Differences in microbial community structure and nitrogen cycling in natural and drained tropical peatland soils

Temporal dynamics of soil microbial C and N cycles with GHG fluxes in the transition from tropical peatland forest to oil palm plantation

Tropical peatlands significantly influence local and global carbon and nitrogen cycles, yet they face growing pressure from anthropogenic activities. Land use changes, such as peatland forests conversion to oil palm plantations, affect the soil microbiome and greenhouse gas (GHG) emissions. However, the temporal dynamics of microbial community changes and their role as GHG indicators are not well understood. This study examines the dynamics of peat chemistry, soil microbial communities, and GHG emissions from 2016 to 2020 in a logged-over secondary peat swamp forest in Sarawak, Malaysia, which transitioned to an oil palm plantation. This study focuses on changes in genetic composition governing plant litter degradation, methane (CH4), and nitrous oxide (N2O) fluxes. Soil CO2 emission increased (doubling from approximately 200 mg C m-2 h-1), while CH4 emissions decreased (from 200 µg C m-2 h-1 to slightly negative) following land use changes. The N2O emissions in the oil palm plantation reached approximately 1,510 µg N m-2 h-1, significantly higher than previous land uses. The CH4 fluxes were driven by groundwater table, humification levels, and C:N ratio, with Methanomicrobia populations dominating methanogenesis and Methylocystis as the main CH4 oxidizer. The N2O fluxes correlated with groundwater table, total nitrogen, and C:N ratio with dominant nirK-type denitrifiers (13-fold nir to nosZ) and a minor role by nitrification (a threefold increase in amoA) in the plantation. Proteobacteria and Acidobacteria encoding incomplete denitrification genes potentially impact N2O emissions. These findings highlighted complex interactions between microbial communities and environmental factors influencing GHG fluxes in altered tropical peatland ecosystems.IMPORTANCETropical peatlands are carbon-rich environments that release significant amounts of greenhouse gases when drained or disturbed. This study assesses the impact of land use change on a secondary tropical peat swamp forest site converted into an oil palm plantation. The transformation lowered groundwater levels and changed soil properties. Consequently, the oil palm plantation site released higher carbon dioxide and nitrous oxide compared to previous land uses. As microbial communities play crucial roles in carbon and nitrogen cycles, this study identified environmental factors associated with microbial diversity, including genes and specific microbial groups related to nitrous oxide and methane emissions. Understanding the factors driving microbial composition shifts and greenhouse gas emissions in tropical peatlands provides baseline information to potentially mitigate environmental consequences of land use change, leading to a broader impact on climate change mitigation efforts and proper land management practices.

Green-house gas fluxes and soil microbial functional genes abundance in saturated and drained peatlands in South-West Iceland

The drainage of peatlands followed by land use conversion significantly impacts on the fluxes of green-house gases (GHGs, i.e. CO2, CH4, and N2O) to and from the atmosphere, driven by changes in soil properties and microbial communities. In this study, we compared saturated peatlands with drained ones used for sheep grazing or cultivated, which are common in South-West Iceland. These areas exhibit different degrees of soil saturation and nitrogen (N) content, reflecting the anthropic pressure gradient. We aimed at covering knowledge gaps about lack of estimates on N2O fluxes and drainage, by assessing the emissions of GHGs, and the impact of land conversion on these emissions. Moreover, we investigated soil microbial community functional diversity, and its connection with processes contributing to GHGs emission. GHGs emissions differed between saturated and drained peatlands, with increased soil respiration rates (CO2 emissions) and N mineralization (N2O), consistent with the trend of anthropogenic pressure. Drainage drastically reduced methane (CH4) emissions but increased CO2 emissions, resulting in a higher global warming potential (GWP). Cultivation, involving occasional tillage and fertilization, further increased N2O emissions, mediated by higher N availability and conditions favorable to nitrification. Functional genes mirrored the overall trend, showing a shift from prevalent methanogenic archaea (mcrA) in saturated peatlands to nitrifiers (amoA) in drained-cultivated areas. Environmental variables and nutrient content were critical factors affecting community composition in both environments, which overall affected the GHGs emissions and the relative contribution of the three gases.

Microbial nitrogen transformations tracked by natural abundance isotope studies and microbiological methods: A review

Nitrogen is an essential nutrient in the environment that exists in multiple oxidation states in nature. Numerous microbial processes are involved in its transformation. Knowledge about very complex N cycling has been growing rapidly in recent years, with new information about associated isotope effects and about the microbes involved in particular processes. Furthermore, molecular methods that are able to detect and quantify particular processes are being developed, applied and combined with other analytical approaches, which opens up new opportunities to enhance understanding of nitrogen transformation pathways. This review presents a summary of the microbial nitrogen transformation, including the respective isotope effects of nitrogen and oxygen on different nitrogen-bearing compounds (including nitrates, nitrites, ammonia and nitrous oxide), and the microbiological characteristics of these processes. It is supplemented by an overview of molecular methods applied for detecting and quantifying the activity of particular enzymes involved in N transformation pathways. This summary should help in the planning and interpretation of complex research studies applying isotope analyses of different N compounds and combining microbiological and isotopic methods in tracking complex N cycling, and in the integration of these results in modelling approaches.

Biochar-based materials as remediation strategy in petroleum hydrocarbon-contaminated soil and water: Performances, mechanisms, and environmental impact

Petroleum contamination is considered as a major risk to the health of humans and environment. Biochars as low-cost and eco-friendly carbon materials, have been widely used for the removal of petroleum hydrocarbon in the environment. The purpose of this paper is to review the performance, mechanisms, and potential environmental toxicity of biochar, modified biochar and its integration use with other materials in petroleum contaminated soil and water. Specifically, the use of biochar in oil-contaminated water and soil as well as the factors that could influence the removal ability of biochar were systematically evaluated. In addition, the modification and integrated use of biochar for improving the removal efficiency were summarized from the aspects of sorption, biodegradation, chemical degradation, and reusability. Moreover, the functional impacts and associated ecotoxicity of pristine and modified biochars in various environments were demonstrated. Finally, some shortcoming of current approaches, and future research needs were provided for the future direction and challenges of modified biochar research. Overall, this paper gain insight into biochar application in petroleum remediation from the perspectives of performance enhancement and environmental sustainability.

Unraveling microbial processes involved in carbon and nitrogen cycling and greenhouse gas emissions in rewetted peatlands by molecular biology

Restoration of drained peatlands through rewetting has recently emerged as a prevailing strategy to mitigate excessive greenhouse gas emissions and re-establish the vital carbon sequestration capacity of peatlands. Rewetting can help to restore vegetation communities and biodiversity, while still allowing for extensive agricultural management such as paludiculture. Belowground processes governing carbon fluxes and greenhouse gas dynamics are mediated by a complex network of microbial communities and processes. Our understanding of this complexity and its multi-factorial controls in rewetted peatlands is limited. Here, we summarize the research regarding the role of soil microbial communities and functions in driving carbon and nutrient cycling in rewetted peatlands including the use of molecular biology techniques in understanding biogeochemical processes linked to greenhouse gas fluxes. We emphasize that rapidly advancing molecular biology approaches, such as high-throughput sequencing, are powerful tools helping to elucidate the dynamics of key biogeochemical processes when combined with isotope tracing and greenhouse gas measuring techniques. Insights gained from the gathered studies can help inform efficient monitoring practices for rewetted peatlands and the development of climate-smart restoration and management strategies.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10533-024-01122-6.

