Schlatter, Daniel C.Hansen, JeremyCarlson, BryanLeslie, Ian N....
15页
查看更多>>摘要：Soil health is an increasingly important concept that provides aspirational targets for agricultural management. Due in part to the incredible diversity of soil microbial communities, however, the biological components of soil health remain poorly understood. In the last decade the refinement of high-throughput DNA sequencing approaches for examining soil microbial communities has led to sequence-variant resolution insights into their diversity. In this work we employ high-throughput sequencing of bacterial (16S rRNA genes) and fungal (internal transcribed spacer [ITS]) regions to evaluate soil microbial communities in relation to other soil chemical parameters, biological soil health tests, and crop yields in fields under long-term reduced tillage (business-as-usual) and no tillage (aspirational) management at two soil depths. We found that tillage systems and soil depth were crucial determinants of microbial community composition and diversity in conjunction with soil chemical measures. Moreover, although some measures of biological soil health (CO2-burst, Haney Soil Health Score) did not differentiate fields under reduced tillage and no-till systems, amplicon sequencing revealed clear differences in microbial communities between management regimes. The relative abundances of many microbial taxa were significantly related to soil chemical variables and crop yields. Fungal communities showed stronger correlations with yield than bacterial communities at both depth increments. Fungi from the families Sordariaceae, Hydnodontaceae, Hypocreaceae, and Clavicipitaceae were positively correlated with yield, especially in the upper soil depth, while Glomeraceae and Phaeosphaeriaceae were negatively correlated. Many of these correlations were also seen in the subsequent winter wheat and chickpea crops, and some correlations could be detected in the 20-year previous yield history of the no-tillage farm. Among the bacteria, only Microbaceriaceae and Xanthomonadaceae were positively correlated, but Caulobacteriaceae, Flavobacteriaceae, Sphingobacteriaceae, Chitinophagaceae were more abundant in lower yielding locations. This may reflect the strong plant selection in the rhizosphere for these bacterial groups in stressed plants. There were no significant differences, however, between microbial diversity and management practices or significant correlations with crop yields. These results suggest that some specific groups of microbial taxa are responsive to tillage systems, exhibit positive relationships with grain yields, and may be useful indicators of soil health.
Barbosa, Julierme ZimmerRoberto, Ludmila de AlmeidaHungria, MariangelaCorrea, Rodrigo Studart...
10页
查看更多>>摘要：The inoculation of maize with the plant-growth-promoting bacteria (PGPB) Azospirillum brasilense Ab-V5 and AbV6 strains has impressively increased in Brazil in the last decade. In the present study, we conducted a metaanalysis with 60 studies published between 2010 and 2021, comprising 103 field trials in 54 locations in Brazil, aiming to assess the benefits and factors that affect the efficiency of A. brasilense inoculation of maize. Results showed that bacteria inoculation increased 12.1% of root mass, 4.3% N leaf concentration, 5.4% grain yield, and 3.6% of N in grains. The analysis of cultivars, edaphoclimatic conditions, and others detected positive effects of inoculation on maize under all the study conditions and yield ranges. However, inoculation benefits were higher at yields <3000 kg/ha (+21%) than between 3000 and 12,000 kg/ha (+1.5% to +6.2%), and yield responses tend towards greater increases at lower N rates ( 50 kg/ha, +8%) that at higher ones ( 200 kg/ha, +3.8%). Seed inoculation was more efficient than inoculation via leaf spray, especially by applying solid (peat) inoculants (+9.5%) than liquid formulations (+5.5%). Leaf-spray inoculation showed positive effect on grain yield (+3.1%) only when performed at the initial vegetative growth stages (V2-V3). A. brasilense inoculation represents an important biotechnology tool to increase yields and nutritional value of maize crops under most agronomic and environmental tropical and subtropical conditions.
