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Autotrophic carbon dioxide (CO 2 ) fixation by microbes is ubiquitous in the environment and potentially contributes to the soil organic carbon (SOC) pool. However, the multiple autotrophic pathways of microbial carbon assimilation and fixation in paddy soils remain poorly characterized. In this study, we combine metagenomic analysis with 14 C-labelling to investigate all known autotrophic pathways and CO 2 assimilation mechanisms in five typical paddy soils from southern China. Marker genes of six autotrophic pathways are detected in all soil samples, which are dominated by the cbbL genes (67%-82%) coding the ribulose-bisphosphate carboxylase large chain in the Calvin cycle. These marker genes are associated with a broad range of phototrophic and chemotrophic genera. Significant amounts of 14 C-CO 2 are assimilated into SOC (74.3-175.8 mg 14 C kg -1 ) and microbial biomass (5.2-24.1 mg 14 C kg -1 ) after 45 days incubation, where more than 70% of 14 C-SOC was concentrated in the relatively stable humin fractions. These results show that paddy soil microbes contain the genetic potential for autotrophic carbon fixation spreading over broad taxonomic ranges, and can incorporate atmospheric carbon into organic components, which ultimately contribute to the stable SOC pool., (© 2020 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Background: The expected increase in global surface temperature due to climate change may have a tremendous effect on the structure and function of the anaerobic food web in flooded rice field soil. Here, we used the metatranscriptomic analysis of total RNA to gain a system-level understanding of this temperature effect on the methanogenic food web., Results: Mesophilic (30 °C) and thermophilic (45 °C) food web communities had a modular structure. Family-specific rRNA dynamics indicated that each network module represents a particular function within the food webs. Temperature had a differential effect on all the functional activities, including polymer hydrolysis, syntrophic oxidation of key intermediates, and methanogenesis. This was further evidenced by the temporal expression patterns of total bacterial and archaeal mRNA and of transcripts encoding carbohydrate-active enzymes (CAZymes). At 30 °C, various bacterial phyla contributed to polymer hydrolysis, with Firmicutes decreasing and non-Firmicutes (e.g., Bacteroidetes, Ignavibacteriae) increasing with incubation time. At 45 °C, CAZyme expression was solely dominated by the Firmicutes but, depending on polymer and incubation time, varied on family level. The structural and functional community dynamics corresponded well to process measurements (acetate, propionate, methane). At both temperatures, a major change in food web functionality was linked to the transition from the early to late stage. The mesophilic food web was characterized by gradual polymer breakdown that governed acetoclastic methanogenesis (Methanosarcinaceae) and, with polymer hydrolysis becoming the rate-limiting step, syntrophic propionate oxidation (Christensenellaceae, Peptococcaceae). The thermophilic food web had two activity stages characterized first by polymer hydrolysis and followed by syntrophic oxidation of acetate (Thermoanaerobacteraceae, Heliobacteriaceae, clade OPB54). Hydrogenotrophic Methanocellaceae were the syntrophic methanogen partner, but their population structure differed between the temperatures. Thermophilic temperature promoted proliferation of a new Methanocella ecotype., Conclusions: Temperature had a differential effect on the structural and functional continuum in which the methanogenic food web operates. This temperature-induced change in food web functionality may not only be a near-future scenario for rice paddies but also for natural wetlands in the tropics and subtropics.

This study demonstrated that a combined heterotrophic and autotrophic denitrification (HAD) process is highly effective for the simultaneous removal of acetate, nitrate, and sulfide at an efficiency of 100, 80, and 100 %, respectively. In the HAD system, simultaneous sulfide, acetate, and nitrate removals were observed, which indicated that heterotrophic and autotrophic denitrification occurred simultaneously. When the sulfide was existed in HAD reactor, the main product of sulfide biooxidation was S(0). Once the sulfide was exhausted, the sulfate concentration in the HAD reactor increased and became the main end product. These results provided an alternative method to control the end sulfide biooxidation product by online monitoring sulfide concentration. Nearly half (43 %) of the total clones in our mix-trophic reactor were amphitrophy denitrifiers. The autotrophic denitrifiers, heterotrophic denitrifiers, and amphitrophy denitrifiers coexisted in the HAD reactor to complete the denitrification process. Retrieved bacterial 16S rRNA gene clones affiliated with uncultured Xanthomonadaceae, Thauera, Thiobacillus, and Chromatiales were dominant.

