Soil Biology & Biochemistry最新文献

Viruses are abundant and diverse members of soil communities, but their influences on soil biogeochemical cycling are poorly understood. To assess the potential for viruses to influence soil carbon (C) cycling in varying environmental contexts, we sampled soils from four contrasting ecosystem types across the continental United States: conifer forest, broadleaf deciduous forest, tallgrass prairie, and agricultural cropland. We then experimentally increased virus abundance in the soils by inoculating microcosms with virus concentrates isolated from the same original soils and incubated the soils for 14 days. The virus-treated conifer forest and prairie soils respired significantly less C (14 μg and 10 μg less C per gram of soil, respectively) over the course of the 14-day incubation compared with control soils, though the effects were proportionally small in magnitude (3% and 6% reductions in cumulative respiration, respectively). Following the initial 14-day incubation, we conducted a¹³C-glucose tracer incubation. In contrast to the initial incubation, after glucose addition we observed effects on respiration only in the agricultural soil, where respiration of soil organic matter-derived C nearly doubled in the virus-treated soils compared with control soils. We also observed overall reduced incorporation of ¹³C into microbial biomass (i.e., lower growth yield) and lower carbon use efficiency on average in all virus-treated soils. These results demonstrate that viruses can influence overall microbial metabolism but with different aggregate effects on soil C balance across soil types depending on soil physicochemical properties. Overall, our study demonstrates that viral influences on soil microorganisms can manifest in altered fates of soil C, with either increased or decreased respiratory C loss depending on ecosystem type.

In addition to supporting plant productivity and nutrient cycling, arbuscular mycorrhizal (AM) fungi contribute to multiple functions within terrestrial ecosystems. However, as ecosystems face increasing temperatures and changes in precipitation, these factors may affect how AM fungi interact with ecosystem multifunctionality. Here, we investigated how warming and precipitation changes affected plant and AM fungal communities, as well as ecosystem multifunctionality in a field experiment in an alpine meadow on the eastern Tibetan Plateau that had warming and precipitation change (40% increase or decrease) manipulated experimentally from 2017. Less AM fungal diversity and evenness resulted from warming combined with increased precipitation. Increased precipitation had a significant negative indirect effect on ecosystem multifunctionality through its direct effect on grass biomass and then on AM fungal community composition. Both warming and precipitation had a positive indirect effect on ecosystem multifunctionality through their direct negative effect on AM fungal diversity and positive effect on soil moisture. We conclude that alterations in the species diversity and community composition of AM fungi due to warming and precipitation change mediate ecosystem multifunctionality. Warmer, humid conditions contribute to higher ecosystem multifunctionality, driven by climate change-induced interactions between plants and AM fungi.

Soil pH stands as a decisive factor in shaping bacterial diversity and community composition, yet predicting the pH preferences and traits of individual bacterial taxa is still incomplete. We surveyed 942 samples from seven biomes worldwide to unravel the responses of individual bacterial genus to soil pH. Our findings indicate that soil pH surpasses the influences of spatial and climatic factors (biomes) in affecting bacterial composition and diversity. We observed that a comparable proportion of genera had low pH optima (21%), high pH optima (18%), and neutral pH optima (18%). However, apart from genera with optima groups, only a small percentage of genera were low pH tolerant (0.8%) compared to those that were high pH tolerant (21%). This suggests that a greater number of non-extremophiles genera can tolerate alkaline conditions compared to acidic conditions. Bacterial richness forms unimodal relationship with soil pH, consistently increasing from acidic levels to neutral across all biomes. However, the decline in richness when pH rises beyond neutral was less pronounced. This can be attributed to the higher number of alkaline-tolerant genera compared to acidic-tolerant genera. As expected, genera with acidic optima are more prevalent in humid climates, such as tropical forests, arctic tundra, and boreal forests, whereas genera with alkaline optima are generally dominant in arid grasslands and drylands. Collectively, our results indicate that the probability of existence of at least 75% of genera in specific soil pH conditions can be predicted, irrespective of biome. The identification of the actual niche spaces occupied by individual soil bacterial genera forms the foundation for developing comprehensive hypotheses regarding the response of soil communities to changing soil conditions worldwide.

