Generalists and keystone species drive rhizosphere microbial diversity and stability in feral Brassica napus

Brassica napus (rapeseed) is a globally important crop, primarily valued for its oil production. However, feral B. napus in non-agricultural areas remains under-researched. This study aims to examine the roles of microbial generalists and network keystone species in shaping microbial diversity and network stability of feral B. napus. We analyzed prokaryotic, fungal, and eukaryotic communities in the rhizosphere and bulk soil from five grassland sites. The rhizosphere microbial communities differed significantly from those in adjacent bulk soil, showing lower diversity and richness. Pseudomonas brassicacearum (bacterium), Olpidium brassicae (fungus), and Glissomonadida (eukaryote) were predominantly found in the rhizosphere. Inter- and intra-kingdom association occurred almost exclusively within the rhizosphere, with low interconnectivity compared to the bulk soil, and network keystone species served to bridge these connections. Furthermore, structural equation modeling highlighted the role of generalists and network keystone species in maintaining microbial diversity and stability. Feral B. napus selectively influenced rhizospheric generalists, which, along with keystone species, played key roles in determining microbial diversity and network stability, controlling community structure and interspecies interactions.

Additive Effects of Multiple Global Change Drivers on Terrestrial Nitrogen Cycling Worldwide

Global change has dramatically altered the Earth's biogeochemical cycles. However, the interactive effects of multiple global change factors (GCFs) on terrestrial nitrogen (N) cycling worldwide remain unclear, limiting the ability to predict how future global change will affect the global N cycle. We conducted a meta-analysis of 108 published articles to evaluate the main and interactive effects of elevated CO2, N addition, warming, and altered precipitation on soil N pools (NH4 +, NO3 -, and organic N) and transformation rates (N mineralization, nitrification, and denitrification) across terrestrial ecosystems. Results showed that single GCFs impacted the soil N cycle in different directions and magnitudes, with N addition and increased precipitation having the strongest positive effects on N pools and transformation rates, respectively. Moreover, the positive effects of N addition on the soil N cycle were generally enhanced when combined with other GCFs. Although the interactions of multiple GCFs were commonly additive (66.2%-83.3%), both synergistic (10.5%-15.1%) and antagonistic (2.8%-18.9%) effects were also observed. The types of treatment and ecosystem, geographic location, and climate all regulated the responses of soil N pools to GCFs to some degree, while only the types of treatment and ecosystem significantly affected the response of soil transformation rates to GCFs. These findings emphasize the importance of considering interactive effects among GCFs on terrestrial N cycling and highlight the necessity of incorporating these interactions into Earth system models for accurate predictions of N cycling responses to global changes.

Shifts in soil ammonia-oxidizing community maintain the nitrogen stimulation of nitrification across climatic conditions

Anthropogenic nitrogen (N) loading alters soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) abundances, likely leading to substantial changes in soil nitrification. However, the factors and mechanisms determining the responses of soil AOA:AOB and nitrification to N loading are still unclear, making it difficult to predict future changes in soil nitrification. Herein, we synthesize 68 field studies around the world to evaluate the impacts of N loading on soil ammonia oxidizers and nitrification. Across a wide range of biotic and abiotic factors, climate is the most important driver of the responses of AOA:AOB to N loading. Climate does not directly affect the N-stimulation of nitrification, but does so via climate-related shifts in AOA:AOB. Specifically, climate modulates the responses of AOA:AOB to N loading by affecting soil pH, N-availability and moisture. AOB play a dominant role in affecting nitrification in dry climates, while the impacts from AOA can exceed AOB in humid climates. Together, these results suggest that climate-related shifts in soil ammonia-oxidizing community maintain the N-stimulation of nitrification, highlighting the importance of microbial community composition in mediating the responses of the soil N cycle to N loading.

Nitrogen availability mediates soil carbon cycling response to climate warming: A meta-analysis

Global climate warming may induce a positive feedback through increasing soil carbon (C) release to the atmosphere. Although warming can affect both C input to and output from soil, direct and convincing evidence illustrating that warming induces a net change in soil C is still lacking. We synthesized the results from field warming experiments at 165 sites across the globe and found that climate warming had no significant effect on soil C stock. On average, warming significantly increased root biomass and soil respiration, but warming effects on root biomass and soil respiration strongly depended on soil nitrogen (N) availability. Under high N availability (soil C:N ratio < 15), warming had no significant effect on root biomass, but promoted the coupling between effect sizes of root biomass and soil C stock. Under relative N limitation (soil C:N ratio > 15), warming significantly enhanced root biomass. However, the enhancement of root biomass did not induce a corresponding C accumulation in soil, possibly because warming promoted microbial CO₂ release that offset the increased root C input. Also, reactive N input alleviated warming-induced C loss from soil, but elevated atmospheric CO₂ or precipitation increase/reduction did not. Together, our findings indicate that the relative availability of soil C to N (i.e., soil C:N ratio) critically mediates warming effects on soil C dynamics, suggesting that its incorporation into C-climate models may improve the prediction of soil C cycling under future global warming scenarios.