Nitrite reduction is regulated by nitrite reductase encoded by nirK and nirS genes. This study aimed to investigate the abundance and composition of nirK- and nirS-containing denitrifiers in response to Spartina alterniflora invasion at the Jiulong River estuary, China. The sediment samples (depth: 0-5.0 and 5.1-20 cm) were collected from 3 vegetation zones, 1 dominated by the exotic plant S. alterniflora, 1 dominated by the native plant Kandelia candel, and 1 dominated by the native plant Cyperus malaccensis, and from an unvegetated flat zone. nirK- and nirS-containing denitrifier population sizes were lower in the invaded and nonvegetated zones than in those dominated by native K. candel and C. malaccensis, which were impacted by depth - vegetation species interaction. The ratios of nirS to nirK abundance ranged from 42.10 to 677.27, with the lowest ratio found for the upper layer in the invaded zone. The nirK-containing denitrifier compositions showed a 35% similarity between invaded zone and others. Most of the sequences of nirK genes recovered from the S. alterniflora zone were specific and distinct from those of nirK genes recovered from other vegetation types; nirS genes in the invaded zone were highly divergent. These results reveal that S. alterniflora invasion has a significant effect on the abundance and composition of both nirK- and nirS-containing denitrifiers, and nirS-containing denitrifiers were less responsive to invasion than nirK-containing denitrifiers.

An in-vessel composting bioremediation of (13)C4-4,5,9,10-pyrene and unlabeled pyrene spiked soil amended with fresh wastes was investigated by DNA-based stable isotope probing (SIP) of active bacteria involved. Highest dissipation of (13)C4-pyrene was detected at 55 °C after 42 days composting. The active bacterial communities in the composting changed over time, showing a distinct difference among different stages. α-, β-, γ-Proteobacteria, and Actinobacteria were detected mainly involving in pyrene degradation at 38 °C over 14 days composting. Streptomyces appeared to dominate the pyrene degradation at 55 °C. β- and γ-Proteobacteria and Actinobacteria were the dominant pyrene degraders at 70 °C after 42 days composting and at 38 °C after 60 days composting. The results of this study suggest the pyrene degradation was performed by phylogenetically distinct bacterial guilds from the phyla Actinobacteria and Proteobacteria during in-vessel composition processes., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

The incorporation of rice residues into paddy fields strongly enhances methane production and emissions. Although the decomposition processes of plant residues in rice field soil has been documented, the structure and dynamics of the microbial communities involved are poorly understood. The purpose of the present study was to determine the dynamics of short-chain fatty acids and the structure of bacterial communities during residue decomposition in a rice field soil. The soil was anaerobically incubated with the incorporation of rice root or straw residues for 90 days at three temperatures (15, 30, and 45 degrees C). The dynamics of fatty acid intermediates showed an initial cumulative phase followed by a rapid consumption phase and a low-concentration quasi-steady state. Correspondingly, the bacterial populations displayed distinct successions during residue decomposition. Temperature showed a strong effect on the dynamics of bacterial populations. Members of Clostridium (clusters I and III) were most dominant in the incubations, particularly in the early successions. Bacteroidetes and Chlorobi were abundant in the later successions at 15 and 30 degrees C, while Acidobacteria were selected at 45 degrees C. We suggest that the early successional groups are responsible for the decomposition of the easily degradable fraction of residues, while the late successional groups become more important in decomposing the less-degradable or resistant fraction of plant residues. The bacterial succession probably is related to resource availability during residue decomposition. The fast-growing organisms are favored at the beginning, while the slow-growing bacteria are better adapted in the later stages, when substrate availability is limiting.