Genes and genome-resolved metagenomics reveal the microbial functional make up of Amazon peatlands under geochemical gradients

The Pastaza-Marañón Foreland Basin (PMFB) holds the most extensive tropical peatland area in South America. PMFB peatlands store ~7.07 Gt of organic carbon interacting with multiple microbial heterotrophic, methanogenic, and other aerobic/anaerobic respirations. Little is understood about the contribution of distinct microbial community members inhabiting tropical peatlands. Here, we studied the metagenomes of three geochemically distinct peatlands spanning minerotrophic, mixed, and ombrotrophic conditions. Using gene- and genome-centric approaches, we evaluate the functional potential of the underlying microbial communities. Abundance analyses show significant differences in C, N, P, and S acquisition genes. Furthermore, community interactions mediated by toxin-antitoxin and CRISPR-Cas systems were enriched in oligotrophic soils, suggesting that non-metabolic interactions may exert additional controls in low-nutrient environments. Additionally, we reconstructed 519 metagenome-assembled genomes spanning 28 phyla. Our analyses detail key differences across the geochemical gradient in the predicted microbial populations involved in degradation of organic matter, and the cycling of N and S. Notably, we observed differences in the nitric oxide (NO) reduction strategies between sites with high and low N2 O fluxes and found phyla putatively capable of both NO and sulfate reduction. Our findings detail how gene abundances and microbial populations are influenced by geochemical differences in tropical peatlands.

Patters of reactive nitrogen removal at the waters in the semi-constructed wetland

Protection and rectification patters of urban wetlands have been considered in strategies to balance services to society and negative consequences of excess reactive nitrogen (Nr) loading. However, the knowledge about strategies of semi-constructed wetlands on nitrogen (N) cycling pathways and removal Nr from the overlying water is limited. This study aimed to reveal considerable differences among rectification patterns of the typical semi-constructed wetland (Xixi wetland), comprising rational exploitation area (REA), rehabilitation and reconstruction area (RRA), and conservation area (CA) by analyzing the N distribution and N protentional pathways among them. Results pointed out that both NH4+ and NO3- concentration were prominently higher in REA, as opposed to CA and RRA. Sediments in RRA had relatively higher NH4+ content, indicating the efficiency of dissimilatory nitrate reduction (DNRA) in RRA. Moreover, there was a significant shift in the microbial community structure across different sites and sediments. Metagenomic analysis distinguished the N cycling pathways, with nitrification (M00804), denitrification (M00529), and DNRA (M00530) being the crucial pathways in the semi-constructed wetland. The relative abundance of N metabolic pathways (ko00910) varied among different types of sediments, being more abundant in shore and rhizosphere areas and less abundant in bottom sediments. Methylobacter and Nitrospira were the predominant nitrifiers in shore sediments, while Methylocystis was enriched in the bottom sediments and rhizosphere soils. Furthermore, Anaeromyxobacter, Anaerolinea, Dechloromonas, Nocardioides, and Methylocystis were identified as the primary denitrifiers with N reductase genes (nirK, nirS, or nosZ). Among these, Anaeromyxobacter, Dechloromonas, and Methylocystis were the primary contributors containing the nosZ gene in semi-constructed wetlands, driving the conversion of N2O to N2. This study provides important insights into rectification-dependent Nr removal from the overlying water in terms of N distribution and N metabolic functional microbial communities in the semi-constructed wetlands.

BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes

BACKGROUND

Exploring metagenomic contigs and "binning" them into metagenome-assembled genomes (MAGs) are essential for the delineation of functional and evolutionary guilds within microbial communities. Despite the advances in automated binning algorithms, their capabilities in recovering MAGs with accuracy and biological relevance are so far limited. Researchers often find that human involvement is necessary to achieve representative binning results. This manual process however is expertise demanding and labor intensive, and it deserves to be supported by software infrastructure.

RESULTS

We present BinaRena, a comprehensive and versatile graphic interface dedicated to aiding human operators to explore metagenome assemblies via customizable visualization and to associate contigs with bins. Contigs are rendered as an interactive scatter plot based on various data types, including sequence metrics, coverage profiles, taxonomic assignments, and functional annotations. Various contig-level operations are permitted, such as selection, masking, highlighting, focusing, and searching. Binning plans can be conveniently edited, inspected, and compared visually or using metrics including silhouette coefficient and adjusted Rand index. Completeness and contamination of user-selected contigs can be calculated in real time. In demonstration of BinaRena's usability, we show that it facilitated biological pattern discovery, hypothesis generation, and bin refinement in a complex tropical peatland metagenome. It enabled isolation of pathogenic genomes within closely related populations from the gut microbiota of diarrheal human subjects. It significantly improved overall binning quality after curating results of automated binners using a simulated marine dataset.

CONCLUSIONS

BinaRena is an installation-free, dependency-free, client-end web application that operates directly in any modern web browser, facilitating ease of deployment and accessibility for researchers of all skill levels. The program is hosted at https://github.com/qiyunlab/binarena , together with documentation, tutorials, example data, and a live demo. It effectively supports human researchers in intuitive interpretation and fine tuning of metagenomic data. Video Abstract.

Heavy metal effects on multitrophic level microbial communities and insights for ecological restoration of an abandoned electroplating factory site

The response of soil microbes to heavy metal pollution provides a metric to evaluate the soil health and ecological risks associated with heavy metal contamination. However, a multitrophic level perspective of how soil microbial communities and their functions respond to long-term exposure of multiple heavy metals remains unclear. Herein, we examined variations in soil microbial (including protists and bacteria) diversity, functional guilds and interactions along a pronounced metal pollution gradient in a field surrounding an abandoned electroplating factory. Given the stressful soil environment resulting from extremely high heavy metal concentrations and low nutrients, beta diversity of protist increased, but that of bacteria decreased, at high versus low pollution sites. Additionally, the bacteria community showed low functional diversity and redundancy at the highly polluted sites. We further identified indicative genus and "generalists" in response to heavy metal pollution. Predatory protists in Cercozoa were the most sensitive protist taxa with respect to heavy metal pollution, whereas photosynthetic protists showed a tolerance for metal pollution and nutrient deficiency. The complexity of ecological networks increased, but the communication among the modules disappeared with increasing metal pollution levels. Subnetworks of tolerant bacteria displaying functional versatility (Blastococcus, Agromyces and Opitutus) and photosynthetic protists (microalgae) became more complex with increasing metal pollution levels, indicating their potential for use in bioremediation and restoration of abandoned industrial sites contaminated by heavy metals.