Nitrification, denitrification, and related functional genes under elevated CO2 : A meta-analysis in terrestrial ecosystems

Global change may have profound effects on soil nitrogen (N) cycling that can induce positive feedback to climate change through increased nitrous oxide (N₂ O) emissions mediated by nitrification and denitrification. We conducted a meta-analysis of the effects of elevated CO₂ on nitrification and denitrification based on 879 observations from 58 publications and 46 independent elevated CO₂ experiments in terrestrial ecosystems. We investigated the effects of elevated CO₂ alone or combined with elevated temperature, increased precipitation, drought, and N addition. We assessed the response to elevated CO₂ of gross and potential nitrification, potential denitrification, and abundances of related functional genes (archaeal amoA, bacterial amoA, nirK, nirS, and nosZ). Elevated CO₂ increased potential nitrification (+28%) and the abundance of bacterial amoA functional gene (+62%) in cropland ecosystems. Elevated CO₂ increased potential denitrification when combined with N addition and higher precipitation (+116%). Elevated CO₂ also increased the abundance of nirK (+25%) and nirS (+27%) functional genes in terrestrial ecosystems and of nosZ (+32%) functional gene in cropland ecosystems. The increase in the abundance of nosZ under elevated CO₂ was larger at elevated temperature and high N (+62%). Four out of 14 two-way interactions tested between elevated CO₂ and elevated temperature, elevated CO₂ and increased precipitation, and elevated CO₂ and N addition were marginally significant and mostly synergistic. The effects of elevated CO₂ on potential nitrification and abundances of bacterial amoA and nirS functional genes increased with mean annual temperature and mean annual precipitation. Our meta-analysis thus suggests that warming and increased precipitation in large areas of the world could reinforce positive responses of nitrification and denitrification to elevated CO₂ and urges the need for more investigations in the tropical zone and on interactive effects among multiple global change factors, as we may largely underestimate the effects of global change on soil N₂ O emissions.

Active predation, phylogenetic diversity, and global prevalence of myxobacteria in wastewater treatment plants

The operation of modern wastewater treatment plants (WWTPs) is driven by activated sludge microbiota, a complex assemblage of trophically interacting microorganisms. Microbial predation is crucial to fundamental understanding of how biological interactions drive microbiome structuring and functioning of WWTPs. However, predatory bacteria have received little attention regarding their diversity, activity, and ecological function in activated sludge, limiting the exploitation of food web interactions for wastewater microbiome engineering. Here, by using rRNA-stable isotope probing of activated sludge microbiota with ¹³C-labeled prey bacteria, we uncovered diverse as-yet-uncultivated putative predatory bacteria that actively incorporated ¹³C-biomass. Myxobacteria, especially Haliangium and the mle1-27 clade, were found as the dominant active predators, refreshing conventional views based on a few predatory isolates of Bdellovibrionota from WWTPs. The identified predatory bacteria showed more selective predation on prey compared with the protists dominated by ciliates, providing in situ evidence for inter-domain predation behavior divergence in activated sludge. Putative predatory bacteria were tracked over a two-year microbiome monitoring effort at a local WWTP, revealing the predominance of Myxococcota (6.5 ± 1.3%) over Bdellovibrionota (1.0 ± 0.2%) lineages. Phylogenetic analysis unveiled highly diverse myxobacteria inhabiting activated sludge and suggested a habitat filtering effect in global WWTPs. Further mining of a global activated sludge microbiome dataset revealed the prevalence of Myxococcota (5.4 ± 0.1%) species and potential impacts of myxobacterial predation on process performance. Collectively, our findings provided unique insights into the predating activity, diversity, and prevalence of Myxococcota species in activated sludge, highlighting their links with wastewater treatment processes via trophic regulation of enteric and functional bacteria.

