

Soil microbiome analysis reveals effects of periodic waterlogging stress on sugarcane growth

Sugarcane is one of the major agricultural crops with high economic importance in Thailand. Periodic waterlogging has a long-term negative effect on sugarcane development, soil properties, and microbial diversity, impacting overall sugarcane production. Yet, the microbial structure in periodically waterlogged sugarcane fields across soil compartments and growth stages in Thailand has not been documented. This study investigated soil and rhizosphere microbial communities in a periodic waterlogged field in comparison with a normal field in a sugarcane plantation in Ratchaburi, Thailand, using 16S rRNA and ITS amplicon sequencing. Alpha diversity analysis revealed comparable values in periodic waterlogged and normal fields across all growth stages, while beta diversity analysis highlighted distinct microbial community profiles in both fields throughout the growth stages. In the periodic waterlogged field, the relative abundance of Chloroflexi, Actinobacteria, and Basidiomycota increased, while Acidobacteria and Ascomycota decreased. Beneficial microbes such as Arthrobacter, Azoarcus, Bacillus, Paenibacillus, Pseudomonas, and Streptomyces thrived in the normal field, potentially serving as biomarkers for favorable soil conditions. Conversely, phytopathogens and growth-inhibiting bacteria were prevalent in the periodic waterlogged field, indicating unfavorable conditions. The co-occurrence network in rhizosphere of the normal field had the highest complexity, implying increased sharing of resources among microorganisms and enhanced soil biological fertility. Altogether, this study demonstrated that the periodic waterlogged field had a long-term negative effect on the soil microbial community which is a key determining factor of sugarcane growth.

Winter drainage and film mulching cultivation mitigated CH4 emission by regulating the function and structure of methanogenic archaeal and fermenting bacterial communities in paddy soil

Winter flooding of harvested rice fields is a typical cropping system in mountainous areas, which emits considerable amounts of CH₄. Plastic film mulching cultivation is recognized as an important rice cultivation practice in paddy field for water-saving irrigation. However, the effects of these managements on CH₄ emissions in paddy soil and the underlying microbial mechanism are unclear. A field experiment was carried out with the application of winter drainage followed by traditional rice cultivation (WD), winter drainage followed by plastic film mulching cultivation (MC), as well as winter flooding followed by traditional rice cultivation (WF) as control in hilly paddy fields. We investigated the CH₄ emissions, functional (CH₄ production rate, ¹³C isotope) and structural (abundance, structure) responses of soil methanogenic archaeal and fermenting bacterial communities during rice season. Shifting the fields from WF into WD and MC substantially mitigated CH₄ emissions by 62.3% and 59.2%, respectively, paralleled with the enhancement of soil Eh and the reductions of soil DOC content. Compared with WF, WD and MC both significantly decreased CH₄ production rates and the copy numbers of mcrA gene. Moreover, an increasing contribution of hydrogenotrophic methanogenesis (from 30.7% to 50.0%) to total CH₄ production was observed during the conversion from WF to MC under an anaerobic incubation, paralleled with the decreased acetate content and increased δ¹³C values of acetate-methyl and total acetate. The communities of methanogenic archaea and fermenting bacteria strongly responded to the shift from WF to WD, while MC only showed significant effects on the methanogenic archaeal communities. Compared with WF, WD and MC significantly increased the relative abundance of Methanothrix, Methanosarcina and Methanocella, while those of Methanoregula, Massilia and Geobacter were decreased. The co-occurrence networks showed that WD and MC induced the loss of mixed methanogenic fermentation modules, indicating the decrease in functional biodiversity and redundancy of fermenting bacterial and methanogenic archaeal communities.The findings suggest that WD and MC approach mitigate CH₄ emission by regulating the function and structure of methanogenic archaeal and fermenting bacterial communities in paddy soil, which represent the effective management strategies considering the water availability and CH₄ mitigation in paddy-field agriculture.

Soil microbial diversity and functional capacity associated with the production of edible mushroom Stropharia rugosoannulata in croplands

