Coupling Between and Among Ammonia Oxidizers and Nitrite Oxidizers in Grassland Mesocosms Submitted to Elevated CO2 and Nitrogen Supply

Niche Differentiation Among Canonical Nitrifiers and N2O Reducers Is Linked to Varying Effects of Nitrification Inhibitors DCD and DMPP in Two Arable Soils

The efficacy of nitrification inhibitors (NIs) dicyandiamide (DCD) and 3,4-dimethylpyrazole phosphate (DMPP) varies with soil types. Understanding the microbial mechanisms for this variation may lead to better modelling of NI efficacy and therefore on-farm adoption. This study addressed the response patterns of mineral nitrogen, nitrous oxide (N₂O) emission, abundances of N-cycling functional guilds and soil microbiota characteristics, in relation to urea application with or without DCD or DMPP in two arable soils (an alkaline and an acid soil). The inhibition of nitrification rate and N₂O emission by NI application occurred by suppressing ammonia-oxidizing bacteria (AOB) abundances and increasing the abundances of nosZI-N₂O reducers; however, abundances of ammonia-oxidizing archaea (AOA) were also stimulated with NIs-added in these two arable soils. DMPP generally had stronger inhibition efficiency than DCD, and both NIs' addition decreased Nitrobacter, while increased Nitrospira abundance only in alkaline soil. N₂O emissions were positively correlated with AOB and negatively correlated with nosZI in both soils and AOA only in acid soil. Moreover, N₂O emissions were also positively correlated with nirK-type denitrifiers in alkaline soil, and clade A comammox in acid soil. Amendment with DCD or DMPP altered soil microbiota community structure, but had minor effect on community composition. These results highlight a crucial role of the niche differentiation among canonical ammonia oxidizers (AOA/AOB), Nitrobacter and Nitrospira, as well as nosZI- and nosZII-N₂O reducers in determining the varying efficacies of DCD and DMPP in different arable soils.

Elevated atmospheric CO2 concentrations caused a shift of the metabolically active microbiome in vineyard soil

BACKGROUND

Elevated carbon dioxide concentrations (eCO₂), one of the main causes of climate change, have several consequences for both vine and cover crops in vineyards and potentially also for the soil microbiome. Hence soil samples were taken from a vineyard free-air CO₂ enrichment (VineyardFACE) study in Geisenheim and examined for possible changes in the soil active bacterial composition (cDNA of 16S rRNA) using a metabarcoding approach. Soil samples were taken from the areas between the rows of vines with and without cover cropping from plots exposed to either eCO₂ or ambient CO₂ (aCO₂).

RESULTS

Diversity indices and redundancy analysis (RDA) demonstrated that eCO₂ changed the active soil bacterial diversity in grapevine soil with cover crops (p-value 0.007). In contrast, the bacterial composition in bare soil was unaffected. In addition, the microbial soil respiration (p-values 0.04-0.003) and the ammonium concentration (p-value 0.003) were significantly different in the samples where cover crops were present and exposed to eCO₂. Moreover, under eCO₂ conditions, qPCR results showed a significant decrease in 16S rRNA copy numbers and transcripts for enzymes involved in N₂ fixation and NO₂^- reduction were observed using qPCR. Co-occurrence analysis revealed a shift in the number, strength, and patterns of microbial interactions under eCO₂ conditions, mainly represented by a reduction in the number of interacting ASVs and the number of interactions.

CONCLUSIONS

The results of this study demonstrate that eCO₂ concentrations changed the active soil bacterial composition, which could have future influence on both soil properties and wine quality.