Microorganisms carrying nosZ I and nosZ II share similar ecological niches in a subtropical coastal wetland

Nitrous oxide (N₂O) reducers are the only known sink for N₂O and pivotal contributors to N₂O mitigation in terrestrial and water ecosystems. However, the niche preference of nosZ I and nosZ II carrying microorganisms, two divergent clades of N₂O reducers in coastal wetlands, is not yet well documented. In this study, we investigated the abundance, community structure and co-occurrence network of nosZ I and nosZ II carrying microorganisms and their driving factors at three depths in a subtropical coastal wetland with five plant species and a bare tidal flat. The taxonomic identities differed between nosZ I and nosZ II carrying microorganisms, with nosZ I sequences affiliated with Alphaproteobacteria and Betaproteobacteria while nosZ II sequences with Gemmatimonadetes, Verrucomicrobia, Gammaproteobacteria, and Chloroflexi. The abundances of nosZ I and nosZ II decreased with increasing soil depths, and were positively associated with salinity, total carbon (TC) and total nitrogen (TN). Random forest analysis showed that salinity was the strongest predictor for the abundances of nosZ I and nosZ II. Salinity, TC and TN were the major driving forces for the community structure of nosZ I and nosZ II carrying microorganisms. Moreover, co-occurrence analysis showed that 92.2 % of the links between nosZ I and nosZ II were positive, indicating that nosZ I and nosZ II carrying microorganisms likely shared similar ecological niches. Taken together, we provided new evidence that nosZ I and nosZ II carrying microorganisms shared similar ecological niches in a subtropical estuarine wetland, and identified salinity, TC and TN serving as the most important environmental driving forces. This study advances our understanding of the environmental adaptation and niche preference of nosZ I and nosZ II carrying microorganisms in coastal wetlands.

Denitrification dynamics in unsaturated soils with different porous structures and water saturation degrees: A focus on the shift in microbial community structures

Despite its environmental significance, little is known about denitrification in vadose zones owing to the complexity of such environments. Here, we investigated denitrification in unsaturated soils with different pore distributions. To this end, we performed batch-type denitrification experiments and analyzed microbial community shifts before and after possible reactions with nitrates to clarify the relevant denitrifying mechanism in the microcosms. For quantitative comparison, pore distribution in the test soil samples was characterized based on the uniformity coefficient (C_u) and water saturation degree (SD). Micro-CT analysis of the soil pore distribution confirmed that the proportion of bigger-sized pores increased with decreasing C_u. However, oxygen diffusion into the system was controlled by SD rather than C_u. Within a certain SD range (51-67%), the pore condition changed abruptly from an oxic to an anoxic state. Consequently, denitrification occurred even under unsaturated soil conditions when the SD increased beyond 51-67%. High throughput sequencing revealed that the same microbial species were potentially responsible for denitrification under both partially (SD 67%), and fully saturated (SD of 100%) conditions, implying that the mechanism of denitrification in a vadose zone, if it exists, might be possibly similar under varying conditions.

The impact of alternating drainage and inundation cycles on geochemistry and microbiology of intact peat cores

The rewetting of degraded peatlands has been adopted as a method to address climate change. Concerns have been raised about the effects of peat inundation and drying cycles, in more extreme climate events, on the potential release of nitrogen (N) species, in particular ammonium (NH₄-N), once rewetted, as well as the physico-chemical and biological properties of the peat. This study used intact peat cores to measure the impact of two different cycles of peat inundation and drying (1 month and 2 month) over a total study duration of 56 weeks on the (1) NH₄-N, nitrate-N (NO₃-N) and dissolved reactive phosphorus (DRP) in the soil pore water; (2) microbial community structure; (3) physico-chemical properties of the peat; and (4) the structure of the peat, and therefore its ability to mitigate flood risks and storm surges. The study found that rewetted cores released NO₃-N in the pore water up to a concentration of 6.25 mg L^-1, but had no appreciable impact on NH₄-N, which remained below 1.7 mg L^-1 over the study duration. DRP moved quickly though the upper layers of the cores, but physico-chemical analysis suggested it was adsorbed to more iron-rich soil, which was present at depths below 0.4 m in the cores. Time intervals between inundation produced no significant difference on the forms of inorganic N released, nor did it compact the soil or change the microbial community structure. The depth of the water table, however, had a significant impact on inorganic N release, particularly NO₃-N, which indicates that this N species, and not NH₄-N, may be problematic in rewetted peatlands.

Diversity and Distribution Characteristics of Soil Microbes across Forest-Peatland Ecotones in the Permafrost Regions

Permafrost peatlands are a huge carbon pool that is uniquely sensitive to global warming. However, despite the importance of peatlands in global carbon sequestration and biogeochemical cycles, few studies have characterized the distribution characteristics and drivers of soil microbial community structure in forest-peatland ecotones. Here, we investigated the vertical distribution patterns of soil microbial communities in three typical peatlands along an environmental gradient using Illumina high-throughput sequencing. Our findings indicated that bacterial richness and diversity decreased with increasing soil depth in coniferous swamp (LT) and thicket swamp (HT), whereas the opposite trend was observed in a tussock swamp (NT). Additionally, these parameters decreased at 0-20 and 20-40 cm and increased at 40-60 cm along the environmental gradient (LT to NT). Principal coordinate analysis (PCoA) indicated that the soil microbial community structure was more significantly affected by peatland type than soil depth. Actinomycetota, Proteobacteria, Firmicutes, Chloroflexota, Acidobacteriota, and Bacteroidota were the predominant bacterial phyla across all soil samples. Moreover, there were no significant differences in the functional pathways between the three peatlands at each depth, except for amino acid metabolism, membrane transport, cell motility, and signal transduction. Redundancy analysis (RDA) revealed that pH and soil water content were the primary environmental factors influencing the bacterial community structure. Therefore, this study is crucial to accurately forecast potential changes in peatland ecosystems and improve our understanding of the role of peat microbes as carbon pumps in the process of permafrost degradation.

