查看更多>>摘要：? 2022 Elsevier LtdBiological soil crusts (biocrusts) recently discovered in agroecosystems have the potential to enrich soil moisture and nitrogen (N) concentrations and structure the subsurface microbiome. In citrus agroecosystems, year-round N availability is vital for production, with vegetative flushes in the spring and fall and fruit development in the fall and winter. Due to the N demand and natural formation of biocrusts in citrus orchards, we investigated the influence of biocrusts on soil moisture content, N cycling, and microbiome composition in the upper root zone of a sandy soil citrus orchard (Florida, USA). Soils sampled from below biocrusts (1–5 cm) were collected at eight sampling dates over a one-year period in the orchard from biocrust-covered and proximate bare areas. Samples were analyzed for moisture content, soluble and microbial N pools, and potential ammonia oxidation. Bacterial and fungal communities were characterized using the 16S rRNA gene and ITS region sequences, respectively, at five sampling dates from September 2019 through March 2020. Biocrust presence and sampling date significantly impacted soil moisture and soluble and microbial N pools (p < 0.05). Soil moisture and inorganic N were enriched below biocrusts compared to below bare soil controls during the dry season from fruit set through harvest. Microbial biomass N and potential ammonia oxidation activity were also higher in September and November during fruit set. During fruit set and maturation, there was a corresponding greater abundance of copiotrophic bacteria and fungi capable of heterotrophic nitrification in soil below biocrusts. Overall, these results indicate soil under biocrusts had increased moisture, N concentrations, and relative abundances of microbiota with functional potential for cycling N. These results support a potential role for biocrust influence on crop N availability and soil health during periods of plant nutrient demand.
查看更多>>摘要：? 2022 Elsevier LtdRelative microbiome profiling (RMP) using new sequencing approaches has limited capacity to detect shifts in microbial abundances. The growing need for absolute abundances has led to advances in absolute microbiome profiling (AMP). However, the performance and universal applicability of these various AMP methods remain unclear. Here, the two most popular AMP methods, spike-in method (spike-AMP) and quantitative PCR combined with high-throughput sequencing (qPCR-AMP), were evaluated in soil microbiota research. Our results showed that the quantitative results based on spike-AMP were inconsistent with expected trends. The spike-derived absolute abundance was indeterminate and highly dependent on the amount of spike added. Furthermore, no good correlation was found between the addition of spike copies and output of spike reads, especially at low spike levels, contradicting the theoretical assumption of the spike-in method. Spike addition consumed substantial sequencing resources, and more importantly, it altered the original microbial community structure, explaining 16.1%–36.2% of structural variation. In contrast, the more common qPCR-AMP method provided valuable insights into the understanding of soil microbial dynamics in response to straw addition. Our results showed that the straw-induced variations in some dominant phyla such as Proteobacteria, Actinobacteriota and Ascomycota could only be detected by absolute rather than relative microbial profiling. We inferred microbial networks based on absolute and relative data matrices, respectively, and observed that the choice of data type essentially impacted the patterns of co-occurrence networks and the recognition of module hubs. The keystones and enriched phyla only detected by absolute microbial profiling were confirmed to be involved in straw decomposition by a stable isotope probing experiment. Overall, AMP can provide valuable insights into the understanding of soil microbial dynamics in response to environmental fluctuations. Given its stability and technical feasibility, qPCR-AMP may be broadly applicable to soil microbiota quantitative research.
查看更多>>摘要：? 2022 Elsevier LtdLittle is known about the microscale heterogeneity of O2 and pH in the interfaces between soil and amendments. In this study, planar optodes were applied to continuously measure the micro-scale O2 and pH dynamics in soil amended with a patch of straw and its biochar. The recalcitrant biochar with high porosity had stronger capability to maintain the oxic zone around the patch area. Mainly through diffusion of alkali carbonates, the biochar increased the soil pH within a few hours but in constrained area (<4.5 mm from the surface of the biochar patch). Such high pH coupled with oxic conditions largely restricted N2O emissions in the biochar treatment. The sufficient labile carbon from straw induced fast O2 consumption with microoxic development in the straw-soil interfaces, while its porous structure could enhance O2 diffusive inputs in the core area, therefore, the microoxic area was formed as a concentric ring around the straw patch. Such enriched oxic-microoxic transient zones would induce nitrification coupled denitrification, which led to the high N2O emissions. Additionally, the microbial degradation of straw resulted in a pulse decline of soil pH, which possibly inhibited the N2O reductases, consequently enhanced N2O emissions. Those results demonstrate the contrasting effects of straw and straw derived biochar on microscale O2 and pH localization as well as the associated N2O emissions. It will contribute to a better understanding of the driving factors for N transformations on a microscale and has the potential to become valuable tool in environmental monitoring.