Soil metatranscriptome demonstrates a shift in C, N, and S metabolisms of a grassland ecosystem in response to elevated atmospheric CO2

Soil organisms play an important role in the equilibrium and cycling of nutrients. Because elevated CO₂ (eCO₂) affects plant metabolism, including rhizodeposition, it directly impacts the soil microbiome and microbial processes. Therefore, eCO₂ directly influences the cycling of different elements in terrestrial ecosystems. Hence, possible changes in the cycles of carbon (C), nitrogen (N), and sulfur (S) were analyzed, alongside the assessment of changes in the composition and structure of the soil microbiome through a functional metatranscriptomics approach (cDNA from mRNA) from soil samples taken at the Giessen free-air CO₂ enrichment (Gi-FACE) experiment. Results showed changes in the expression of C cycle genes under eCO₂ with an increase in the transcript abundance for carbohydrate and amino acid uptake, and degradation, alongside an increase in the transcript abundance for cellulose, chitin, and lignin degradation and prokaryotic carbon fixation. In addition, N cycle changes included a decrease in the transcript abundance of N₂O reductase, involved in the last step of the denitrification process, which explains the increase of N₂O emissions in the Gi-FACE. Also, a shift in nitrate (NO3-) metabolism occurred, with an increase in transcript abundance for the dissimilatory NO3- reduction to ammonium (NH4+) (DNRA) pathway. S metabolism showed increased transcripts for sulfate (SO42-) assimilation under eCO₂ conditions. Furthermore, soil bacteriome, mycobiome, and virome significantly differed between ambient and elevated CO₂ conditions. The results exhibited the effects of eCO₂ on the transcript abundance of C, N, and S cycles, and the soil microbiome. This finding showed a direct connection between eCO₂ and the increased greenhouse gas emission, as well as the importance of soil nutrient availability to maintain the balance of soil ecosystems.

Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity

BACKGROUND

Anthropogenic activities have increased the inputs of atmospheric reactive nitrogen (N) into terrestrial ecosystems, affecting soil carbon stability and microbial communities. Previous studies have primarily examined the effects of nitrogen deposition on microbial taxonomy, enzymatic activities, and functional processes. Here, we examined various functional traits of soil microbial communities and how these traits are interrelated in a Mediterranean-type grassland administrated with 14 years of 7 g m^-2 year^-1 of N amendment, based on estimated atmospheric N deposition in areas within California, USA, by the end of the twenty-first century.

RESULTS

Soil microbial communities were significantly altered by N deposition. Consistent with higher aboveground plant biomass and litter, fast-growing bacteria, assessed by abundance-weighted average rRNA operon copy number, were favored in N deposited soils. The relative abundances of genes associated with labile carbon (C) degradation (e.g., amyA and cda) were also increased. In contrast, the relative abundances of functional genes associated with the degradation of more recalcitrant C (e.g., mannanase and chitinase) were either unchanged or decreased. Compared with the ambient control, N deposition significantly reduced network complexity, such as average degree and connectedness. The network for N deposited samples contained only genes associated with C degradation, suggesting that C degradation genes became more intensely connected under N deposition.

CONCLUSIONS

We propose a conceptual model to summarize the mechanisms of how changes in above- and belowground ecosystems by long-term N deposition collectively lead to more soil C accumulation. Video Abstract.

The Deterioration of Agronomical Traits of the Continuous Cropping of Stevia Is Associated With the Dynamics of Soil Bacterial Community

Stevia rebaudiana Bertoni is grown worldwide as an important, natural sweetener resource plant. The yield of steviol glycosides (SVglys) is greatly influenced by continuous cropping. In this study, we collected the roots, rhizosphere soils, and bulk soils from 2 years of continuous cropping (Y2) and 8 years of continuous cropping (Y8). A high-throughput sequencing technology based on Illumina Hiseq 2500 platform was used to study the structure and diversity of bacterial communities in the roots and soils of stevia with different years of continuous cropping. The results demonstrated that although the content of a group of SVglys was significantly increased in stevia of long-term continuous cropping, it inhibited the growth of plants and lowered the leaf dry weight; as a result, the total amount of SVglys was significantly decreased. Meanwhile, continuous cropping changed the physicochemical properties and the bacterial composition communities of soil. The different sampling sources of the root, rhizosphere soil, and bulk soil had no impact on the richness of bacterial communities, while it exhibited obvious effects on the diversity of bacterial communities. Continuous cropping had a stronger effect on the bacterial community composition in rhizosphere soil than in root and bulk soil. Based on linear discriminant analysis effect size (LEfSe), in the rhizosphere soil of Y8, the relative abundance of some beneficial bacterial genera of Sphingomonas, Devosia, Streptomyces, and Flavobacterium decreased significantly, while the relative abundance of Polycyclovorans, Haliangium, and Nitrospira greatly increased. Moreover, the soil pH and nutrient content, especially the soil organic matter, were correlated with the relative abundance of predominant bacteria at the genus level. This study provides a theoretical basis for uncovering the mechanism of obstacles in continuous stevia cropping and provides guidance for the sustainable development of stevia.