Nitrate removal by combining chemical and biostimulation approaches using micro-zero valent iron and lactic acid

The occurrence of nitrate is the most significant type of pollution affecting groundwater globally, being a major contributor to the poor condition of water bodies. This pollution is related to livestock-agricultural and urban activities, and the nitrate presence in drinking water has a clear impact on human health. For example, it causes the blue child syndrome. Moreover, the high nitrate content in aquifers and surface waters significantly affects aquatic ecosystems since it is responsible for the eutrophication of surface water bodies. A treatability test was performed in the laboratory to study the decrease of nitrate in the capture zone of water supply wells. For this purpose, two boreholes were drilled from which groundwater and sediments were collected to conduct the test. The goal was to demonstrate that nitrate in groundwater can be decreased much more efficiently using combined abiotic and biotic methods with micro-zero valent iron and biostimulation with lactic acid, respectively, than when both strategies are used separately. The broader implications of this goal derive from the fact that the separate use of these reagents decreases the efficiency of nitrate removal. Thus, while nitrate is removed using micro-valent iron, high concentrations of harmful ammonium are also generated. Furthermore, biostimulation alone leads to overgrowth of other microorganisms that do not result in denitrification, therefore complete denitrification requires more time to occur. In contrast, the combined strategy couples abiotic denitrification of nitrate with biostimulation of microorganisms capable of biotically transforming the abiotically generated harmful ammonium. The treatability test shows that the remediation strategy combining in situ chemical reduction using micro-zero valent iron and biostimulation with lactic acid could be a viable strategy for the creation of a reactive zone around supply wells located in regions where groundwater and porewater in low permeability layers are affected by diffuse nitrate contamination.

Degradation reduces the diversity of nitrogen-fixing bacteria in the alpine wetland on the Qinghai-Tibet Plateau

Biological nitrogen fixation is a key process in the nitrogen cycle and the main source of soil available nitrogen. The number and diversity of nitrogen-fixing bacteria directly reflect the efficiency of soil nitrogen fixation. The alpine wetland on the Qinghai-Tibet Plateau (QTP) is degrading increasingly, with a succession toward alpine meadows. Significant changes in soil physicochemical properties accompany this process. However, it is unclear how does the soil nitrogen-fixing bacteria change during the degradation processes, and what is the relationship between these changes and soil physicochemical properties. In this study, the nifH gene was used as a molecular marker to further investigate the diversity of nitrogen-fixing bacteria at different stages of degradation (none, light, and severe degeneration) in the alpine wetland. The results showed that wetland degradation significantly reduced the diversity, altered the community composition of nitrogen-fixing bacteria, decreased the relative abundance of Proteobacteria, and increased the relative abundance of Actinobacteria. In addition to the dominant phylum, the class, order, family, and genus of nitrogen-fixing bacteria had significant changes in relative abundance. Analysis of Mantel test showed that most soil factors (such as pH, soil water content (SWC), the organic carbon (TOC), total nitrogen (TN), and soil C:P ratio) and abundance had a significant positive correlation. TOC, TN, total phosphorus (TP), soil C:P ratio and Shannon had a significant positive correlation with each other. The RDA ranking further revealed that TOC, SWC, and TN were the main environmental factors influencing the community composition of nitrogen-fixing bacteria. It is found that the degradation of the alpine wetland inhibited the growth of nitrogen-fixing bacteria to a certain extent, leading to the decline of their nitrogen-fixing function.

Structure and function of the soil microbiome underlying N2O emissions from global wetlands

Wetland soils are the greatest source of nitrous oxide (N₂O), a critical greenhouse gas and ozone depleter released by microbes. Yet, microbial players and processes underlying the N₂O emissions from wetland soils are poorly understood. Using in situ N₂O measurements and by determining the structure and potential functional of microbial communities in 645 wetland soil samples globally, we examined the potential role of archaea, bacteria, and fungi in nitrogen (N) cycling and N₂O emissions. We show that N₂O emissions are higher in drained and warm wetland soils, and are correlated with functional diversity of microbes. We further provide evidence that despite their much lower abundance compared to bacteria, nitrifying archaeal abundance is a key factor explaining N₂O emissions from wetland soils globally. Our data suggest that ongoing global warming and intensifying environmental change may boost archaeal nitrifiers, collectively transforming wetland soils to a greater source of N₂O.

Biofilm carrier type affects biogenic sulfur-driven denitrification performance and microbial community dynamics in moving-bed biofilm reactors

Autotrophic denitrification with biosulfur (ADBIOS) provides a sustainable technological solution for biological nitrogen removal from wastewater driven by biogenic S⁰, derived from biogas desulfurization. In this study, the effect of different biofilm carriers (conventional AnoxK™ 1 and Z-200 with a pre-defined maximum biofilm thickness) on ADBIOS performance and microbiomics was investigated in duplicate moving bed-biofilm reactors (MBBRs). The MBBRs were operated parallelly in continuous mode for 309 days, whilst gradually decreasing the hydraulic retention time (HRT) from 72 to 21 h, and biosulfur was either pumped in suspension (days 92-223) or supplied in powder form. Highest nitrate removal rates were approximately 225 (±11) mg/L·d and 180 (±7) mg NO₃^--N/L·d in the MBBRs operated with K1 and Z-200 carriers, respectively. Despite having the same protected surface area for biofilm development in each MBBR, the biomass attached onto the K1 carrier was 4.8-fold more than that on the Z-200 carrier, with part of the biogenic S⁰ kept in the biofilm. The microbial communities of K1 and Z-200 biofilms could also be considered similar at cDNA level in terms of abundance (R = 0.953 with p = 0.042). A relatively stable microbial community was formed on K1 carriers, while the active portion of the microbial community varied significantly over time in the MBBRs using Z-200 carriers.

High-Throughput Sequencing-Based Analysis of Rhizosphere and Diazotrophic Bacterial Diversity Among Wild Progenitor and Closely Related Species of Sugarcane (Saccharum spp. Inter-Specific Hybrids)

Considering the significant role of genetic background in plant-microbe interactions and that most crop rhizospheric microbial research was focused on cultivars, understanding the diversity of root-associated microbiomes in wild progenitors and closely related crossable species may help to breed better cultivars. This study is aimed to fill a critical knowledge gap on rhizosphere and diazotroph bacterial diversity in the wild progenitors of sugarcane, the essential sugar and the second largest bioenergy crop globally. Using a high-throughput sequencing (HTS) platform, we studied the rhizosphere and diazotroph bacterial community of Saccharum officinarum L. cv. Badila (BRS), Saccharum barberi (S. barberi) Jesw. cv Pansahi (PRS), Saccharum robustum [S. robustum; (RRS), Saccharum spontaneum (S. spontaneum); SRS], and Saccharum sinense (S. sinense) Roxb. cv Uba (URS) by sequencing their 16S rRNA and nifH genes. HTS results revealed that a total of 6,202 bacteria-specific operational taxonomic units (OTUs) were identified, that were distributed as 107 bacterial groups. Out of that, 31 rhizobacterial families are commonly spread in all five species. With respect to nifH gene, S. barberi and S. spontaneum recorded the highest and lowest number of OTUs, respectively. These results were validated by quantitative PCR analysis of both genes. A total of 1,099 OTUs were identified for diazotrophs with a core microbiome of 9 families distributed among all the sugarcane species. The core microbiomes were spread across 20 genera. The increased microbial diversity in the rhizosphere was mainly due to soil physiochemical properties. Most of the genera of rhizobacteria and diazotrophs showed a positive correlation, and few genera negatively correlated with the soil properties. The results showed that sizeable rhizospheric diversity exists across progenitors and close relatives. Still, incidentally, the rhizosphere microbial abundance of progenitors of modern sugarcane was at the lower end of the spectrum, indicating the prospect of Saccharum species introgression breeding may further improve nutrient use and disease and stress tolerance of commercial sugarcane. The considerable variation for rhizosphere microbiome seen in Saccharum species also provides a knowledge base and an experimental system for studying the evolution of rhizobacteria-host plant association during crop domestication.