In recent years, a rare edible mushroom Stropharia rugosoannulata has become popular. S. rugosoannulata has the characteristics of easy cultivation, low cost, high output value, and low labor requirement, making its economic benefits significantly superior to those of other planting industries. Accumulating research demonstrates that cultivating edible fungus is advantageous for farming soil. The present experiment used idle croplands in winter for S. rugosoannulata cultivation. We explored the effects of S. rugosoannulata cultivation on soil properties and soil microbial community structure in paddy and dry fields, respectively. We cultivated S. rugosoannulata in the fields after planting chili and rice, respectively. The results showed that Chili-S. rugosoannulata and Rice-S. rugosoannulata planting patterns increased the yield, quality and amino acid content of S. rugosoannulata. By analyzing the soil properties, we found that the Chili-S. rugosoannulata and Rice-S. rugosoannulata cropping patterns increased the total nitrogen, available phosphorus, soil organic carbon, and available potassium content of the soil. We used 16s amplicons for bacteria and internal transcribed spacer (ITS) region for fungi to analyze the microbial communities in rhizosphere soils. Notably, S. rugosoannulata cultivation significantly increased the abundance of beneficial microorganisms such as Chloroflexi, Cladosporium and Mortierella and reduce the abundance of Botryotrichumin and Archaeorhizomyces. We consider S. rugosoannulata cultivation in cropland can improve soil properties, regulate the community structure of soil microorganisms, increase the expression abundance of beneficial organisms and ultimately improve the S. rugosoannulata yield and lay a good foundation for a new round of crops after this edible mushroom cultivation.

Effect of water management on microbial diversity and composition in an Italian rice field system

Traditional rice cultivation consumes up to 2500 L of water per kg yield and new strategies such as the ‘Alternate Wetting and Drying’ (AWD) might be promising water-saving alternatives. However, they might have large impacts on the soil microbiology. In this study, we compared the bacterial and archaeal communities in experimental field plots, cultivated under continuously flooding (CF) and AWD management, by high-throughput sequencing of the 16S rRNA gene. We analysed alpha and beta diversity in bulk soil and on plant roots, in plots cultivated with two different rice cultivars. The strongest difference was found between soil and root communities. Beside others, the anaerobic methanotroph Methanoperedens was abundant in soil, however, we detected a considerable number of ANME-2a-2b on plant roots. Furthermore, root communities were significantly affected by the water management: Differential abundance analysis revealed the enrichment of aerobic and potentially plant-growth-promoting bacteria under AWD treatment, such as Sphingomonadaceae and Rhizobiaceae (both Alphaproteobacteria), and Bacteroidetes families. Microorganisms with an overall anaerobic lifestyle, such as various Delta- and Epsilonproteobacteria, and Firmicutes were depleted. Our study indicates that the bulk soil communities seem overall well adapted and more resistant to changes in the water treatment, whereas the root microbiota seems more vulnerable.

Community structure and activity potentials of archaeal communities in hadal sediments of the Mariana and Mussau trenches

Hadal trenches are the least explored marine habitat on earth. Archaea has been shown to be the dominant group in trench sediments. However, the activity potentials and detailed diversity of these communities as well as their inter-trench variations are still not known. In this study, we combined datasets from two pairs of primers to investigate at high resolution the structure and activity potentials of the archaeal communities in vertically sectioned sediment cores taken from the deepest points of the Mariana (10,853 m) and Mussau (7011 m) trenches. The compositions of the potentially active communities revealed, via 16S ribosomal RNA gene (rDNA) and RNA (rRNA), significant differences between samples. Marine Group I (MGI), with nine identified subgroups, was the most dominant class in the active archaeal communities of the two trenches. Significantly different species composition and vertical variations were observed between the two trenches. Vertical transitions from aerobic MGI α to anaerobic MGI η and υ subgroups were observed in MST but not in MT sediments, which might be related to the faster microbial oxygen consumption in MST. These results provide a better understanding on archaeal activity and diversity in trench sediments.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-021-00105-y.

Contrasting Patterns of the Resident and Active Rhizosphere Bacterial Communities of Phragmites Australis

Rhizosphere microbes play a key role in maintaining plant health and regulating biogeochemical cycles. The active bacterial community (ABC) in rhizosphere, as a small fraction of the rhizosphere resident bacterial community (RBC), has the potential to actively participate in nutrient cycling processes at the root-sediment interface. Here, we investigated the ABC and RBC within the rhizosphere of Phragmites australis (P. australis) subjected to different environmental conditions (i.e., seasons and flooding conditions) in Lake Taihu, China. Our results indicated that RBC exhibited significantly higher alpha diversity as well as lower beta diversity than ABC. The active ratios of 16S rRNA to 16S rDNA (also RNA/DNA) of the bacterial communities in summer and winter suggested a lower proportion of potential active taxa in the rhizosphere bacterial community during summer. Network analysis showed that negative correlations in each network were observed to dominate the species correlations between the rhizosphere and bulk sediment bacterial communities. Our results revealed that niche differentiation and seasonal variation played crucial roles in driving the assembly of ABC and RBC associated with the rhizospheres of P. australis. These findings broaden our knowledge about how rhizosphere bacterial communities respond to environmental variations through changing their diversity and composition.