A scoping review on biochar-based fertilizers: enrichment techniques and agro-environmental application

Biochar is a carbonized biomass that can be used as a soil amendment. However, the exclusive use of biochar may present some limitations, such as the lack of nutrients. Thus, biochar enrichment techniques have made it possible to obtain biochar-based fertilizers (BCFs), with great potential to improve soil fertility. Nevertheless, there is still a lack of information about the description, advantages, and limitations of the methods used for biochar enrichment. This review provides a comprehensive overview of the production methods of enriched biochar and its performance in agriculture as a soil amendment. Studies demonstrate that the application of BCF is more effective in improving soil properties and crop yields than the exclusive application of pure biochar or other fertilizers. The post-pyrolysis method is the most used technique for enriching biochar. Future studies should focus on understanding the mechanisms of the long-term application of BCFs.

Combined analysis of microbial community and microbial metabolites based on untargeted metabolomics during pig manure composting

Compost has been widely used in agriculture in recent years, but the nutrients it provides are far from enough for plant growth. Therefore, it is necessary to systematically explore the fermentation process of composting. In this study, the succession of microbial community and metabolite characteristics in compost were analyzed by using microbial sequencing and metabolomics techniques. The results showed that compared with mesophilic phase and cooling phase, the richness and diversity of bacterial community decreased in thermophilic phase. At the genus level, Pseudomonas (8.90%), Lactobacillus (3.99%), Bacteroidetes (3.39%), Flavobacterium (3.25%) and Prevotella (Prevotella_9, 2.33%, Prevotellaceae_NK3B31_group, 2.44%) were the dominant genera in the pig manure composting. The abundance of Pseudomonas and Flavobacterium increased significantly while Lactobacillus and Prevotella were significantly decreased after composting, and the abundance of Bacteroidetes increased first and then decreased. Fatty acyls, sterol lipids, glycerophospholipids, polyketides and prenol lipids were common microbial metabolites in compost. Moreover, the linoleic acid metabolic pathway was significantly enriched in the three stages of composting, and linoleic acid metabolism might be the primary function of the microbial community in composting. The network analysis showed that between the microbial communities or between the microbial community and metabolites were closely related to each other.

Effects of reducing chemical fertilizer combined with organic amendments on ammonia-oxidizing bacteria and archaea communities in a low-fertility red paddy field

Ammonia oxidation process in soil has a great contribution to the emission of nitrous oxide, which is a hot issue in the study of N cycle of rice field ecosystem. Organic amendments which partially substitute chemical nitrogen fertilizer are widely adopted to optimizing N management and reduce the use of chemical nitrogen fertilizers in the paddy ecosystem, but their long-term effects on ammonia-oxidizing archaea (AOA) and bacteria (AOB) were not well understood. Thus, based on a 6-year field trial that comprised four fertilization strategies (CF, chemical fertilizer; PM, pig manure substituting for 20% chemical N; BF, biogas slurry substituting for 20% chemical N; and GM, milk vetch substituting for 20% chemical N) and no N fertilizer application as CK, the abundance and community structure of ammonia oxidizers were examined by using qPCR and Illumina Miseq sequencing approaches based on the functional marker genes (amoA) in a low-fertility paddy field. The results revealed that 6 years of organic-substitute fertilization significantly increased AOA abundance in comparison with NF and CF. However, only CF and PM had a higher AOB abundance than those in NF and no significant difference between CF and organic-substitute treatments was observed. Both AOA and AOB were significantly correlated with soil potential nitrification rate (PNR). Moreover, organic-substitute treatments showed the evident changes in the AOA community, while little were observed in the AOB community. Soil pH was the main predictor for AOA abundance, while NH₄⁺-N and NO₃^--N were the main predictors for AOB abundance. This study suggests that both AOA and AOB were jointly contributed to the variation of soil potential nitrification rate, while the AOA community was shown to be more responsive to organic-substitute fertilization strategies than AOB in the tested soils.