Restoring wetlands on intensive agricultural lands modifies nitrogen cycling microbial communities and reduces N2O production potential

The concentration of nitrous oxide (N₂O), an ozone-depleting greenhouse gas, is rapidly increasing in the atmosphere. Most atmospheric N₂O originates in terrestrial ecosystems, of which the majority can be attributed to microbial cycling of nitrogen in agricultural soils. Here, we demonstrate how the abundance of nitrogen cycling genes vary across intensively managed agricultural fields and adjacent restored wetlands in the Sacramento-San Joaquin Delta in California, USA. We found that the abundances of nirS and nirK genes were highest at the intensively managed organic-rich cornfield and significantly outnumber any other gene abundances, suggesting very high N₂O production potential. The quantity of nitrogen transforming genes, particularly those responsible for denitrification, nitrification and DNRA, were highest in the agricultural sites, whereas nitrogen fixation and ANAMMOX was strongly associated with the wetland sites. Although the abundance of nosZ genes was also high at the agricultural sites, the ratio of nosZ genes to nir genes was significantly higher in wetland sites indicating that these sites could act as a sink of N₂O. These findings suggest that wetland restoration could be a promising natural climate solution not only for carbon sequestration but also for reduced N₂O emissions.

Multifarious functional traits of free-living rhizospheric fungi, with special reference to Aspergillus spp. isolated from North Indian soil, and their inoculation effect on plant growth

Purpose

Rhizospheric soil fungi are critical for plant and soil health. However, their multiple functional traits and impact on plant growth have not been systematically explored.

Methods

During this study, biochemical traits of 73 indigenous soil fungal isolates and 15 unidentified isolates related to plant growth promotion and production of extracellular enzymes were studied.

Results

Forty four (65.67%) of the total isolates produced indole acetic acid (IAA) followed by siderophore (52.23%), phosphate solubilization (37.31%), and antibiotic (11.93%). 91.04% of the studied isolates produced ammonia whereas 28.35% produced organic acid. Extracellular enzyme activities of lipase, amylase, chitinase, and cellulase were detected among 95.52%, 61.11%, 35.82%, and 41.79% isolates, respectively. Based on these activities, 73 fungal isolates were categorized into different biotypes. Quantitative analysis of IAA production and phosphate solubilization was carried out for Aspergillus, Penicillium, and Rhizopus isolates. Aspergillus isolates exhibited varying activities of IAA production and phosphate solubilization. Most of the Aspergillus isolates and some other fungi demonstrated multiple activities. Based on the multiple traits of selected fungal isolates, Aspergillus sp-07, Penicillium sp-03, and Rhizopus sp-02 were further evaluated in different combinations for their inoculation effect on the growth and yield of wheat under field conditions.

Conclusions

The results indicated that these isolates could be developed into bio-inoculants to enhance plant growth. The consortium of these three isolates was also found to be compatible and beneficial for plant growth.

Characterization of Bacterial and Fungal Communities Reveals Novel Consortia in Tropical Oligotrophic Peatlands

Despite their importance for global biogeochemical cycles and carbon sequestration, the microbiome of tropical peatlands remains under-determined. Microbial interactions within peatlands can regulate greenhouse gas production, organic matter turnover, and nutrient cycling. Here we analyze bacterial and fungal communities along a steep P gradient in a tropical peat dome and investigate community level traits and network analyses to better understand the composition and potential interactions of microorganisms in these understudied systems and their relationship to peatland biogeochemistry. We found that both bacterial and fungal community compositions were significantly different along the P gradient, and that the low-P bog plain was characterized by distinct fungal and bacterial families. At low P, the dominant fungal families were cosmopolitan parasites and endophytes, including Clavicipitaceae (19%) in shallow soils (0-4 cm), Hypocreaceae (50%) in intermediate-depth soils (4-8 cm), and Chaetothyriaceae (45%) in deep soils (24-30 cm). In contrast, high- and intermediate-P sites were dominated by saprotrophic families at all depths. Bacterial communities were consistently dominated by the acidophilic Koribacteraceae family, with the exception of the low-P bog site, which was dominated by Acetobacteraceae (19%) and Syntrophaceae (11%). These two families, as well as Rhodospirillaceae, Syntrophobacteraceae, Syntrophorhabdaceae, Spirochaetaceae, and Methylococcaceae appeared within low-P bacterial networks, suggesting the presence of a syntrophic-methanogenic consortium in these soils. Further investigation into the active microbial communities at these sites, when paired with CH₄ and CO₂ gas exchange, and the quantification of metabolic intermediates will validate these potential interactions and provide insight into microbially driven biogeochemical cycling within these globally important tropical peatlands.

Flooding variations affect soil bacterial communities at the spatial and inter-annual scales

Hydrological variations have substantial effects on the diversity and composition of soil bacterial communities in wetlands. At the spatial scale, the responses of soil bacterial diversity and composition to hydrological variations in wetlands have been extensively investigated. However, at the temporal scale, especially at the inter-annual scale, the corresponding bacterial responses are rarely reported. Therefore, we explored the effects of flooding variations on the diversity and composition of soil bacterial communities at a lakeshore wetland in two hydrological contrasting years. Three flooding variables, i.e. flooding duration (FD), total duration of the growing season (TGD), and exposure duration of the growing season (EGD), were used to characterize flooding regime. Soil bacterial communities were determined using 16S rRNA gene sequencing method. We found a very high soil bacterial diversity at the lakeshore wetland. The Shannon's indexes of soil bacterial communities varied from 5.61 to 7.11 in two years. Soil bacterial α-diversity followed a unimodal curve along the elevation gradient, and was significantly lower in the flooding year than in the drought year. Principal coordinate analysis demonstrated that the compositions of soil bacterial communities were separated in order of elevation and year along the first and second axes, respectively. The apparent habitat preferences of soil bacterial families were closely connected with their respiratory traits, and this trend was stronger at the inter-annual scale than at the spatial scale. Soil bacterial compositions were predominantly determined by the direct (by changing respiratory traits) and indirect (by changing soil pH) effects of TGD at the spatial scale, while they were simultaneously regulated by the direct effects of three flooding variables at the inter-annual scale. Our results enhance the understanding of soil microbial communities in wetlands and have large implications for developing general theories to predicting soil microbial functions.