Stimulation of ammonia oxidizer and denitrifier abundances by nitrogen loading: Poor predictability for increased soil N2 O emission

Unprecedented nitrogen (N) inputs into terrestrial ecosystems have profoundly altered soil N cycling. Ammonia oxidizers and denitrifiers are the main producers of nitrous oxide (N₂ O), but it remains unclear how ammonia oxidizer and denitrifier abundances will respond to N loading and whether their responses can predict N-induced changes in soil N₂ O emission. By synthesizing 101 field studies worldwide, we showed that N loading significantly increased ammonia oxidizer abundance by 107% and denitrifier abundance by 45%. The increases in both ammonia oxidizer and denitrifier abundances were primarily explained by N loading form, and more specifically, organic N loading had stronger effects on their abundances than mineral N loading. Nitrogen loading increased soil N₂ O emission by 261%, whereas there was no clear relationship between changes in soil N₂ O emission and shifts in ammonia oxidizer and denitrifier abundances. Our field-based results challenge the laboratory-based hypothesis that increased ammonia oxidizer and denitrifier abundances by N loading would directly cause higher soil N₂ O emission. Instead, key abiotic factors (mean annual precipitation, soil pH, soil C:N ratio, and ecosystem type) explained N-induced changes in soil N₂ O emission. Altogether, these findings highlight the need for considering the roles of key abiotic factors in regulating soil N transformations under N loading to better understand the microbially mediated soil N₂ O emission.

Stimulation of ammonia oxidizer and denitrifier abundances by nitrogen loading: Poor predictability for increased soil N2 O emission

Unprecedented nitrogen (N) inputs into terrestrial ecosystems have profoundly altered soil N cycling. Ammonia oxidizers and denitrifiers are the main producers of nitrous oxide (N₂ O), but it remains unclear how ammonia oxidizer and denitrifier abundances will respond to N loading and whether their responses can predict N-induced changes in soil N₂ O emission. By synthesizing 101 field studies worldwide, we showed that N loading significantly increased ammonia oxidizer abundance by 107% and denitrifier abundance by 45%. The increases in both ammonia oxidizer and denitrifier abundances were primarily explained by N loading form, and more specifically, organic N loading had stronger effects on their abundances than mineral N loading. Nitrogen loading increased soil N₂ O emission by 261%, whereas there was no clear relationship between changes in soil N₂ O emission and shifts in ammonia oxidizer and denitrifier abundances. Our field-based results challenge the laboratory-based hypothesis that increased ammonia oxidizer and denitrifier abundances by N loading would directly cause higher soil N₂ O emission. Instead, key abiotic factors (mean annual precipitation, soil pH, soil C:N ratio, and ecosystem type) explained N-induced changes in soil N₂ O emission. Altogether, these findings highlight the need for considering the roles of key abiotic factors in regulating soil N transformations under N loading to better understand the microbially mediated soil N₂ O emission.

Slope aspect determines the abundance and composition of nitrogen-cycling microbial communities in an alpine ecosystem

Slope aspect is an important topographic feature that can influence local environmental conditions. While strong effects of slope aspect on aboveground and belowground communities have been frequently elucidated, how slope aspect affects soil nitrogen (N) cycling microbes remains unclear. Here, we characterized the communities of soil N-cycling microbes on south- and north-facing slopes in an alpine ecosystem, by quantifying (qPCR) and high-throughput sequencing six genes involved in N-fixation (nifH), nitrification (archaeal and bacterial amoA) and denitrification (nirK, nirS and nosZ). We found that the abundance, diversity and community composition of major N-cycling microbes differed dramatically between the two slope aspects, and these variances could be well explained by the aspect-driven differences in environmental conditions, especially soil temperature and moisture. The response patterns of different N-cycling groups to slope aspect were much inconsistent, especially for those with similar functions (i.e. ammonia-oxidizing archaea vs. bacteria, nirK- vs. nirS-reducers), indicating strong niche differentiation between these counterparts. We also observed strong preferences and distinct co-occurrence patterns of N-cycling microbial taxa for the two slope aspects. These findings highlight the importance of slope aspect in determining the abundance, species distribution and community structure of N-cycling microbes, and consequently influencing N-cycling processes and ecosystem functioning. This article is protected by copyright. All rights reserved.