Effects of biochar-based controlled release nitrogen fertilizer on nitrogen-use efficiency of oilseed rape (Brassica napus L.)

Biochar-based controlled release nitrogen fertilizers (BCRNFs) have received increasing attention due to their ability to improve nitrogen-use efficiency (NUE) and increase crop yields. We previously developed a novel BCRNF, but its effects on soil microbes, NUE, and crop yields have not been reported. Therefore, we designed a pot experiment with five randomised treatments: CK (without urea and biochar), B (addition biochar without urea), B + U (biochar mixed urea), Urea (addition urea without biochar), and BCRNF (addition BCRNF), to investigate the effects of BCRNF on nitrifiers and denitrifiers, and how these impact nitrogen supply and NUE. Results of high-throughput sequencing revealed bacterial community groups with higher nutrient metabolic cycling ability under BCRNF treatment during harvest stage. Compared to Urea treatment, BCRNF treatment stimulated nitrification by increasing the copy number of the bacterial amoA gene and reducing nitrous oxide emission by limiting the abundance of nirS and nirK. Eventually, BCRNF successfully enhanced the yield (~ 16.6%) and NUE (~ 58.79%) of rape by slowly releasing N and modulating the abundance of functional microbes through increased soil nitrification and reduced denitrification, as compared with Urea treatment. BCRNF significantly improved soil NO₃⁻, leading to an increase in N uptake by rape and NUE, thereby promoting rape growth and increasing grain yield.

Heavy nitrogen application increases soil nitrification through ammonia-oxidizing bacteria rather than archaea in acidic tea (Camellia sinensis L.) plantation soil

Nitrogen (N) fertilizer is widely used in agricultural ecosystems and influences N transformation processes in the soil such as nitrification. However, whether nitrification is primarily dominated by ammonia-oxidizing bacteria (AOB) or archaea (AOA) under heavy N application is still under debate. In the present work, the effect of long-term (12 years) N fertilization on soil nitrification and the key influencing factors were investigated in acidic tea plantation soil that received four different rates of N application (0, 119, 285, and 569 kg N ha^-1 yr^-1). Nitrification potential was measured and partitioned using chemical inhibitors. The abundance of functional genes involved in ammonia oxidation was quantified using quantitative polymerase chain reaction (qPCR). Ammonia-oxidizing communities were identified by shotgun metagenome sequencing. Potential nitrification rate in tea plantation soil was mainly dominated by autotrophic nitrification (PNR_A) (71-79%). PNR_A and heterotrophic nitrification (PNR_H) were both significantly increased by heavy N (569 kg ha^-1) application. Moreover, PNR_A was mainly due to the contribution of AOB (52-66%) in N-treated soils, and N569 significantly increased the AOB contribution without affecting the AOA contribution. N569 increased the functional gene abundance of AOB and TAO100 (a non-halophilic γ-AOB) but decreased that of AOA. The dominant AOB (Nitrosomonas, Nitrosospira, and Nitrosococcus), AOA (Nitrososphaera and Nitrosopumilus) and commamox (Nitrospira) groups were profoundly altered by long-term N application rates. Partial least squares regression showed that total nitrification (PNR_T), PNR_A, and PNR_AOB were primarily explained by the functional gene abundance of nitrifiers whereas PNR_H and PNR_AOA were closely associated with soil and pruned litter properties. Moreover, structural equation modeling (SEM) revealed that long-term N application significantly and indirectly affected nitrification potential by directly influencing soil properties, pruned litter properties, and functional gene abundance. Understanding the relative contribution of AOA and AOB to nitrification may help to better regulate N fertilizer use in agricultural ecosystems.