Trees as net sinks for methane (CH4 ) and nitrous oxide (N2 O) in the lowland tropical rain forest on volcanic Réunion Island

Trees are known to emit methane (CH₄ ) and nitrous oxide (N₂ O), with tropical wetland trees being considerable CH₄ sources. Little is known about CH₄ and especially N₂ O exchange of trees growing in tropical rain forests under nonflooded conditions. We determined CH₄ and N₂ O exchange of stems of six dominant tree species, cryptogamic stem covers, soils and volcanic surfaces at the start of the rainy season in a 400-yr-old tropical lowland rain forest situated on a basaltic lava flow (Réunion Island). We aimed to understand the unknown role in greenhouse gas fluxes of these atypical tropical rain forests on basaltic lava flows. The stems studied were net sinks for atmospheric CH₄ and N₂ O, as were cryptogams, which seemed to be co-responsible for the stem uptake. In contrast with more commonly studied rain forests, the soil and previously unexplored volcanic surfaces consumed CH₄ . Their N₂ O fluxes were negligible. Greenhouse gas uptake potential by trees and cryptogams constitutes a novel and unique finding, thus showing that plants can serve not only as emitters, but also as consumers of CH₄ and N₂ O. The volcanic tropical lowland rain forest appears to be an important CH₄ sink, as well as a possible N₂ O sink.

Depression of soil nitrogen fixation by drying soil in a degraded alpine peatland

Soil biological nitrogen fixation (BNF) represents a major pathway through which nitrogen enters pristine peatlands. Many peatlands have been undergoing human-induced changes in environmental factors, while environmental changes dramatically affect the community composition and activity of nitrogen-fixing prokaryotes (i.e., diazotrophs). However, the impact of peatland degradation on soil BNF remains unclear. By carrying out a field campaign, we examined how soil BNF varies along a natural gradient from pristine marshes to moderately-degraded meadows and sandy meadows on the Zoige Plateau. Plant and topsoil samples from four pristine marshes, three moderately-degraded meadows, and three sandy meadows were collected to determine the potential rate of nitrogen fixation (R_Nfix), abundance of the nifH gene, diazotrophic community composition, and soil and plant characteristics. Our results showed that topsoil R_Nfix varied in the range 0.018-3.00 μmol N g d.w.^-1 day^-1 (i.e. 21.74-1632.37 mg N m^-2 day^-1) across the ten sites, being lowest in sandy meadows and highest in pristine marshes. Topsoil R_Nfix and diazotrophic abundance were positively correlated with soil water content, sedge cover, plant biomass, soil organic carbon content, and total nitrogen and phosphorus contents. Soil water content, which affected most plant and soil characteristics, had dominant influences on the abundance and community structure of diazotrophs. The R_Nfix was closely correlated with the abundance of dominant diazotroph groups. The community composition of diazotrophs differed markedly among sites of different degradation levels. Proteobacteria was the most abundant diazotrophic phylum across the ten sites. Heterotrophic diazotrophs acted as the major contributor to BNF, especially in pristine marshes and moderately-degraded meadows. We conclude that soil water content was the main factor driving the depressed soil BNF during peatland degradation in Zoige, due to soil water effects on plant cover and biomass, soil organic carbon and total phosphorus, and the abundance and community structure of diazotrophs.

Soil Bacterial and Archaeal Communities and Their Potential to Perform N-Cycling Processes in Soils of Boreal Forests Growing on Well-Drained Peat

Peatlands are unique wetland ecosystems that cover approximately 3% of the world’s land area and are mostly located in boreal and temperate regions. Around 15 Mha of these peatlands have been drained for forestry during the last century. This study investigated soil archaeal and bacterial community structure and abundance, as well as the abundance of marker genes of nitrogen transformation processes (nitrogen fixation, nitrification, denitrification, and dissimilatory nitrate reduction to ammonia) across distance gradients from drainage ditches in nine full-drained, middle-aged peatland forests dominated by Scots pine, Norway spruce, or Downy birch. The dominating tree species had a strong effect on the chemical properties (pH, N and C/N status) of initially similar Histosols and affected the bacterial and archaeal community structure and abundance of microbial groups involved in the soil nitrogen cycle. The pine forests were distinguished by having the lowest fine root biomass of trees, pH, and N content and the highest potential for N fixation. The distance from drainage ditches affected the spatial distribution of bacterial and archaeal communities (especially N-fixers, nitrifiers, and denitrifiers possessing nosZ clade II), but this effect was often dependent on the conditions created by the dominance of certain tree species. The composition of the nitrifying microbial community was dependent on the soil pH, and comammox bacteria contributed significantly to nitrate formation in the birch and spruce soils where the pH was higher than 4.6. The highest N₂O emission was recorded from soils with higher bacterial and archaeal phylogenetic diversity such as birch forest soils. This study demonstrates that the long-term growth of forests dominated by birch, pine, and spruce on initially similar organic soil has resulted in tree-species-specific changes in the soil properties and the development of forest-type-specific soil prokaryotic communities with characteristic functional properties and relationships within microbial communities.

Effect of Cathode Material and Its Size on the Abundance of Nitrogen Removal Functional Genes in Microcosms of Integrated Bioelectrochemical-Wetland Systems

Constructed wetland-microbial electrochemical snorkel (CW-MES) systems, which are short-circuited microbial fuel cells (MFC), have emerged as a novel tool for wastewater management, although the system mechanisms are insufficiently studied in process-based or environmental contexts. Based on quantitative polymerase chain reaction assays, we assessed the prevalence of different nitrogen removal processes for treating nitrate-rich waters with varying cathode materials (stainless steel, graphite felt, and copper) and sizes in the CW-MES systems and correlated them to the changes of N2O emissions. The nitrate and nitrite removal efficiencies were in range of 40% to 75% and over 98%, respectively. In response to the electrochemical manipulation, the abundances of most of the nitrogen-transforming microbial groups decreased in general. Graphite felt cathodes supported nitrifiers, but nirK-type denitrifiers were inhibited. Anaerobic ammonium oxidation (ANAMMOX) bacteria were less abundant in the electrochemically manipulated treatments compared to the controls. ANAMMOX and denitrification are the main nitrogen reducers in CW-MES systems. The treatments with 1:1 graphite felt, copper, plastic, and stainless-steel cathodes showed higher N2O emissions. nirS- and nosZI-type denitrifiers are mainly responsible for producing and reducing N2O emissions, respectively. Hence, electrochemical manipulation supported dissimilatory nitrate reduction to ammonium (DNRA) microbes may play a crucial role in producing N2O in CW-MES systems.