Community RNA-Seq: multi-kingdom responses to living versus decaying roots in soil

Roots are a primary source of organic carbon input in most soils. The consumption of living and detrital root inputs involves multi-trophic processes and multiple kingdoms of microbial life, but typical microbial ecology studies focus on only one or two major lineages. We used Illumina shotgun RNA sequencing to conduct PCR-independent SSU rRNA community analysis ("community RNA-Seq") and simultaneously assess the bacteria, archaea, fungi, and microfauna surrounding both living and decomposing roots of the annual grass, Avena fatua. Plants were grown in 13CO2-labeled microcosms amended with 15N-root litter to identify the preferences of rhizosphere organisms for root exudates (13C) versus decaying root biomass (15N) using NanoSIMS microarray imaging (Chip-SIP). When litter was available, rhizosphere and bulk soil had significantly more Amoebozoa, which are potentially important yet often overlooked top-down drivers of detritusphere community dynamics and nutrient cycling. Bulk soil containing litter was depleted in Actinobacteria but had significantly more Bacteroidetes and Proteobacteria. While Actinobacteria were abundant in the rhizosphere, Chip-SIP showed Actinobacteria preferentially incorporated litter relative to root exudates, indicating this group's more prominent role in detritus elemental cycling in the rhizosphere. Our results emphasize that decomposition is a multi-trophic process involving complex interactions, and our methodology can be used to track the trajectory of carbon through multi-kingdom soil food webs.

Effects of the interaction among climate, terrain and human activities on biodiversity on the Qinghai-Tibet Plateau

Disentangling the driving factors of biodiversity is critical for understanding biogeographical patterns of vegetation and ecosystem function. However, the biotic and abiotic attributes that shape biodiversity on the Qinghai-Tibet Plateau (QTP) are still not been quantified. Previous studies have not distinguished the direct and indirect effects of climate, terrain, and human disturbance on biodiversity. In this study, we applied a structural equation model (SEM) to assess the interactions among 4 attributes and biodiversity. A conceptual framework with 8 explanatory variables was built to identify the driving forces of biodiversity. A geographically weighted regression (GWR) model was applied to explore the response sensitivity of biodiversity to climate, terrain, and human attributes. We found that the SEM passed the tests of validity, reliability and fit, indicating that the hypothetical model was reasonable and credible. Among terrain conditions, elevation had the greatest, most-negative effect on biodiversity. Among the human factors, distance to town showed the strongest and most negative influence on biodiversity. Among the climate factors, precipitation had the greatest influence on biodiversity. Moreover, the direct effects of terrain and human activity were 0.348 and 0.135, respectively, and their indirect effects were 0.769 and 0.213, respectively, revealing that they had stronger indirect effects on biodiversity than direct effects. Climate exhibited only direct effects on biodiversity and had no indirect effects. The total effects of climate, terrain and human activity on biodiversity were 1.39, 0.35 and 0.13, respectively, indicating that climate was the main driving force of biodiversity on the QTP. The response sensitivity of biodiversity to climate, terrain and human factors showed obvious spatial variations. This study contributes to exploring the interactive effects and driving mechanisms of human-natural attributes on biodiversity and provides further effective guidance and support for biodiversity conservation and restoration.

The soil microbial food web revisited: Predatory myxobacteria as keystone taxa?

Trophic interactions are crucial for carbon cycling in food webs. Traditionally, eukaryotic micropredators are considered the major micropredators of bacteria in soils, although bacteria like myxobacteria and Bdellovibrio are also known bacterivores. Until recently, it was impossible to assess the abundance of prokaryotes and eukaryotes in soil food webs simultaneously. Using metatranscriptomic three-domain community profiling we identified pro- and eukaryotic micropredators in 11 European mineral and organic soils from different climes. Myxobacteria comprised 1.5-9.7% of all obtained SSU rRNA transcripts and more than 60% of all identified potential bacterivores in most soils. The name-giving and well-characterized predatory bacteria affiliated with the Myxococcaceae were barely present, while Haliangiaceae and Polyangiaceae dominated. In predation assays, representatives of the latter showed prey spectra as broad as the Myxococcaceae. 18S rRNA transcripts from eukaryotic micropredators, like amoeba and nematodes, were generally less abundant than myxobacterial 16S rRNA transcripts, especially in mineral soils. Although SSU rRNA does not directly reflect organismic abundance, our findings indicate that myxobacteria could be keystone taxa in the soil microbial food web, with potential impact on prokaryotic community composition. Further, they suggest an overlooked, yet ecologically relevant food web module, independent of eukaryotic micropredators and subject to separate environmental and evolutionary pressures.