Nitrogen fertilizer is a key factor affecting the soil chemical and microbial communities in a Mollisol

Microbial communities drive geochemical cycles in soils. Relatively few studies have assessed the long-term impacts of different types of soil amendments under field conditions in long-term experiments. The response of soil microbial organisms in a Mollisol cultivated with maize for 35 years was examined. Treatments involved the use of N, P, and K fertilizers and two doses of straw residue in isolation or combined. Real-time PCR and Illumina MiSeq sequencing methods were used to characterize the microbial community. The results showed that addition of nitrogen fertilizers decreased soil pH, but this was mitigated when a high dose of straw was also incorporated. Long-term application of inorganic fertilizers was able to alter the abundance of functional soil microbial population. Application of inorganic N fertilizer resulted in distinctive changes on N-cycle microorganisms. Phosphate-solubilizing functional genes abundance was lower in plots with no phosphate fertilizer. Sequencing analysis showed that the presence or absence of N in the fertilizer mix is a key factor affecting bacterial community diversity of agricultural soil, and pH, total organic C, and total N show a high correlation with bacterial community composition. Nitrogen addition increased the N concentration in the soil, which could cause changes in the soil pH and change the soil bacterial community. Our findings proved that interaction of N fertilizer with other fertilizers can affect microbial communities.

The DNRA-Denitrification Dichotomy Differentiates Nitrogen Transformation Pathways in Mountain Lake Benthic Habitats

Effects of nitrogen (N) deposition on microbially-driven processes in oligotrophic freshwater ecosystems are poorly understood. We quantified guilds in the main N-transformation pathways in benthic habitats of 11 mountain lakes along a dissolved inorganic nitrogen gradient. The genes involved in denitrification (nirS, nirK, nosZ), nitrification (archaeal and bacterial amoA), dissimilatory nitrate reduction to ammonium (DNRA, nrfA) and anaerobic ammonium oxidation (anammox, hdh) were quantified, and the bacterial 16S rRNA gene was sequenced. The dominant pathways and associated bacterial communities defined four main N-transforming clusters that differed across habitat types. DNRA dominated in the sediments, except in the upper layers of more productive lakes where nirS denitrifiers prevailed with potential N₂O release. Loss as N₂ was more likely in lithic biofilms, as indicated by the higher hdh and nosZ abundances. Archaeal ammonia oxidisers predominated in the isoetid rhizosphere and rocky littoral sediments, suggesting nitrifying hotspots. Overall, we observed a change in potential for reactive N recycling via DNRA to N losses via denitrification as lake productivity increases in oligotrophic mountain lakes. Thus, N deposition results in a shift in genetic potential from an internal N accumulation to an atmospheric release in the respective lake systems, with increased risk for N₂O emissions from productive lakes.

Long-term elevated CO2 shifts composition of soil microbial communities in a Californian annual grassland, reducing growth and N utilization potentials