The Responses to Long-Term Water Addition of Soil Bacterial, Archaeal, and Fungal Communities in A Desert Ecosystem

The response of microbial communities to continual and prolonged water exposure provides useful insight when facing global climate changes that cause increased and uneven precipitation and extreme rainfall events. In this study, we investigated an in situ manipulative experiment with four levels of water exposure (ambient precipitation +0%, +25%, +50%, and +100% of local annual mean precipitation) in a desert ecosystem of China. After 9 years of water addition, Illumina sequencing was used to analyze taxonomic compositions of the soil bacterial, archaeal, and fungal communities. The results showed significant increases in microbial biomass carbon (MBC) at higher amended precipitation levels, with the highest values reported at 100% precipitation. Furthermore, an increase in the bacterial species richness was observed along the water addition gradient. In addition, the relative abundance of several bacterial phyla, such as Proteobacteria, significantly increased, whereas that of some drought-tolerant taxa, including Actinobacteria, Firmicutes, and Bacteroidetes, decreased. In addition, the phyla Planctomycetes and Nitrospirae, associated with nitrification, positively responded to increased precipitation. Archaeal diversity significantly reduced under 100% treatment, with changes in the relative abundance of Thaumarchaeota and Euryarchaeota being the main contributors to shifts in the archaeal community. The fungal community composition was stable in response to water addition. Results from the Mantel test and structural equation models suggested that bacterial and archaeal communities reacted contrastingly to water addition. Bacterial community composition was directly affected by changing soil moisture and temperature, while archaeal community composition was indirectly affected by changing nitrogen availability. These findings highlight the importance of soil moisture and nitrogen in driving microbial responses to long-term precipitation changes in the desert ecosystem.

Comparison of early season crop types for wheat production and nitrogen use efficiency in the Jianghan Plain in China

The rice-wheat (RW) cropping system is one of the most prevalent double-cropping systems used to farm the Jianghan Plain in China. However, it can lead to low wheat yields and reduced nitrogen use efficiency compared with dryland wheat (DW). We evaluated wheat yield and nitrogen use efficiency for two rotations (summer rice-winter wheat and summer soybean-winter wheat) from 2017 to 2019 and applied the results to improve nitrogen management for planting wheat after rice in the Jianghan Plain. Field experiments were conducted over two years with two nitrogen treatments: traditional nitrogen management (M1: 90 kg N ha⁻¹ was applied at sowing and jointing, respectively ) and optimized nitrogen management (M2: 60 kg N ha⁻¹ was applied at sowing, wintering and jointing, respectively). The highest total wheat production was achieved under M2 for both cropping systems and the two-year average yield was 6,128 kg ha⁻¹ in DW and 6,166 kg ha⁻¹ in RW. The spike number in DW was 15% higher than RW in M1 and 13% higher in M2, but the kernel per spike and 1,000-grain weight was lower than RW. The nitrogen accumulation of DW was 24% higher than RW in M1 and 33% in M2. Compared with RW, DW had higher NO₃⁻ content in the soil surface layer (0–20 cm) and a higher root length density (RLD) in the deeper layer (40–60 cm), which may account for the higher N uptake in DW. Our results show that the grain yield of RW was comparable to that of DW by optimum nitrogen management. The rice-wheat cropping system combined with optimum nitrogen management may be of economic and agronomic benefit to the wheatbelt in the Jianghan Plain in China.

Methane Production in Soil Environments-Anaerobic Biogeochemistry and Microbial Life between Flooding and Desiccation

Flooding and desiccation of soil environments mainly affect the availability of water and oxygen. While water is necessary for all life, oxygen is required for aerobic microorganisms. In the absence of O₂, anaerobic processes such as CH₄ production prevail. There is a substantial theoretical knowledge of the biogeochemistry and microbiology of processes in the absence of O₂. Noteworthy are processes involved in the sequential degradation of organic matter coupled with the sequential reduction of electron acceptors, and, finally, the formation of CH₄. These processes follow basic thermodynamic and kinetic principles, but also require the presence of microorganisms as catalysts. Meanwhile, there is a lot of empirical data that combines the observation of process function with the structure of microbial communities. While most of these observations confirmed existing theoretical knowledge, some resulted in new information. One important example was the observation that methanogens, which have been believed to be strictly anaerobic, can tolerate O₂ to quite some extent and thus survive desiccation of flooded soil environments amazingly well. Another example is the strong indication of the importance of redox-active soil organic carbon compounds, which may affect the rates and pathways of CH₄ production. It is noteworthy that drainage and aeration turns flooded soils, not generally, into sinks for atmospheric CH₄, probably due to the peculiarities of the resident methanotrophic bacteria.