查看更多>>摘要：? 2022 The AuthorsOne of the biggest environmental challenges facing agriculture is how to both supply and retain nitrogen (N), especially as precipitation becomes more variable with climate change. We used a greenhouse experiment to assess how contrasting histories of crop rotational complexity affect plant-soil-microbe interactions that govern N processes, including during water stress. With higher levels of carbon and N cycling hydrolytic enzymes, higher mineral-associated organic matter N concentrations, and an altered microbial community, soils from the most complex rotation enabled 80% more corn N uptake under two moisture regimes, compared to soil from monoculture corn. Higher levels of plant N likely drove the changes in corn leaf gas exchange, particularly increasing intrinsic water use efficiency by 9% in the most complex rotation. The water deficit increased the standing pool of nitrate 44-fold in soils with a history of complex crop rotations, compared to an 11-fold increase in soils from the corn monoculture. The implications of this difference must be considered in a whole cropping systems and field context. Cycling of 15N-labeled fresh clover residue into soil N pools did not depend on the water regime or rotation history, with 2-fold higher recovery in the mineral vs. particulate organic N pool. In contrast, the water deficit reduced recovery of clover 15N in corn shoots by 37%, showing greater impacts of water deficit on plant N uptake compared to organic N cycling in soil. This study provides direct experimental evidence that long-term crop rotational complexity influences microbial N cycling and availability with feedbacks to plant physiology. Collectively, these results could help explain general observations of higher yields in more complex crop rotations, including specifically during dry conditions.
查看更多>>摘要：? 2022 Elsevier LtdTools for accurate measurements of microbial biomass/abundance are imperative in soil ecology. This perspective was prompted by a lack of consistency in how the neutral lipid fatty acid (NLFA) and phospholipid fatty acid (PLFA) 16:1ω5 are used to estimate arbuscular mycorrhizal (AM) fungal abundance, which we argue can lead to erroneous conclusions within studies and complicate among-study comparisons. We show that more than half of all studies published to date use PLFA 16:1ω5 to quantify AM fungal biomass without proper controls. This is problematic because AM fungi cannot be separated from the bacterial contribution to this fatty acid signature. We provide a set of recommendations for future research and specifically urge researchers to extract and analyze NLFA 16:1ω5 for more accurate and sensitive assessments of AM fungal biomass as this can be done without doubling effort.
查看更多>>摘要：? 2022 The AuthorsTemperate forests are increasingly subject to natural disturbance by stand replacing windthrows or bark-beetle attacks. Forests are commonly salvage logged after disturbance, whereby substantial parts of biological legacies, such as surviving trees and deadwood, are removed. Despite increasing concerns about the ecological consequences of salvage logging operations, our knowledge on the effects on the soil microbiome and associated functioning remains limited. Here, we studied soil fungal communities, decomposition processes, and soil organic matter dynamics in 21 intact or disturbed, temperate Norway spruce stands about one decade after they were damaged by windthrow or bark-beetle attacks. Disturbed stands comprised different post-disturbance management, i.e. deadwood retention and salvage logged plots. We used high-throughput sequencing and ergosterol measurements to explore fungal communities and biomass, and enzyme assays to study decomposition processes. Disturbance shifted soil fungal communities from ectomycorrhizal to saprotrophic dominated assemblages. Fungal biomass declined with decreasing tree abundance after disturbance. Activities of organic matter degrading enzymes declined by ca. 30–80% after disturbance. The relative abundance of ectomycorrhizal fungi was positively related to enzymatic activities. Tree biomass parameters and amounts of deadwood retained were positively related to fungal biomass, certain ectomycorrhizal taxa, and relative ectomycorrhizal fungal abundance among disturbed stands, which, in turn, was associated with higher enzymatic activities. Our findings demonstrate a significant response of soil fungal communities to natural forest disturbance and salvage logging, with consequences for decomposition and soil organic matter dynamics. We conclude that the retention of surviving trees and deadwood as biological legacies attenuated associated changes to a significant extent, highlighting their importance for the preservation of ectomycorrhizal fungi and the maintenance of decomposition processes after disturbance.
查看更多>>摘要：? 2022 The AuthorsSoil biota contribute to the delivery of multiple soil functions. However, soil biological methods are highly underrepresented in the assessment of soil functionality in agricultural production systems. Here we present a flexible tool to support decision-making during the selection process of soil biological methods for monitoring soil functions. This tool is based on a structured and conceptual framework that connects soil biota to soil functions through their contribution to different soil processes. The methods assessed by the tool were selected as a result of a thorough literature review. Soil biology experts supported the development of the tool (i) by providing feedback on the reviewed methods through a survey and (ii) by determining the relevance of different soil biota to the soil processes related to soil multifunctionality during a workshop. The tool is freely accessible online at the Biological Soil Information System (BIOSIS) platform, where researchers or users with an understanding of research practices can interact with the tool to define the context of their assessment and preferences for technical criteria of the methods. By incorporating user input, this flexible tool can help inform a wide variety of research and assessment programs interested in applying soil biological methods to monitor soil multifunctionality at different scales.