The continuously increasing concentration of atmospheric CO₂ has considerably altered ecosystem functioning. However, few studies have examined the long-term (i.e. over a decade) effect of elevated CO₂ on soil microbial communities. Using 16S rRNA gene amplicons and a GeoChip microarray, we investigated soil microbial communities from a Californian annual grassland after 14 years of experimentally elevated CO₂ (275 ppm higher than ambient). Both taxonomic and functional gene compositions of the soil microbial community were modified by elevated CO₂. There was decrease in relative abundance for taxa with higher ribosomal RNA operon (rrn) copy number under elevated CO₂, which is a functional trait that responds positively to resource availability in culture. In contrast, taxa with lower rrn copy number were increased by elevated CO₂. As a consequence, the abundance-weighted average rrn copy number of significantly changed OTUs declined from 2.27 at ambient CO₂ to 2.01 at elevated CO₂. The nitrogen (N) fixation gene nifH and the ammonium-oxidizing gene amoA significantly decreased under elevated CO₂ by 12.6% and 6.1%, respectively. Concomitantly, nitrifying enzyme activity decreased by 48.3% under elevated CO₂, albeit this change was not significant. There was also a substantial but insignificant decrease in available soil N, with both nitrate (NO₃^-) (-27.4%) and ammonium (NH₄⁺) (-15.4%) declining. Further, a large number of microbial genes related to carbon (C) degradation were also affected by elevated CO₂, whereas those related to C fixation remained largely unchanged. The overall changes in microbial communities and soil N pools induced by long-term elevated CO₂ suggest constrained microbial N decomposition, thereby slowing the potential maximum growth rate of the microbial community.

Geospatial variation in co-occurrence networks of nitrifying microbial guilds

Microbial communities transform nitrogen (N) compounds, thereby regulating the availability of N in soil. The N cycle is defined by interacting microbial functional groups, as inorganic N‐products formed in one process are the substrate in one or several other processes. The nitrification pathway is often a two‐step process in which bacterial or archaeal communities oxidize ammonia to nitrite, and bacterial communities further oxidize nitrite to nitrate. Little is known about the significance of interactions between ammonia‐oxidizing bacteria (AOB) and archaea (AOA) and nitrite‐oxidizing bacterial communities (NOB) in determining the spatial variation of overall nitrifier community structure. We hypothesize that nonrandom associations exist between different AO and NOB lineages that, along with edaphic factors, shape field‐scale spatial patterns of nitrifying communities. To address this, we sequenced and quantified the abundance of AOA, AOB, and Nitrospira and Nitrobacter NOB communities across a 44‐hectare site with agricultural fields. The abundance of Nitrobacter communities was significantly associated only with AOB abundance, while that of Nitrospira was correlated to AOA. Network analysis and geostatistical modelling revealed distinct modules of co‐occurring AO and NOB groups occupying disparate areas, with each module dominated by different lineages and associated with different edaphic factors. Local communities were characterized by a high proportion of module‐connecting versus module‐hub nodes, indicating that nitrifier assemblages in these soils are shaped by fluctuating conditions. Overall, our results demonstrate the utility of network analysis in accounting for potential biotic interactions that define the niche space of nitrifying communities at scales compatible to soil management.

Succession of organics metabolic function of bacterial community in swine manure composting

Organics metabolic function of bacterial communities was evaluated in 60 days composting of swine manure and pumice by using MiSeq sequencing, PICRUSt and Biolog tools. The diversity of bacterial communities significantly decreased during the first 10 days, and gradually increased in the cooling and curing phase. The PICRUSt and Biolog analysis indicated that carbohydrate, lipid and amino acids metabolisms were relatively higher in the thermophilic phases. Xenobiotics biodegradation and metabolism, lipid metabolism, terpenoids and polyketides and biosynthesis of other secondary metabolites were mainly detected in the curing phases. Canonical correspondence analysis (CCA) indicated that the succession of bacterial community and organics utilization characteristics were highly affected by the temperature, moisture and oxidation reduction potential (ORP) in the swine composting system.