Elucidating the microbiological characteristics of cyromazine affecting the nitrogen cycle during aerobic composting of pig manure

Cyromazine as insect growth inhibitor have been frequently detected in the environment, which show a potential threat to environment and soil health. Nitrogen is an essential component of all living organisms and the main nutrient limiting life on our planet. In this study, quantitative polymerase chain reaction (qPCR) and sequencing of nitrifying and denitrifying bacteria were conducted to investigate the dynamic effects of cyromazine on nitrogen conversion during laboratory-based composting. Results showed that the presence of cyromazine significantly reduced the abundance of amoA gene during the thermophilic phase of composting (p < 0.01), resulting in lower oxidation of NH₄⁺-N. The archaea amoA gene was more resistant to cyromazine. The nirK gene was more abundant than the nirS gene during composting and was significantly reduced only under high concentrations of cyromazine (p < 0.01). The high dose of cyromazine (15 mg/kg) severely damaged the nitrogen fixation capacity of compost products. Cyromazine exhibited an inhibition effect on richness (ACE, Chao) of nitrifying and denitrifying microorganisms during the thermophilic period, while increased the diversity (shannon) at all stages of composting. Pseudomonas_formosensis was the core denitrifiers that harbored nosZ gene, Nitrosomonas_eutropha and Nitrosospira_sp_Nl5 were the dominant nitrifier that harbored amoA gene, and these species have a negative response to cyromazine. Network analysis indicated that the dominant bacteria harboring amoA and nosZ genes were hubs of nitrogen oxidation and reduction processes. Structural equation modeling revealed that NO₂^--N conversion played a crucial role in driving denitrification, and increase of NH₄⁺-N content was attributed to the inhibition of nitrification and denitrification during composting caused by cyromazine.

Effect of Different Combinations of Phosphorus and Nitrogen Fertilization on Arbuscular Mycorrhizal Fungi and Aphids in Wheat

While chemical fertilizers can be used to increase crop yield, the abuse of fertilizers aggravates environmental pollution and soil degradation. Understanding the effects of chemical fertilizers on the interaction between arbuscular mycorrhizal fungi (AMF) and pest insects is of great benefit to crop and environmental protection, because AMF can enhance the nutrition absorption and insect resistance of crops. This study tested the effect of different levels of phosphorus, nitrogen, and their interactions on AMF, secondary metabolites, Sitobion avenae in garden, as well as the wheat traits in field. The results showed that AMF colonization on roots in the P0N1 treatment (0 g P/pot, 1.3083 g N/pot in the garden, and 0 g P/plot, 299.84 g N/plot) was the highest in both the garden and the field. The abundance of aphid was reduced in the P0N1 treatment, and there were negative relationships between aphids and AMF and phenolics, but a positive relationship between AMF and phenolics. Our results indicated that a change in the ratio of phosphorus to nitrogen affects the relationship among AMF, aphid abundance, and metabolites. The results also suggested an approach to save chemical fertilizers that could improve crop health and protect the agroecosystem against pollution at the same time.

Beneficial effects of bacterial agent/bentonite on nitrogen transformation and microbial community dynamics during aerobic composting of pig manure

This study investigated the effects of adding a bacterial agent (B) and bentonite (BT) on nitrogen transformation, nitrogen functional genes, and the microbial community dynamics during the aerobic composting of pig manure, as well as their contributions to NH₃ and N₂O emissions. Treatments B, BT, and BT + B reduced the NH₃ emissions by 31.34%, 18.82%, and 23.67%, respectively, and the N₂O emissions by 53.16%, 72.56%, and 63.41%. N₂O and NH₃ emissions were strongly related to the functional genes. Adding bacterial agent promoted the ammonia oxidation process to reduce NH₃ emissions, whereas the influence of bentonite on nitrogen conversion was mostly related to nirS and nirK in denitrification processes. Nitrification and denitrification were dominated by different functional microorganisms in various stages of composting, where Proteobacteria comprised the most important denitrifying microorganisms. Thus, the additives reduced NH₃ and N₂O emissions by regulating nitrification and denitrification processes, and adding both was highly advantageous.

Is "Wolf-Pack" Predation by Antimicrobial Bacteria Cooperative? Cell Behaviour and Predatory Mechanisms Indicate Profound Selfishness, Even when Working Alongside Kin

For decades, myxobacteria have been spotlighted as exemplars of social "wolf-pack" predation, communally secreting antimicrobial substances into the shared public milieu. This behavior has been described as cooperative, becoming more efficient if performed by more cells. However, laboratory evidence for cooperativity is limited and of little relevance to predation in a natural setting. In contrast, there is accumulating evidence for predatory mechanisms promoting "selfish" behavior during predation, which together with conflicting definitions of cooperativity, casts doubt on whether microbial "wolf-pack" predation really is cooperative. Here, it is hypothesized that public-goods-mediated predation is not cooperative, and it is argued that a holistic model of microbial predation is needed, accounting for predator and prey relatedness, social phenotypes, spatial organization, activity/specificity/transport of secreted toxins, and prey resistance mechanisms. Filling such gaps in our knowledge is vital if the evolutionary benefits of potentially costly microbial behaviors mediated by public goods are to be properly understood.