To identify microbial resources for dehalogenation, develop effective remediation strategies, and reveal their significance in “One Health”, it is crucial to understand the occurrence, distribution, and drivers of soil dehalogenation functional traits and taxonomy groups at a broad scale, which is currently not well understood. To address the gaps, we characterized the biogeography of both dehalogenation traits and taxa assigned to six dehalogenation pathways, by metagenomic profiling global 4821 soils from eight habitats, based on a manually curated dehalogenase database (DhgaseDB). We found dehalogenation genes and microbes assigned to different pathways are everywhere, but varied consistently across habitats. The similarity of dehalogention traits and taxa composition declines with geographic distance, and that patterns are strongly correlated with geo-environmental factors. We identified anthropogenic organohalide pesticide inputs as the most influential factor on dehalogenation gene abundance, while soil properties, particularly pH, exert a larger impact on dehalogenation taxa diversity. Ultimately, we generated predictive maps of soil dehalogenation gene abundance and taxa diversity for the first time, highlighting the microbial dehalogenation hotpots in East Asia, Australia, Southern Africa, and coastal regions. Collectively, our study highlights the significant role of various microbial dehalogenation processes in organohalide biotransformation and environmental microecology, providing the necessary methodological basis for a deeper comprehension of the underlying mechanisms, thereby contributing to the advancement of tailored strategies for organohalide remediation.

Antimicrobial resistance is an urgent threat to global health, causing serious antibiotic-resistant infections and deaths. The phages can serve as genetic reservoirs for bacterial adaptation, facilitating the horizontal transfer of antibiotic resistance genes (ARGs). However, how environmental perturbations impact the variation in viral ARGs via the phage-bacterial ecological network remains obscure. This study applied combined metagenomic and viromic sequencing without amplification bias to investigate the variations in the viral resistome and the ecological phage-bacterial networks in the paddy soils with different fertilizers. Results showed that manure application significantly changed the microbial community composition and increased the abundance of bacterial ARGs. The numbers of shared ARGs between paired virome and metagenome, as well as the diversity of host bacteria for phage-associated ARGs distinctly increased with manure amendment compared to chemical fertilizer treatment and non-fertilizer control. Elevated abundance of genes encoding stress and gene transfer-associated functions was observed in the manured soil viromes. Manure fertilization restructured the phage-bacteria ecological network with increased interactions potentially facilitating the dissemination of ARGs in the manure amended soils.

Fertilizer nitrogen (N) turnover is highly controlled by soil aggregation. However, the functions of the various aggregates that regulate long-term fertilizer N retention under conservation management remain unexplored. In this study, ¹⁵N-labeled fertilizer was initially applied in situ to investigate the effects of maize straw mulching on fertilizer N allocation in soil aggregates at a decadal scale. The topsoil was fractionated into macroaggregate, microaggregate, and silt-clay (SC) fractions. Macroaggregate was further divided into particulate organic matter (POM) and mineral-associated organic matter (MAOM). A higher enrichment factor of fertilizer N than of soil total N in macroaggregate indicated that the fertilizer N was more apt to incorporation into macroaggregate. The fertilizer N in the bulk soil declined gradually to 84.0% by the 13^th year. Temporally, the reduction proportion of fertilizer N in the SC fraction was the largest before 5^th years, whereas macroaggregate was the main reactive spot for fertilizer N transformation from 9 to 13 years. Therefore, the function of aggregates was time-dependent in controlling fertilizer N retention and turnover via the release of previously entrapped fertilizer N, but encapsulated the subsequently applied N (i.e., unlabeled fertilizer), whereas mineral adsorption contributed to the long-term stabilization of fertilizer N. Compared with fertilization alone, straw mulching improved aggregates stability, favored the initial fertilizer N retention in macroaggregate by enriching fertilizer N in POM, and reduced the proportion of N loss in MAOM after 9 years. These finding indicate that the improvement in fertilizer N stability related to straw decomposition was sequentially attributed to the enhancement of aggregate encapsulation and persistent interaction with soil minerals. Therefore, this study provides new insights into the functional heterogeneity of soil aggregates at different time stages and the intricate interplay between carbon availability-controlled fertilizer N retention and the improvement in soil aggregation.