查看更多>>摘要：Phosphorus (P) fertilization rates have been dramatically increasing in intensive agro-ecosystems. However, the impact of such long-term P fertilization in intensive agro-ecosystems on the diversity, composition mycorrhizal traits of arbuscular mycorrhizal fungi (AMF) communities and the relationship between them remains poorly understood. By conducting a long-term field experiment (10 years) in north China in a typical calcareous soil with a wheat-maize rotation, we investigated the effects of six P fertilization rates on AMF community properties. We found that AMF alpha diversity (including OTU number and Shannon index) was positively correlated with both AMF root colonization of maize, hyphal density in soil and expression of the phosphate transporter gene ZmPht1;6 for maize. AMF community structure was significantly correlated with AMF colonization of maize roots, hyphal density and P concentrations in maize shoots. The relative abundance of the most dominant taxon Funneliformis caledonium OTU1 decreased while that of the second dominant taxon Claroideoglomus lamellosum OTU55 increased as the P fertilizer rate increased. AMF colonization of roots and hyphal density was positively correlated with the relative abundances of Glomus sp. (including OUT 29, OTU32, and OTU37) in soil but was negatively correlated with the relative abundances of Septoglomus viscosum OTU14. The relative abundances of Glomus sp. (OTU 5, OTU 25, OTU27, OTU23, and OTU29) were positively correlated with AMF colonization of roots, hyphal density and ZmPht1;6 expression under low rates of P fertilization (P0 and P12.5 treatments), while the relative abundance of Glomus sp. OTU20 was positively correlated with AMF colonization of roots, hyphal density and ZmPht1;6 expression under high rates of P fertilization (P100 and P200 treatments). Long-term P fertilization significantly altered the alpha diversity, structure, and composition of AM communities, which affected AMF colonization of maize roots and expression of a phosphate transporter gene. Our results indicate that different members of AMF communities differentially modulated their mycorrhizal traits with maize under different P fertilization rates. An improved understanding of how AMF taxa and functions are altered by P fertilization and the mycorrhizal traits impact on plant nutrition could help guide P fertilization practices in agroecosystems.
查看更多>>摘要：Denitrification is a key process for soil available nitrogen (N) loss and is greatly influenced by fertilization strategies; however, the effect of straw return rates on soil denitrification potential (DP) and the community composition of denitrifying bacteria remain unclear. A 30-year straw return experiment was used to study changes in soil DP, the abundance and community composition of nirK- and nirS-type denitrifying bacteria in north-central China. The experiment included five treatments: control (CK, without fertilizers and straw application), and the application of N and phosphorus (P) fertilizers combined with 0 (S0), 2250 (S1), 4500 (S2), and 9000 kg ha(-1) (S3) maize straw, respectively. Relative to the CK treatment, the 50 greatly increased soil DP and the abundance of nirK and nirS genes, and these values further increased with the increasing straw rates; however, the chemical fertilization and straw rates had no effects on the a-diversity of two denitrifying communities. Principal component analysis showed that the chemical fertilizers and straw return rates significantly influenced the composition of nirS-type denitrifying community, but had less effect on nirK-type denitrifying community. Soil NO3--N, total N, and organic matter were positive correlated with soil DP and the abundance of nirK- and nirS-type denitrifying bacteria across all treatments, and were the dominant factors affecting the composition of two nir denitrifying communities under the high rates of straw return. Our results indicated that the rate of straw return had different effects on the abundance and composition of nirK- and nirS-type denitrifying communities, and nirS-type denitrifying community was more sensitive to the increasing return rate of straw than nirK-type denitrifying community.
查看更多>>摘要：Soil pore size and arrangement control the heterogeneous distribution of nutrients, water, and air and, therefore, are likely a superimposed and integrated factor dictating the soil microbial community structure. It is known that soil with more large pores can potentially harbor more diverse microbes under low hydraulic connectivity. Still, there is scant information on how soil pore size distribution (PSD) governs the composition and association of the microbial community. This work examined PSD effects on microbial community compositions and networks via marker gene high-throughput sequencing of both DNA and cDNA. Three soils with a large variation in silt content (similar to 11-73%) and their combinations at different mass ratios were used to enhance the continuity in silt content and thus PSD. Investigations were made under different levels of total pore volume and pore hydraulic connectivity by incubating soils at varied bulk densities and moisture contents for 50 days. The total of six soils was dichotomized into two PSD groups based on soil water retention curves, with PSD-1 of more macro- and mesopores ( 30 mu m) and PSD-2 of more micropores (<30 mu m). Effects of moisture treatments on both fungal and bacterial evenness and Shannon diversity index were pore size group specific, supporting the importance of pore hydraulic connectivity in regulating microbial diversity. PSD-1 soils promoted the proliferation of Betaproteobacteria, Bacteroidetes, and Eurotiales, whereas PSD-2 soils favored Alphaproteobacteria, Sordariomycetes, and Chaetothyriales. Pore hydraulic connectivity slightly and yet significantly affected the microbial relative abundance of PSD-2 soils, with Actinobacteria being more abundant under drier conditions. There were less intra- and interkingdom associations in PSD-2 than PSD-1 soils, and such differences were little affected by pore volume and pore hydraulic connectivity. Our work highlighted PSD-dependent soil microbial distributions and associations, but ecological consequences need to be further examined.