Earthworms offset straw-induced increase of greenhouse gas emission in upland rice production

Increasing water scarcity and rapid socio-economic development are driving farmers in Asia to transform traditionally flooded rice cropping systems into non-flooded crop production. The management of earthworms in non-flooded rice fields appears to be a promising strategy to support residue recycling and mitigate greenhouse gas (GHG) emissions triggered by residue amendment. We conducted a field experiment on non-flooded rainfed rice fields, with and without residue amendment. In-situ mesocosms were inoculated with endogeic earthworms (Metaphire sp.), with either low (ET1: 150 individuals m^-2), or high density (ET2: 450 individuals m^-2), and a control (ET0: no earthworms). We measured GHG emissions (methane (CH₄); nitrous oxide (N₂O); carbon dioxide (CO₂)) twice a week during the cropping season with static chambers. Effects of earthworms on yield and root growth were additionally assessed. Earthworms offset the enormous increase of CH₄ emissions induced by straw amendment (from 4.6 ± 5 to 75.3 ± 46 kg CH₄-C ha^-1 in ET0). Earthworm activity significantly reduced CH₄ release, particularly at ET2, by more than one-third (to 22 ± 15 kg CH₄-C ha^-1). In contrast, earthworm inoculation did not affect N₂O emission. Straw amendment more than doubled the global warming potential (GWP). Earthworms reduced GWP by 39% at low (ET1) and 55% at high densities (ET2). Earthworm activity reduced root mass density under conditions of straw amendment but did not affect yield. Earthworms can significantly reduce detrimental effects of rice crop residue amendment on GHG release under upland rice production. Organic carbon (C) might be preserved in earthworm casts and thereby limit C availability for CH₄ production. At the same time, earthworm activity might increase methanotrophic CH₄ consumption, due to improved soil aeration or less root exudates. Consequently, earthworms have a strong potential for regulating ecosystem functions related to rice straw decomposition, nutrient allocation and thus GHG reduction.

Bacterial, archaeal and micro-eukaryotic communities characterize a disease-suppressive or conducive soil and a cultivar resistant or susceptible to common scab

Control of common scab disease can be reached by resistant cultivars or suppressive soils. Both mechanisms are likely to translate into particular potato microbiome profiles, but the relative importance of each is not known. Here, microbiomes of bulk and tuberosphere soil and of potato periderm were studied in one resistant and one susceptible cultivar grown in a conducive and a suppressive field. Disease severity was suppressed similarly by both means yet, the copy numbers of txtB gene (coding for a pathogenicity determinant) were similar in both soils but higher in periderms of the susceptible cultivar from conducive soil. Illumina sequencing of 16S rRNA genes for bacteria (completed by 16S rRNA microarray approach) and archaea, and of 18S rRNA genes for micro-eukarytes showed that in bacteria, the more important was the effect of cultivar and diversity decreased from resistant cultivar to bulk soil to susceptible cultivar. The major changes occurred in proportions of Actinobacteria, Chloroflexi, and Proteobacteria. In archaea and micro-eukaryotes, differences were primarily due to the suppressive and conducive soil. The effect of soil suppressiveness × cultivar resistance depended on the microbial community considered, but differed also with respect to soil and plant nutrient contents particularly in N, S and Fe.

Mediterranean Native Leguminous Plants: A Reservoir of Endophytic Bacteria with Potential to Enhance Chickpea Growth under Stress Conditions

Bacterial endophytes, a subset of a plant’s microbiota, can facilitate plant growth by a number of different mechanisms. The aims of this study were to assess the diversity and functionality of endophytic bacterial strains from internal root tissues of native legume species grown in two distinct sites in South of Portugal and to evaluate their ability to promote plant growth. Here, 122 endophytic bacterial isolates were obtained from 12 different native legume species. Most of these bacteria possess at least one of the plant growth-promoting features tested in vitro, with indole acetic acid production being the most common feature among the isolates followed by the production of siderophores and inorganic phosphate solubilization. The results of in planta experiments revealed that co-inoculation of chickpea plants with specific endophytic bacteria along with N₂-fixing symbionts significantly improved the total biomass of chickpea plants, in particular when these plants were grown under saline conditions. Altogether, this study revealed that Mediterranean native legume species are a reservoir of plant growth-promoting bacteria, that are also tolerant to salinity and to toxic levels of Mn. Thus, these bacterial endophytes are well adapted to common constraints present in soils of this region which constitutes important factors to consider in the development of bacterial inoculants for stressful conditions in the Mediterranean region.