Duration and frequency of drainage and flooding events interactively affect soil biogeochemistry and N flux in subtropical peat soils

With the demand for restoration and future prediction of climate change effects, subtropical peatlands are expected to be subjected to hydrologic regimes with variable duration and frequency of drained and flooded conditions, but knowledge of their interactive effects on soil biogeochemistry and emission of greenhouse gases including nitrous oxide (N₂O) is largely limited. The objective of this study was to investigate how the duration and frequency of drainage and flooding events interactively influence soil biogeochemical properties and denitrification and related net N₂O production rates following rewetting. Surface soils are susceptible to different hydrologic regimes. Significantly higher pH, extractable organic carbon (ext. OC), ammonium (NH₄⁺-N), denitrification enzyme activity (DEA), but lower nitrate (NO₃^--N), microbial biomass C and N were observed when the peat soils were under flooded conditions compared to drained conditions. Two-week and four-week drainage or flooding duration did not result in statistically significant differences in soil biogeochemical properties. A 24-week prolonged drainage led to an accumulation of NO₃^--N and a significantly lower pH. Soil microbial biomass and fungal:bacterial abundance likely increased with the frequency of drainage-flooding cycles. Significant differences in denitrification and net N₂O production rates following reflooding were mainly found in the surface soils. Structural equation modeling indicated that hydroperiod and water-filled pore space (WFPS) prior to reflooding is likely to control denitrification and net N₂O production through its regulation of NO₃^--N and activity of microorganisms involved in denitrification while higher drainage-flooding frequency decreases the availability of organic C and NO₃^--N for denitrification. Our results also suggest high NO₃^--N and low pH within peat soils caused by prolonged drainage likely leads to a significant N₂O emission pulse following reflooding. For peat soils subjected to frequent drainage-flooding cycles, N₂O emission pulses following reflooding would decrease with time, attributing to the loss of substrates for denitrification.

Microbial community composition across a coastal hydrological system affected by submarine groundwater discharge (SGD)

Mobile Bay, the fourth largest estuary in the USA located in the northern Gulf of Mexico, is known for extreme hypoxia in the water column during dry season caused by NH4+-rich and anoxic submarine groundwater discharge (SGD). Nutrient dynamics in the coastal ecosystem point to potentially elevated microbial activities; however, little is known about microbial community composition and their functional roles in this area. In this study, we investigated microbial community composition, distribution, and metabolic prediction along the coastal hydrological compartment of Mobile Bay using 16S rRNA gene sequencing. We collected microbial samples from surface (river and bay water) and subsurface water (groundwater and coastal pore water from two SGD sites with peat and sandy lithology, respectively). Salinity was identified as the primary factor affecting the distribution of microbial communities across surface water samples, while DON and PO43- were the major predictor of community shift within subsurface water samples. Higher microbial diversity was found in coastal pore water in comparison to surface water samples. Gammaproteobacteria, Bacteroidia, and Oxyphotobacteria dominated the bacterial community. Among the archaea, methanogens were prevalent in the peat-dominated SGD site, while the sandy SGD site was characterized by a higher proportion of ammonia-oxidizing archaea. Cyanobium PCC-6307 and unclassified Thermodesulfovibrionia were identified as dominant taxa strongly associated with trends in environmental parameters in surface and subsurface samples, respectively. Microbial communities found in the groundwater and peat layer consisted of taxa known for denitrification and dissimilatory nitrate reduction to ammonium (DNRA). This finding suggested that microbial communities might also play a significant role in mediating nitrogen transformation in the SGD flow path and in affecting the chemical composition of SGD discharging to the water column. Given the ecological importance of microorganisms, further studies at higher taxonomic and functional resolution are needed to accurately predict chemical biotransformation processes along the coastal hydrological continuum, which influence water quality and environmental condition in Mobile Bay.

Methanogens and Methanotrophs Show Nutrient-Dependent Community Assemblage Patterns Across Tropical Peatlands of the Pastaza-Marañón Basin, Peruvian Amazonia

Tropical peatlands are globally important carbon reservoirs that play a crucial role in fluxes of atmospheric greenhouse gases. Amazon peatlands are expected to be large source of atmospheric methane (CH₄) emissions, however little is understood about the rates of CH₄ flux or the microorganisms that mediate it in these environments. Here we studied a mineral nutrient gradient across peatlands in the Pastaza-Marañón Basin, the largest tropical peatland in South America, to describe CH₄ fluxes and environmental factors that regulate species assemblages of methanogenic and methanotrophic microorganisms. Peatlands were grouped as minerotrophic, mixed and ombrotrophic categories by their general water source leading to different mineral nutrient content (rich, mixed and poor) quantified by trace elements abundance. Microbial communities clustered dependent on nutrient content (ANOSIM p < 0.001). Higher CH₄ flux was associated with minerotrophic communities compared to the other categories. The most dominant methanogens and methanotrophs were represented by Methanobacteriaceae, and Methylocystaceae, respectively. Weighted network analysis demonstrated tight clustering of most methanogen families with minerotrophic-associated microbial families. Populations of Methylocystaceae were present across all peatlands. Null model testing for species assemblage patterns and species rank distributions confirmed non-random aggregations of Methylococcacae methanotroph and methanogen families (p < 0.05). We conclude that in studied amazon peatlands increasing mineral nutrient content provides favorable habitats for Methanobacteriaceae, while Methylocystaceae populations seem to broadly distribute independent of nutrient content.

Aeromonas hydrophila, Bacillus thuringiensis, Escherichia coli and Pseudomonas aeruginosa utilization of Ammonium-N, Nitrate-N and Urea-N in culture

Agricultural drainage ditches represent a major source of nutrient pollution. Shifts in nitrogen source and use of animal manures have changed the bacterial composition both in species of bacteria and their abundance in agricultural ditches. This change affects how nitrogen is being cycled and potentially the final forms of available nutrients. In particular, animal manures often have bacteria such as Escherichia coli present, increasing the abundance of a bacterial species in ditches. Research has shown that the effect of different nitrogen sources is to change bacterial community composition (class, family). How this influences the role of an individual bacterial species is poorly understood. Thus, our question was how individual species would respond to different sources of nitrogen. We used Aeromonas hydrophila, Bacillus thuringiensis, Escherichia coli and Pseudomonas aeruginosa that are common in agricultural ditches and exposed them to different concentrations of nitrogen in cultures of 1 × 10⁰ and 1 × 10⁻¹ dilutions from a stock solution of bacteria. Nitrogen sources were ammonium chloride, sodium nitrate and urea. The results showed A. hydrophila and E. coli have strong similarities particularly with nitrate-N and urea-N utilization and the response was often correlated with the amount of nutrient added. P. aeruginosa while similar did not show any strong correlation with amount of nutrient added. B. thuringiensis was different from the other three bacteria in utilization or production. Research has provided insight into the role of some bacteria in nitrogen cycling and may be valuable in the future to developing management strategies to reduce nutrients.