Small, Ian M.Liao, Hui-LingZhang, KaileSchumacher, Lesley...
12页
查看更多>>摘要：Integrating two years of bahiagrass (Paspalum notatum Flugge) into the peanut (Arachis hypogea L.) and cotton (Gossypium hirsutum L.) cropping system improves soil quality and crop production as compared to a conventional peanut-cotton-cotton rotation (CR). However, it is unclear if this system, known as a sod-based rotation (SBR), affects soil biological communities (e.g., soil microorganisms and nematodes) and their trophic interactions. Furthermore, how soil trophic groups respond to agricultural management (e.g., irrigation) is understudied. In April 2017, we collected pre-planting soil samples (0-30 cm) from cotton plots located in Quincy (Florida, United States) that had been under CR (cotton grown in two consecutive years) and SBR (cotton grown only once) for 17 years. We used amplicon sequencing to investigate soil microbial communities and an inverted microscope technique to quantify nematodes. Compared to CR, SBR significantly increased nematode alpha diversity (one-way ANOVA; P < 0.05) and induced different nematode communities. In contrast, there were no significant differences in the diversity and structure of bacterial communities between SBR and CR. SBR plots were significantly enriched in Nitrospira, while the second of two consecutive years of cotton growth in CR had a higher relative abundance of Alphaproteobacteria (one-way ANOVA; P < 0.05). Plant-parasitic (848 counts per 100 g dry soil) and bacterial-feeding nematodes (798 counts per 100 g dry soil) had a similar abundance in SBR, while plant-parasitic nematodes (7772 counts per 100 g dry soil) were predominant in CR (<1000 counts per 100 g dry soil for all other taxa). SBR exhibited a greater number of significant paired Pearson correlations (P < 0.05) among functional groups of bacteria and nematodes compared to CR systems. Irrigation had no effect on the diversity and structure of bacterial and nematode communities in SBR, although some soil bacterial and nematode groups responded to irrigation. Overall, these results suggest that integrating bahiagrass to diversify the conventional peanut-cotton rotation is a sustainable approach to enhance soil biodiversity, with more diverse nematode communities and complex soil trophic interactions that will affect the response to crops and irrigation. Thus, future crop rotations should increase plant functional trait diversity (e.g., by adding perennial grasses) to maximize benefits to soil communities.
查看更多>>摘要：Organic farming aims at improving soil fertility in vineyard soils through a combination of farming practices. We studied the effect of organic management on community traits of free-living nematodes as well as bulk and microstructure properties of soil by comparing them to conventional management, both within vine rows and in interrows. The objectives of this study were to: 1) identify differences between management systems in terms of nematode abundance and molecularly measured community composition, and 2) to scrutinize, whether these changes can be explained by microstructural properties measured with X-ray computed tomography (X-ray CT) of individual soil aggregates. Nematode abundance was mainly governed by habitat constraints, which was reflected in significant correlations with soil moisture and with porosity in the habitable size range of 20-220 mu m obtained with X-ray CT. The lack of bioturbation by fine roots and the absence of irrigation reduced the abundance of water-filled, habitable pores, which resulted in the lowest nematode abundance in conventionally managed interrows without a grass cover. Community composition in terms of diversity and maturity, in turn, was not affected by habitat constraints but mainly governed by resource availability for the soil food web estimated by particulate and dissolved organic matter contents. The permanent grass cover and lack of tillage in interrows of the organic vineyard improved resource availability and promoted the build-up of omnivores and predators that are especially sensitive to disturbance. The organically managed interrows therefore had lower diversity and higher maturity than conventionally managed interrows. Differences between conventional and organic management were in general greater in interrows than within vine rows. These findings highlight the added value of pore structure investigations via X-ray CT in understanding trophic interactions of nematodes. At the same time, they stress the importance of exact sampling locations on nematode traits especially for perennial, woody crops.