Three-Source Partitioning of Methane Emissions from Paddy Soil: Linkage to Methanogenic Community Structure

Identification of the carbon (C) sources of methane (CH₄) and methanogenic community structures after organic fertilization may provide a better understanding of the mechanism that regulate CH₄ emissions from paddy soils. Based on our previous field study, a pot experiment with isotopic ¹³C labelling was designed in this study. The objective was to investigate the main C sources for CH₄ emissions and the key environmental factor with the application of organic fertilizer in paddies. Results indicated that 28.6%, 64.5%, 0.4%, and 6.5% of ¹³C was respectively distributed in CO₂, the plants, soil, and CH₄ at the rice tillering stage. In total, organically fertilized paddy soil emitted 3.51 kg·CH₄ ha⁻¹ vs. 2.00 kg·CH₄ ha⁻¹ for the no fertilizer treatment. Maximum CH₄ fluxes from organically fertilized (0.46 mg·m⁻²·h⁻¹) and non-fertilized (0.16 mg·m⁻²·h⁻¹) soils occurred on day 30 (tillering stage). The total percentage of CH₄ emissions derived from rice photosynthesis C was 49%, organic fertilizer C < 0.34%, and native soil C > 51%. Therefore, the increased CH₄ emissions from paddy soil after organic fertilization were mainly derived from native soil and photosynthesis. The 16S rRNA sequencing showed Methanosarcina (64%) was the dominant methanogen in paddy soil. Organic fertilization increased the relative abundance of Methanosarcina, especially in rhizosphere. Additionally, Methanosarcina sp. 795 and Methanosarcina sp. 1H1 co-occurred with Methanobrevibacter sp. AbM23, Methanoculleus sp. 25XMc2, Methanosaeta sp. HA, and Methanobacterium sp. MB1. The increased CH₄ fluxes and labile methanogenic community structure in organically fertilized rice soil were primarily due to the increased soil C, nitrogen, potassium, phosphate, and acetate. These results highlight the contributions of native soil- and photosynthesis-derived C in paddy soil CH₄ emissions, and provide basis for more complex investigations of the pathways involved in ecosystem CH₄ processes.

Effects of redox potential on soil cadmium solubility: Insight into microbial community

Understanding the role of microbes in the solubility of cadmium (Cd) is of fundamental importance for remediation of Cd toxicity. The present study aimed to identify the microbes that involved in regulating Cd solubility and to reveal possible mechanisms. Therefore, microbial communities were investigated through high-throughput sequencing approach, the molecular ecological network was constructed and metagenomes were predicted. Our results indicated that redox conditions affected both the solubility of soil Cd and the microbial communities. Anaerobic microbes, such as Anaerolineaceae, did not only play important roles in shaping the microbial community in soils, but might also be involved in regulating the Cd solubility. Two possible mechanisms that how Anaerolineaceae involved in Cd solubility are (1) Anaerolineaceae are important organic matter degraders under anoxic conditions and (2) Anaerolineaceae can co-exist with methane metabolism microbes, while methane metabolism promotes the precipitation of soluble Cd. Thus, application of Anaerolineaceae in bioremediation of soil Cadmium contamination is a potential approach. The study provided a novel insight into the role of microbial community in the regulation of Cd solubility under different redox conditions, and suggested a potential approach for the remediation of soil Cd contamination.

Crop Rotation and Straw Application Impact Microbial Communities in Italian and Philippine Soils and the Rhizosphere of Zea mays

Rice is one of the most important nourishments and its cultivation binds large agricultural areas in the world. Its cultivation leads to huge water consumption and high methane emissions. To diminish these problems, crop rotation between paddy rice and maize is introduced in Asia, but can lead to losses of carbon and water by the formation of desiccation cracks. To counteract these problems rice straw can be applied. We analyzed soil microbial responses to different crop rotation systems [rice–rice (RR), maize–maize (MM), maize–rice (MR)] and to rice straw application in the soil and rhizosphere of maize. Zea mays was grown in microcosms using soils from different field locations, each including different crop rotation regimes. The bacterial and fungal community composition was analyzed by 16S rRNA gene and ITS based amplicon sequencing in the bulk soil and rhizosphere. The microbiota was clearly different in soils from the different field locations (analysis of similarity, ANOSIM: R = 0.516 for the bacterial community; R = 0.817 for the fungal community). Within the field locations, crop rotation contributed differently to the variation in microbial community composition. Strong differences were observed in communities inhabiting soils under monosuccession (RR vs. MM) (ANOSIM: R = 0.923 for the bacterial and R = 0.714 for the fungal community), while the communities in soils undergoing MR crop rotation were more similar to those of the corresponding RR soils (ANOSIM: R = 0.111–0.175). The observed differences could be explained by altered oxygen availabilities in RR and MR soils, resulting in an enrichment of anaerobic bacteria in the soils, and the presence of the different crops, leading to the enrichment of host-plant specific microbial communities. The responses of the microbial communities to the application of rice straw in the microcosms were rather weak compared to the other factors. The taxa responding in bulk soil and rhizosphere were mostly distinct. In conclusion, this study revealed that the different agricultural management practices affect microbial community composition to different extent, not only in the bulk soil but also in the rhizosphere, and that the microbial responses in bulk soil and rhizosphere are distinct.