Large quantities of soil carbon (C) can persist within paleosols for millennia due to burial and subsequent isolation from plant-derived inputs, atmospheric conditions, and microbial activity at the modern surface. Erosion exposes buried soils to modern root-derived C influx via root exudation and root turnover, thus stimulating microbial activity leading to SOC decomposition and accumulation through organo-mineral stabilization of modern C. With this study we aim to quantify how modern root-derived C inputs impact paleosol C decomposition and stabilization across varying degrees of isolation from modern surface conditions in southwestern Nebraska, USA, where hillslope erosion is bringing a buried Late-Pleistocene-early Holocene paleosol (the “Brady Soil”) closer to the modern surface. We collected Brady Soil samples from 0.2 m, 0.4 m, and 1.2 m below the modern surface and conducted two lab-based incubations. Soils were amended with either (1) a lab-synthesized mixture of low molecular weight compounds (12 atom% ¹³C), or (2) ¹³C enriched root residues (92 atom% ¹³C), in 30-day and 240-day incubation experiments, respectively. We determined microbial responses to synthetic root exudates and residues by partitioning the ¹³C label from Brady Soil C, including measurements of total, root, and primed C respiration, microbial biomass C (MBC), microbial C use efficiency (CUE). To assess the capacity of isolated paleosols to accrue modern plant C, we used Nano-scale Secondary Ion Mass Spectrometry imaging. We found that: (1) adding root-derived C inputs primed Brady Soil C across all depths, and was mediated by depth and composition of root additions; (2) root-derived C inputs stimulated microbial biomass C (MBC) growth similarly across depths, but the magnitude of CUE and MBC varied by chemistry of root-derived additions; (3) new particulate organic matter was incorporated into mineral-associated pools over time; (4) material from the added root residues was found in association with bacterial cells and fungal hyphae as well as with soil aggregate and mineral surfaces. Our study shows that paleosols defy expectations of C content and reactivity with depth, and changes in land cover and climate will expose buried paleosols to modern surface conditions, increasing respired C. This work highlights the importance of evaluating the role resurfacing buried soils through landscape change plays in C cycle feedbacks to the climate system.

Organic fertilizer can enhance soil health and multifunctionality in agroecosystems, but its impact on soil-borne greenhouse gas emissions needs mitigation. Fungal denitrification significantly contributes to N₂O emissions in carbon-rich soils; yet, the interactions between bacterial and fungal denitrifers under organic fertilizer amendment, remain unclear. Here, we investigated the rates and proportions of N₂O and N₂ emissions, along with the interactions between fungal and bacterial denitrifiers in a high nitrogen (N) loading arable soil subjected to four treatments: ⅰ) Control, ⅱ) organic fertilizer (Manure), ⅲ) synthetic fertilizer (Urea), and ⅳ) synthetic plus organic fertilizer (Urea + Manure). Results showed that N₂O and N₂ fluxes increased by 35.4 and 7.7 folds, respectively, in the Manure treatment compared to Control treatment. And these fluxes increased by 62.9 and 37.0 folds, respectively, in the Manure + Urea treatment compared to Urea treatment. Meanwhile, the contribution of fungal denitrification to N₂O emissions significantly increased in both Manure and Urea + Manure treatments, due to the significant enrichment of keystone fungal denitrifiers like Chaetomium among bacterial and fungal denitrifiers’ co-occurrence networks. Additionally, N₂O/(N₂O + N₂) ratio significantly decreased in the Manure and Urea + Manure treatments, which was primarily driven by significant enrichment of keystone bacterial denitrifiers carrying nosZ gene such as Achromobacter, Chelatococcus, and Shinella. These bacteria possess complete denitrification capability and can synergize with fungal denitrifiers, enhancing N₂O reduction. Overall, our findings suggest that organic fertilizer amendment in high N loading arable soils decreases N₂O/(N₂O + N₂) ratio mainly by enhancing fungal-bacterial denitrifier mutualism.