Rhizosphere Bacterial Communities Differ According to Fertilizer Regimes and Cabbage (Brassica oleracea var. capitata L.) Harvest Time, but Not Aphid Herbivory

Rhizosphere microbial communities are known to be highly diverse and strongly dependent on various attributes of the host plant, such as species, nutritional status, and growth stage. High-throughput 16S rRNA gene amplicon sequencing has been used to characterize the rhizosphere bacterial community of many important crop species, but this is the first study to date to characterize the bacterial and archaeal community of Brassica oleracea var. capitata. The study also tested the response of the bacterial community to fertilizer type (organic or synthetic) and N dosage (high or low), in addition to plant age (9 or 12 weeks) and aphid (Myzus persicae) herbivory (present/absent). The impact of aboveground herbivory on belowground microbial communities has received little attention in the literature, and since the type (organic or mineral) and amount of fertilizer applications are known to affect M. percicae populations, these treatments were applied at agricultural rates to test for synergistic effects on the soil bacterial community. Fertilizer type and plant growth were found to result in significantly different rhizosphere bacterial communities, while there was no effect of aphid herbivory. Several operational taxonomic units were identified as varying significantly in abundance between the treatment groups and age cohorts. These included members of the S-oxidizing genus Thiobacillus, which was significantly more abundant in organically fertilized 12-week-old cabbages, and the N-fixing cyanobacteria Phormidium, which appeared to decline in synthetically fertilized soils relative to controls. These responses may be an effect of accumulating root-derived glucosinolates in the B. oleracea rhizosphere and increased N-availability, respectively.

Distinct distribution patterns of ammonia-oxidizing archaea and bacteria in sediment and water column of the Yellow River estuary

Ammonia oxidation is a critical process of estuarine nitrogen cycling involving ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the distribution patterns of ammonia-oxidizing microorganisms (AOMs) between different habitats in the same area remain unclear. The present study investigated the AOMs’ abundance and community compositions in both sediment and water habitats of the Yellow River estuary. Quantitative PCR (qPCR) revealed that AOA showed significant higher abundance than AOB both in sediment and water samples. AOA and AOB abundance distribution trends were consistent in sediment but distinct in water along the sampling sites. Clone library-based analyses showed that AOA sequences were affiliated with Nitrososphaera, Nitrosopumilus and Nitrosotalea clusters. Generally, Nitrososphaera was predominant in sediment, while Nitrosopumilus and Nitrosotalea dominated in water column. AOB sequences were classified into genera Nitrosospira and Nitrosomonas, and Nitrosospira dominated in both habitats. Principal coordinate analysis (PCoA) also indicated AOA community structures exhibited significant differences between two habitats, while AOB were not. Ammonium and carbon contents were the potential key factors to influence AOMs’ abundance and compositions in sediment, while no measured variables were determined to have major influences on communities in water habitat. These findings increase the understanding of the AOMs’ distribution patterns in estuarine ecosystems.

Adaptation of soil nitrifiers to very low nitrogen level jeopardizes the efficiency of chemical fertilization in west african moist savannas

The moist savanna zone covers 0.5 × 10⁶ km² in West Africa and is characterized by very low soil N levels limiting primary production, but the ecology of nitrifiers in these (agro)ecosystems is largely unknown. We compared the effects of six agricultural practices on nitrifier activity, abundance and diversity at nine sites in central Ivory Coast. Treatments, including repeated fertilization with ammonium and urea, had no effect on nitrification and crop N status after 3 to 5 crop cycles. Nitrification was actually higher at low than medium ammonium level. The nitrifying community was always dominated by ammonia oxidizing archaea and Nitrospira. However, the abundances of ammonia oxidizing bacteria, AOB, and Nitrobacter increased with fertilization after 5 crop cycles. Several AOB populations, some affiliated to Nitrosospira strains with urease activity or adapted to fluctuating ammonium levels, emerged in fertilized plots, which was correlated to nitrifying community ability to benefit from fertilization. In these soils, dominant nitrifiers adapted to very low ammonium levels have to be replaced by high-N nitrifiers before fertilization can stimulate nitrification. Our results show that the delay required for this replacement is much longer than ever observed for other terrestrial ecosystems, i.e. > 5 crop cycles, and demonstrate for the first time that nitrifier characteristics jeopardize the efficiency of fertilization in moist savanna soils.