Effects of different fertilizers on methane emissions and methanogenic community structures in paddy rhizosphere soil

Paddy soil accounts for 10% of global atmospheric methane (CH₄) emissions. Many types of fertilizers may enhance CH₄ emissions, especially organic fertilizer. The aim of this study was to explore the effects of different fertilizers on CH₄ and methanogen patterns in paddy soil. This experiment involved four treatments: chemical fertilizer (CT), organic fertilizer (OT), mixed with chemical and organic fertilizer (MT), and no fertilizer (ctrl). The three fertilization treatments were applied with total nitrogen at the same rate of 300 kg N ha^-1. Paddy CH₄, soil physicochemical variables and methanogen communities were quantitatively analyzed. Rhizosphere soil mcrA and pmoA gene copy numbers were determined by qPCR. Methanogenic 16S rRNA genes were identified by MiSeq sequencing. The results indicated CH₄ emissions were significantly higher in OT (145.31 kg ha^-1) than MT (84.62 kg ha^-1), CT (77.88 kg ha^-1) or ctrl (32.19 kg ha^-1). Soil organic acids were also increased by organic fertilization. CH₄ effluxes were significantly and negatively related to mcrA and pmoA gene copy numbers, and positively related to mcrA/pmoA. Above all, hydrogenotrophic Methanocella and acetoclastic Methanosaeta were the predominant methanogenic communities; these communities were strictly associated with soil potassium, oxalate, acetate, and succinate. Application of organic fertilizer promoted the dominant acetoclastic methanogens, but suppressed the dominant hydrogenotrophic methanogens. The transformation in methanogenic community structure and enhanced availability of C substrates may explain the increased CH₄ production in OT compared to other treatments. Compared to OT, MT may partially mitigate CH₄ emissions while guaranteeing a high rice yield. On this basis, we recommend the local fertilization pattern should change from 300 N kg ha^-1 of organic manure to the same level of mixed fertilization. Moreover, we suggest multiple combinations of mixed fertilization merit more investigation in the future.

Decrease in the annual emissions of CH4 and N2O following the initial land management change from rice to vegetable production

In recent years, rice paddies have been increasingly converted to vegetable production resulting from economic benefits and changes in demand of diets, potentially altering soil greenhouse gas (GHG) balance. Here, we implemented a parallel field experiment to simultaneously quantify the differences in emissions of CH₄ and N₂O among rice paddy (RP) and conventional vegetable field (CV) and greenhouse vegetable field (GV), both of which have been recently converted from rice paddy in subtropical China over a full year. The results revealed that CH₄ emission was reduced dramatically by nearly 100% following the initial land management change from rice to vegetable production, with annual emissions of 720.9, 0.9, and 0.2 kg CH₄-C ha^-1 for RP, CV, and GV, respectively. This conversion however substantially increased N₂O emissions, resulting in the transition from a minor sink of N₂O in RP (-0.1 kg N ha^-1 yr^-1) to considerable N₂O sources in CV (31.8 kg N ha^-1 yr^-1) and GV (52.2 kg N ha^-1 yr^-1). Furthermore, annual N₂O emission from GV significantly exceeded that from CV due to lower soil pH and higher soil temperature facilitating N₂O production in GV relative to CV. Land management change significantly decreased the annual total emissions of CH₄ and N₂O from CV and GV by 19-51% as compared to RP, attributing to the reduced CH₄ emissions outweighing the increased N₂O emissions in CV and GV. These results indicate that expansion of vegetable production at the expense of rice paddies for higher economic benefits also helps mitigate the total emissions of CH₄ and N₂O.