Characterization of Denitrifying Community for Application in Reducing Nitrogen: a Comparison of nirK and nirS Gene Diversity and Abundance

Studies have shown that the addition of biochar to agricultural soils has the potential to mitigate climate change by decreasing nitrous oxide (N₂O) emissions resulting from denitrification. Rice paddy field soils have been known to have strong denitrifying activity, but the response of microbes to biochar for weakening denitrification in rice paddy field soils is not well known. In this work, compared with the chemical fertilizer alone, the chemical fertilizer + 20 t hm^-2 biochar fertilizer slightly decreased denitrifying the nitrite reductase activity (S-NiR) and N₂O emission without statistic difference, whereas the chemical fertilizer + 40 t hm^-2 biochar significantly boosted them. The abundance of nir-denitrifiers contributed to S-NiR and N₂O emission, especially nirS-denitrifiers, rather than the variation of community structure. Pearson correlation analysis showed that NO₂^--N was a key factor for controlling the abundance of nir-denitrifiers, S-NiR and N₂O emission. The biochar addition fertilization treatments strongly shaped the community structure of nirK-denitrifiers, while the community structure of nirS-denitrifiers remained relatively stable. In addition, Paracoccus and Sinorhizobium were revealed to be as the predominant lineage of nirS- and nirK-containing denitrifiers, respectively. Distance-based redundancy analysis (db-RDA) showed that changes in the nir-denitrifier community structure were significantly related to soil organic carbon, NO₃^--N, and total phosphorus. Our findings suggest that, although the nirS- and nirK-denitrifiers are both controlling nitrite reductase, their responses to biochar addition fertilization treatments showed significant discrepancies of diversity, abundance, and contribution to N₂O and S-NiR in a paddy soil.

Under the Christmas Tree: Belowground Bacterial Associations With Abies nordmanniana Across Production Systems and Plant Development

Abies nordmanniana is an economically important tree crop widely used for Christmas tree production. After initial growth in nurseries, seedlings are transplanted to the field. Rhizosphere bacterial communities generally impact the growth and health of the host plant. However, the dynamics of these communities during A. nordmanniana growth in nurseries, and during transplanting, has not previously been addressed. By a 16S rRNA gene amplicon sequencing approach, we characterized the composition and dynamics of bacterial communities in the rhizosphere during early plant growth in field and greenhouse nurseries and for plants transplanted from the greenhouse to the field. Moreover, the N-cycling potential of rhizosphere bacteria across plant age was addressed in both nurseries. Overall, a rhizosphere core microbiome of A. nordmanniana, comprising 19.9% of the taxa at genus level, was maintained across plant age, nursery production systems, and even during the transplantation of plants from the greenhouse to the field. The core microbiome included the bacterial genera Bradyrhizobium, Burkholderia, Flavobacterium, Pseudomonas, Rhizobium, Rhodanobacter, and Sphingomonas, which harbor several N-fixing and plant growth–promoting taxa. Nevertheless, both plant age and production system caused significant changes in the rhizosphere bacterial communities. Concerning community composition, the relative abundance of Rhizobiales (genera Rhizobium, Bradyrhizobium, and Devosia) was higher in the rhizosphere of field-grown A. nordmanniana, whereas the relative abundance of Enterobacteriales and Pseudomonadales (genus Pseudomonas) was higher in the greenhouse. Analysis of community dynamics across plant age showed that in the field nursery, the most abundant bacterial orders showed more dynamic changes in their relative abundance in the rhizosphere than in the bulk soil. In the greenhouse, age-dependent dynamics even occurred but affected different taxa than for the field-grown plants. The N-cycling potential of rhizosphere bacterial communities showed an increase of the relative abundance of genes involved in nitrogen fixation and denitrification by plant age. Similarly, the relative abundance of reported nitrogen-fixing or denitrifying bacteria increased by plant age. However, different community structures seemed to lead to an increased potential for nitrogen fixation and denitrification in the field versus greenhouse nurseries.

Characterization of a nifH-Harboring Bacterial Community in the Soil-Limited Gotjawal Forest

Using a high-throughput metagenomic approach, we evaluated nifH-harboring bacterial communities and their assembly in the Gotjawal forest, which was naturally formed on basalt rocks with thin layer of soil. Significant differences in soil properties and community structure were observed in comparison with similar communities in various habitats, including other lava-formed forests (on Jeju Island and in Hawaii) and in regions with high humidity (Florida) or low temperatures (Alaska). nifH-harboring bacterial communities were found to assemble along gradients of environmental factors, particularly cation-exchange capacity. Unlike in other regions, in the Gotjawal forest, Paenibacillus and Clostridium, which belong to the phylum Firmicutes, were present in significantly higher proportion than in other regions. Network analysis suggested that much fewer co-occurrence relationships occurred in the Gotjawal forest than in other lava-formed forests. Our results indicate that the unique nifH-harboring bacterial community and its assembly in the Gotjawal forest are due to its distinctive soil properties, which has implications for microbial interactions and functional potentials.

Ecological and physiological implications of nitrogen oxide reduction pathways on greenhouse gas emissions in agroecosystems

Microbial reductive pathways of nitrogen (N) oxides are highly relevant to net emissions of greenhouse gases (GHG) from agroecosystems. Several biotic and abiotic N-oxide reductive pathways influence the N budget and net GHG production in soil. This review summarizes the recent findings of N-oxide reduction pathways and their implications to GHG emissions in agroecosystems and proposes several mitigation strategies. Denitrification is the primary N-oxide reductive pathway that results in direct N2O emissions and fixed N losses, which add to the net carbon footprint. We highlight how dissimilatory nitrate reduction to ammonium (DNRA), an alternative N-oxide reduction pathway, may be used to reduce N2O production and N losses via denitrification. Implications of nosZ abundance and diversity and expressed N2O reductase activity to soil N2O emissions are reviewed with focus on the role of the N2O-reducers as an important N2O sink. Non-prokaryotic N2O sources, e.g. fungal denitrification, codenitrification and chemodenitrification, are also summarized to emphasize their potential significance as modulators of soil N2O emissions. Through the extensive review of these recent scientific advancements, this study posits opportunities for GHG mitigation through manipulation of microbial N-oxide reductive pathways in soil.

Short-Term Response of the Soil Microbial Abundances and Enzyme Activities to Experimental Warming in a Boreal Peatland in Northeast China

Global warming is likely to influence the soil microorganisms and enzyme activity and alter the carbon and nitrogen balance of peatland ecosystems. To investigate the difference in sensitivities of carbon and nitrogen cycling microorganisms and enzyme activity to warming, we conducted three-year warming experiments in a boreal peatland. Our findings demonstrated that both mcrA and nirS gene abundance in shallow soil and deep soil exhibited insensitivity to warming, while shallow soil archaea 16S rRNA gene and amoA gene abundance in both shallow soil and deep soil increased under warming. Soil pmoA gene abundance of both layers, bacterial 16S rRNA gene abundance in shallow soil, and nirK gene abundance in deep soil decreased due to warming. The decreases of these gene abundances would be a result of losing labile substrates because of the competitive interactions between aboveground plants and underground soil microorganisms. Experimental warming inhibited β-glucosidase activity in two soil layers and invertase activity in deep soil, while it stimulated acid phosphatase activity in shallow soil. Both temperature and labile substrates regulate the responses of soil microbial abundances and enzyme activities to warming and affect the coupling relationships of carbon and nitrogen. This study provides a potential microbial mechanism controlling carbon and nitrogen cycling in peatland under climate warming.