查看更多>>摘要：ABSTR A C T Assessment of bacterial community distribution patterns along elevation gradients is invaluable in understanding the underlying mechanism involved in their diversity formation, sustenance, and response to environmental changes. However, no consensus has been reached as studies show contrasting patterns with different regulating factors due to habitat specificity and associated environmental conditions. Moreover, limited studies have considered spatial and temporal variability in bacterial diversity simultaneously. Here, we provide three years of meta-barcoding-based insight into the effects of environmental changes on soil bacterial communities and their driving factors across elevation-vegetation gradient (3373-4020 m) in the Himalaya. We also assess their sea-sonal and inter-annual variations. Results indicate that extreme elevations viz., low and high, having similar edaphic factors but different climatic regimes, showed similar bacterial diversity compared to a dip at mid-elevations caused by low moisture and substrate availability. Bacterial alpha-diversity and relative abundances of major phyla showed mid-elevation dip mainly caused by the direct impact of edaphic factors (soil organic carbon, total nitrogen, and moisture) but not temperature. Community composition showed three distinct clusters across elevation gradient and was also influenced directly by edaphic properties in addition to tem-perature. Moreover, we observed no significant seasonal and inter-annual variability in alpha and beta-diversity, sug-gesting stability in bacterial communities over time. The mid-elevations harbored predominantly competitive interactions, while low and high elevations exhibited co-operative interactions. Taken together, the results show the critical role of edaphic properties over the temperature in influencing bacterial diversity and indicate the community resilience towards climate warming. Our study will enhance the predictability of the community dynamics across broader spatio-temporal scales under changing climate.
查看更多>>摘要：In grafted apple combinations, rootstocks can increase the stress tolerance of plants, influence scion growth, and harbor a rich microbial community. However, whether scions modify plant growth, rootstock phenotypes and rhizosphere bacterial communities has not been clearly investigated. Here, 14 different combinations of two scion cultivars grafted on 7 rootstock genotypes were used as research materials, and we analyzed the plant traits, rhizosphere bacterial community, and potential functionalities across these plants in the same orchard. We found that apple scion cultivars influenced the tree height and trunk circumference, and the sugar concentration in roots varied significantly between scion cultivars, especially fructose and sucrose. Apple scion cultivars were the largest source of variation in the rhizosphere bacterial diversity and taxonomic composition of grafted combinations, and exerted a greater impact on the rhizosphere bacterial community than the rootstock genotype. The rhizosphere bacterial community networks were also significantly influenced by the scion cultivars. The dominant rhizosphere bacterial taxa were correlated with the root sugar concentration, especially sucrose. Further potential functional analysis of the bacterial community revealed that rhizosphere bacteria contained fructose and sucrose metabolism and had plant growth-promoting traits. Additionally, the predicted metabolism of the rhizosphere-associated bacterial communities varied depending on the scion cultivar. These results indicated that apple scion varieties regulate the rhizosphere bacterial community and function in grafted combinations through controlling the soluble sugar content, especially sucrose.
查看更多>>摘要：Earthworms are crucial regulators of many soil ecosystem processes; however, the effects of fertilization regimes on earthworm gut microbiota remains poorly understood. Here, we investigated the effects of 10 years of fertilization on the gut microbiota of two different earthworm species, Metaphire californica and Amynthas phaselus, belonging to anecic and endogeic ecological groups, respectively. Five fertilization treatments were designed as follows: non-nitrogen fertilizer (CK), nitrogen fertilizer only (NPK), and the combined application of inorganic fertilizers and three different application rates of pig manure (NPKM1, NPKM2, NPKM3). We observed that, compared with the CK and NPK treatments, the organic manure treatments had strong effects on both earthworm gut microbial communities and the associated metabolic functions. The lower application rate of organic manure significantly increased the gut microbial diversity of both earthworm species, which may have further improved their gut microbial metabolic potential, especially for the metabolism of various carbon resources. With the increasing application of organic fertilizers, the abundance of several bacterial families, such as Comamonadaceae, Oxalobacteraceae, and Cytophagaceae, significantly increased in the gut of M. californica. These families have also been identified as the primary indicator taxa of high organic matter inputs and play a crucial role in regulating microbial community functionalities. However, a similar trend was not observed in the gut of A. phaselus, indicating that A. phaselus might be less sensitive to fertilization regimes because it lives deeper in the soil and has a long digestive tract compared with those of M. californica. Our results demonstrated that long-term organic amendment application significantly shapes earthworm gut microbial communities and results in greater decomposition potential of the earthworm gut. Furthermore, our study found that lower application rates of organic matter may be beneficial for earthworm gut microbial diversity and functional structures.
NSTL
Elsevier