查看更多>>摘要：? 2022 Elsevier LtdNitrification and denitrification driven by microbes are important processes mediating soil N availability and N2O emission. Enhanced N deposition usually stimulates both nitrification and denitrification rates, but whether these stimulation effects are generally persistent or not, and the underlying biological mechanism remain unclear. To clarify these issues, we compiled the responses of soil nitrification rate, denitrification rate, and microbial functional gene abundances as well as corresponding N2O emission to N deposition at global scale. The results showed that both nitrification rate and AOB amoA abundance were stimulated by N deposition on average, while denitrification rate was stimulated without any change in denitrification related functional gene abundance. When the data set was partitioned by N addition duration, there were larger significant positive responses of nitrification rate and AOB amoA abundance as well as those of denitrification rate and narG abundance with longer duration. The response ratio of nitrification rate was positively correlated with that of AOB amoA abundance (p < 0.01). The response ratio of N2O emission was positively correlated with that of AOB amoA abundance (p = 0.04) as well as that of narG abundance (p < 0.01). These results indicated the crucial role of AOB amoA and narG abundances for the responses of nitrification and denitrification rates to N deposition, as well as the response of N2O emission. The larger gene abundances of AOB amoA and narG with longer term N deposition sustain long-term positive responses of nitrification and denitrification to N deposition. This challenges the traditional cognition that long term N deposition diminished the positive response of N2O emission to N deposition by dampening the microbial activity. The responses of AOB amoA and narG abundances to N deposition should be considered to better predict the dynamic of nitrification rate, denitrification rate or N2O emission in the context of enhanced N deposition.
查看更多>>摘要：? 2022 Elsevier LtdRhizosphere microbial communities play essential roles in plant growth and health, with plant-derived carbon serving as the primary resource fueling the growth and activity of these root-associated communities. However, not all rhizosphere microbes are likely equivalent in their ability to metabolize root-derived carbon inputs, and far fewer studies have sought to identify the rhizosphere taxa, and the traits of those taxa that actively consume plant photosynthates. Here, we labeled wheat plants (Triticum aestivum L.) with 13C–CO2, combining stable isotope probing, quantitative PCR, marker gene sequencing, and shotgun metagenomic sequencing to identify rhizosphere microbes that metabolized plant-derived carbon and their genomic attributes. Those rhizosphere taxa that incorporated the plant-derived 13C were not necessarily the most abundant taxa in the rhizosphere. Rhizosphere microbes clearly differed in their capacity to consume plant-derived carbon, with the bacterial photosynthate consumers having distinct metabolic and genomic profiles with higher estimated potential growth rates and more genes associated with carbon metabolism, resource uptake, and potential for plant growth promotion. Together, this work highlights the important roles and the differential contributions of rhizosphere microbes to belowground carbon dynamics, building a more nuanced understanding of the complexity of plant-microbe interactions in the rhizosphere.
查看更多>>摘要：? 2022 Elsevier LtdUnderstanding what controls the soil organic matter (SOM) storage and its stability is important to predict how SOM will respond to environmental changes. The role of mycorrhizal fungi in mediating soil carbon (C) and nitrogen (N) cycling is increasingly recognized. However, how mycorrhizal fungi could affect C distribution and N demand of different soil fractions is largely unknown. Here, we compiled a global dataset of C and N concentrations in different SOM fractions from arbuscular mycorrhizal (AM) and ectomycorrhizal (EcM) dominated ecosystems, covering major biomes, including tropical forest, temperate forest, boreal forest, and grassland. Based on this dataset, we evaluated the effect of mycorrhiza symbiosis on C storage and C: N stoichiometry of SOM fractions with different stability. We found that for both topsoil and subsoil, bulk soil C storage and C: N ratio in EcM ecosystems were higher than those in AM ecosystems, and a similar pattern was also observed in the particulate organic matter fraction (POM). However, the C storage in the mineral-associated organic matter fraction (MAOM) was not different between AM and EcM ecosystems. Moreover, with the increase in bulk soil C concentration, the C storage in topsoil MAOM reached a stable level in EcM ecosystems but continued to increase in AM ecosystems. With the increase in soil N concentration, bulk soil C storage of EcM ecosystems increased more rapidly than that of AM ecosystems, which was mainly driven by the increase in POM C storage. Our study highlights that soil C storage and relative stability are different between AM and EcM ecosystems. Although EcM ecosystems have a higher soil C storage and lower N demand per unit soil C, most C is distributed in relative labile POM. Therefore, SOM in EcM ecosystems could be more susceptible to disturbances caused by land use and climate changes.
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