Transcription of mcrA Gene Decreases Upon Prolonged Non-flooding Period in a Methanogenic Archaeal Community of a Paddy-Upland Rotational Field Soil

Methanogenic archaea survive under aerated soil conditions in paddy fields, and their community is stable under these conditions. Changes in the abundance and composition of an active community of methanogenic archaea were assessed by analyzing mcrA gene (encoding α subunit of methyl-coenzyme M reductase) and transcripts during a prolonged drained period in a paddy-upland rotational field. Paddy rice (Oryza sativa L.) was planted in the flooded field and rotated with soybean (Glycine max [L.] Merr.) under upland soil conditions. Soil samples were collected from the rotational plot in the first year, with paddy rice, and in the two successive years, with soybean, at six time points, before seeding, during cultivation, and after harvest as well as from a consecutive paddy (control) plot. By the time that soybean was grown in the second year, the methanogenic archaeal community in the rotational plot maintained high mcrA transcript levels, comparable with those of the control plot community, but the levels drastically decreased by over three orders of magnitude after 2 years of upland conversion. The composition of active methanogenic archaeal communities that survived upland conversion in the rotational plot was similar to that of the active community in the control plot. These results revealed that mcrA gene transcription of methanogenic archaeal community in the rotational field was affected by a prolonged non-flooding period, longer than 1 year, indicating that unknown mechanisms maintain the stability of methanogenic archaeal community in paddy fields last up to 1 year after the onset of drainage.

Bacterial Community of the Rice Floodwater Using Cultivation-Independent Approaches

In agricultural systems, interactions between plants and microorganisms are important to maintaining production and profitability. In this study, bacterial communities in floodwaters of rice fields were monitored during the vegetative and reproductive stages of rice plant development using 16S amplicon sequencing. The study was conducted in the south of Brazil, during the crop years 2011/12 and 2012/13. Comparative analyses showed strong differences between the communities of floodwaters associated with the two developmental stages. During the vegetative stage, 1551 operational taxonomic units (OTUs) were detected, while less than half that number (603) were identified in the reproductive stage. The higher bacterial richness observed in floodwater collected during the vegetative stage may have been favored by the higher concentration of nutrients, such as potassium, due to rhizodeposition and fertilizer application. Eighteen bacterial phyla were identified in both samples. Both communities were dominated by Gammaproteobacteria. In the vegetative stage, Alphaproteobacteria and Betaproteobacteria were more abundant and, in contrast, Bacilli and Clostridia were the more dominant classes in the reproductive stage. The major bacterial taxa identified have been previously identified as important colonizers of rice fields. The richness and composition of bacterial communities over cultivation time may contribute to the sustainability of the crop.

Response of basal metabolic rate to complete submergence of riparian species Salix variegata in the Three Gorges reservoir region

One-year old seedlings of Salix variegata (submergence-tolerant) and Cinnamomum camphora (submergence-intolerant) were selected and subjected to complete submergence (2 m) for 1, 5, 10, and 20 days, to elucidate the submergence- tolerance mechanism of S. variegata in the Three Gorges reservoir region. The basal CO2 emission ratios (BCERs) and O2 consumption rates (OCRs) of leaf, stem, and root were determined. The basal O2 consumption rates (BOCRs) were calculated from the OCRs of different parts and their biomass allocations and used for evaluating the basal metabolic rate (BMR) of species with BCERs. The results showed that: (1) The BCERs of both species responded to flooding similarly, and no significant differences occurred between the submerged S. variegata (SS) and the submerged C. camphora (SC) seedlings, and between the control S. variegata (CS) and the control C. camphora (CC) seedlings. (2) The BOCRs of SS were significantly lower than those of SC on days 1 and 20, while no significant differences occurred between CS and CC for every duration. Therefore, the BMRs, evaluated from BOCRs rather than from BCERs, were related to submergence-tolerance of species, and the response of BMR to submergence would contribute to the survival of S. variegata seedlings under flooding.

Responses of CH4 and N2O fluxes to land-use conversion and fertilization in a typical red soil region of southern China

Land-use conversion and fertilization have been widely reported as important management practices affecting CH₄ and N₂O fluxes; however, few long-term in situ measurements are available after land-use conversion from rice paddies to upland cultivation, especially those including the initial stages after conversion. A 3-year field experiment was conducted in rice paddies and a newly converted citrus orchard to measure CH₄ and N₂O fluxes in response to land-use conversion and fertilization in a red soil region of southern China. Annual CH₄ and N₂O emissions averaged 303.9 kg C ha^-1 and 3.8 kg N ha^-1, respectively, for the rice paddies over three cultivation years. Although annual N₂O emissions increased two- to threefold after the conversion of rice paddies to citrus orchard, the substantial reduction in CH₄ emissions and even shift into a sink for atmospheric CH₄ led to significantly lower CO₂-eq emissions of CH₄ and N₂O in the citrus orchard compared to the rice paddies. Moreover, distinct CH₄ emissions were observed during the initial stages and sustained for several weeks after conversion. Our results indicated that the conversion of rice paddies to citrus orchards in this region for higher economic benefits may also lead to lower aggregate CH₄ and N₂O emissions.