Soil C and N statuses determine the effect of maize inoculation by plant growth-promoting rhizobacteria on nitrifying and denitrifying communities

Maize inoculation by Azospirillum stimulates root growth, along with soil nitrogen (N) uptake and root carbon (C) exudation, thus increasing N use efficiency. However, inoculation effects on soil N-cycling microbial communities have been overlooked. We hypothesized that inoculation would (i) increase roots-nitrifiers competition for ammonium, and thus decrease nitrifier abundance; and (ii) increase roots-denitrifiers competition for nitrate and C supply to denitrifiers by root exudation, and thus limit or benefit denitrifiers depending on the resource (N or C) mostly limiting these microorganisms. We quantified (de)nitrifiers abundance and activity in the rhizosphere of inoculated and non-inoculated maize on 4 sites over 2 years, and ancillary soil variables. Inoculation effects on nitrification and nitrifiers (AOA, AOB) were not consistent between the three sampling dates. Inoculation influenced denitrifiers abundance (nirK, nirS) differently among sites. In sites with high C limitation for denitrifiers (i.e. limitation of denitrification by C > 66%), inoculation increased nirS-denitrifier abundance (up to 56%) and gross N2O production (up to 84%), likely due to increased root C exudation. Conversely, in sites with low C limitation (<47%), inoculation decreased nirS-denitrifier abundance (down to -23%) and gross N2O production (down to -18%) likely due to an increased roots-denitrifiers competition for nitrate.

A New Perspective on Microbes Formerly Known as Nitrite-Oxidizing Bacteria

Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, nitrite oxidation to nitrate, which is an important process of the biogeochemical nitrogen cycle. NOB were traditionally perceived as physiologically restricted organisms and were less intensively studied than other nitrogen-cycling microorganisms. This picture is in contrast to new discoveries of an unexpected high diversity of mostly uncultured NOB and a great physiological versatility, which includes complex microbe-microbe interactions and lifestyles outside the nitrogen cycle. Most surprisingly, close relatives to NOB perform complete nitrification (ammonia oxidation to nitrate) and this finding will have far-reaching implications for nitrification research. We review recent work that has changed our perspective on NOB and provides a new basis for future studies on these enigmatic organisms.

Plant Invasions Associated with Change in Root-Zone Microbial Community Structure and Diversity

The importance of plant-microbe associations for the invasion of plant species have not been often tested under field conditions. The research sought to determine patterns of change in microbial communities associated with the establishment of invasive plants with different taxonomic and phenetic traits. Three independent locations in Virginia, USA were selected. One site was invaded by a grass (Microstegium vimineum), another by a shrub (Rhamnus davurica), and the third by a tree (Ailanthus altissima). The native vegetation from these sites was used as reference. 16S rRNA and ITS regions were sequenced to study root-zone bacterial and fungal communities, respectively, in invaded and non-invaded samples and analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Though root-zone microbial community structure initially differed across locations, plant invasion shifted communities in similar ways. Indicator species analysis revealed that Operational Taxonomic Units (OTUs) closely related to Proteobacteria, Acidobacteria, Actinobacteria, and Ascomycota increased in abundance due to plant invasions. The Hyphomonadaceae family in the Rhodobacterales order and ammonia-oxidizing Nitrospirae phylum showed greater relative abundance in the invaded root-zone soils. Hyphomicrobiaceae, another bacterial family within the phyla Proteobacteria increased as a result of plant invasion, but the effect associated most strongly with root-zones of M. vimineum and R. davurica. Functional analysis using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed bacteria responsible for nitrogen cycling in soil increased in relative abundance in association with plant invasion. In agreement with phylogenetic and functional analyses, greater turnover of ammonium and nitrate was associated with plant invasion. Overall, bacterial and fungal communities changed congruently across plant invaders, and support the hypothesis that nitrogen cycling bacteria and functions are important factors in plant invasions. Whether the changes in microbial communities are driven by direct plant microbial interactions or a result of plant-driven changes in soil properties remains to be determined.