Response of Methanogenic Microbial Communities to Desiccation Stress in Flooded and Rain-Fed Paddy Soil from Thailand

Rice paddies in central Thailand are flooded either by irrigation (irrigated rice) or by rain (rain-fed rice). The paddy soils and their microbial communities thus experience permanent or arbitrary submergence, respectively. Since methane production depends on anaerobic conditions, we hypothesized that structure and function of the methanogenic microbial communities are different in irrigated and rain-fed paddies and react differently upon desiccation stress. We determined rates and relative proportions of hydrogenotrophic and aceticlastic methanogenesis before and after short-term drying of soil samples from replicate fields. The methanogenic pathway was determined by analyzing concentrations and δ¹³C of organic carbon and of CH₄ and CO₂ produced in the presence and absence of methyl fluoride, an inhibitor of aceticlastic methanogenesis. We also determined the abundance (qPCR) of genes and transcripts of bacterial 16S rRNA, archaeal 16S rRNA and methanogenic mcrA (coding for a subunit of the methyl coenzyme M reductase) and the composition of these microbial communities by T-RFLP fingerprinting and/or Illumina deep sequencing. The abundances of genes and transcripts were similar in irrigated and rain-fed paddy soil. They also did not change much upon desiccation and rewetting, except the transcripts of mcrA, which increased by more than two orders of magnitude. In parallel, rates of CH₄ production also increased, in rain-fed soil more than in irrigated soil. The contribution of hydrogenotrophic methanogenesis increased in rain-fed soil and became similar to that in irrigated soil. However, the relative microbial community composition on higher taxonomic levels was similar between irrigated and rain-fed soil. On the other hand, desiccation and subsequent anaerobic reincubation resulted in systematic changes in the composition of microbial communities for both Archaea and Bacteria. It is noteworthy that differences in the community composition were mostly detected on the level of operational taxonomic units (OTUs; 97% sequence similarity). The treatments resulted in change of the relative abundance of several archaeal OTUs. Some OTUs of Methanobacterium, Methanosaeta, Methanosarcina, Methanocella and Methanomassiliicoccus increased, while some of Methanolinea and Methanosaeta decreased. Bacterial OTUs within Firmicutes, Cyanobacteria, Planctomycetes and Deltaproteobacteria increased, while OTUs within other proteobacterial classes decreased.

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.

Greenhouse gas emissions and global warming potential of traditional and diversified tropical rice rotation systems

Global rice agriculture will be increasingly challenged by water scarcity, while at the same time changes in demand (e.g. changes in diets or increasing demand for biofuels) will feed back on agricultural practices. These factors are changing traditional cropping patterns from double-rice cropping to the introduction of upland crops in the dry season. For a comprehensive assessment of greenhouse gas (GHG) balances, we measured methane (CH4 )/nitrous oxide (N2 O) emissions and agronomic parameters over 2.5 years in double-rice cropping (R-R) and paddy rice rotations diversified with either maize (R-M) or aerobic rice (R-A) in upland cultivation. Introduction of upland crops in the dry season reduced irrigation water use and CH4 emissions by 66-81% and 95-99%, respectively. Moreover, for practices including upland crops, CH4 emissions in the subsequent wet season with paddy rice were reduced by 54-60%. Although annual N2 O emissions increased two- to threefold in the diversified systems, the strong reduction in CH4 led to a significantly lower (P < 0.05) annual GWP (CH4  + N2 O) as compared to the traditional double-rice cropping system. Measurements of soil organic carbon (SOC) contents before and 3 years after the introduction of upland crop rotations indicated a SOC loss for the R-M system, while for the other systems SOC stocks were unaffected. This trend for R-M systems needs to be followed as it has significant consequences not only for the GWP balance but also with regard to soil fertility. Economic assessment showed a similar gross profit span for R-M and R-R, while gross profits for R-A were reduced as a consequence of lower productivity. Nevertheless, regarding a future increase in water scarcity, it can be expected that mixed lowland-upland systems will expand in SE Asia as water requirements were cut by more than half in both rotation systems with upland crops.