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| Cladogram indicating the phylogenetic distribution of microbial lineages as affected by legume and grass. Each circle's diameter is proportional to the given taxon's relative abundance; circles represent phylogenetic levels from phylum to genus inside out. Red indicates control without plants, green indicates grass, blue indicates legume, and yellow indicates non-significant. (A) Bacteria; (B) Fungi.
Source publication
Plants are the essential factors shaping soil microbial community (SMC) structure. When most studies focus on the difference in the SMC structure associated different plant species, the variation in the SMC structure associated with phylogenetically close species is less investigated. Legume (Fabaceae) and grass (Poaceae) are functionally important...
Contexts in source publication
Context 1
... performed linear discriminant analysis (LDA) to reveal the microbial biomarkers of legume and grass. For bacteria, Figure 3A shows that legume enriched Actinobacteria and Nitrospirae phyla, in contrast to Bacteroidetes phylum enriched by grass. In more details, legume enriched Actinobacteria, Gammaproteobacteria, Betaproteobacteria, and Nitrospira classes, and grass enriched Sphingobacteria class; while Spartobacteria and Alphaproteobacteria classes were enriched in soils without plants (Figure 3A). ...
Context 2
... bacteria, Figure 3A shows that legume enriched Actinobacteria and Nitrospirae phyla, in contrast to Bacteroidetes phylum enriched by grass. In more details, legume enriched Actinobacteria, Gammaproteobacteria, Betaproteobacteria, and Nitrospira classes, and grass enriched Sphingobacteria class; while Spartobacteria and Alphaproteobacteria classes were enriched in soils without plants (Figure 3A). For fungi, Figure 3B shows that legume, grass and control enriched Ascomycota, Basidiomycota and Zygomycota phyla, respectively. ...
Context 3
... more details, legume enriched Actinobacteria, Gammaproteobacteria, Betaproteobacteria, and Nitrospira classes, and grass enriched Sphingobacteria class; while Spartobacteria and Alphaproteobacteria classes were enriched in soils without plants (Figure 3A). For fungi, Figure 3B shows that legume, grass and control enriched Ascomycota, Basidiomycota and Zygomycota phyla, respectively. In more detail, legume enriched Sordariomycetes class, and grass enriched Dothideomycetes, Glomeromycetes, Agaricomycetes; Data followed with lower letters in each column are separated by one-way ANOVA (Turkey HSD multiple range test, P = 0.05). ...
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Citations
... Soil fungal communities play key roles in making plant nutrients available, facilitating soil nutrient cycling and promoting beneficial ecosystem services in many agricultural systems. Previous studies have shown that legume cultivars play a key role in shaping soil microbial communities [53,54]. Our results demonstrated that RP cultivars were important determinants of soil fungal community structure and function. ...
Background
Crop-associated microorganisms play a crucial role in soil nutrient cycling, and crop growth, and health. Fine-scale patterns in soil microbial community diversity and composition are commonly regulated by plant species or genotype. Despite extensive reports in different crop or its cultivar effects on the microbial community, it is uncertain how rhizoma peanut (RP, Arachis glabrata Benth.), a perennial warm-season legume forage that is well-adapted in the southern USA, affects soil microbial community across different cultivars.
Results
This study explored the influence of seven different RP cultivars on the taxonomic composition, diversity, and functional groups of soil fungal communities through a field trial in Marianna, Florida, Southern USA, using next-generation sequencing technique. Our results showed that the taxonomic diversity and composition of the fungal community differed significantly across RP cultivars. Alpha diversity (Shannon, Simpson, and Pielou’s evenness) was significantly higher in Ecoturf but lower in UF_Peace and Florigraze compared to other cultivars (p < 0.001). Phylogenetic diversity (Faith’s PD) was lowest in Latitude compared to other cultivars (p < 0.0001). The dominant phyla were Ascomycota (13.34%), Mortierellomycota (3.82%), and Basidiomycota (2.99%), which were significantly greater in Florigraze, UF_Peace, and Ecoturf, respectively. The relative abundance of Neocosmospora was markedly high (21.45%) in UF_Tito and showed large variations across cultivars. The relative abundance of the dominant genera was significantly greater in Arbrook than in other cultivars. There were also significant differences in the co-occurrence network, showing different keystone taxa and more positive correlations than the negative correlations across cultivars. FUNGuild analysis showed that the relative abundance of functional guilds including pathogenic, saprotrophic, endophytic, mycorrhizal and parasitic fungi significantly differed among cultivars. Ecoturf had the greatest relative abundance of mycorrhizal fungal group (5.10 ± 0.44), whereas UF_Peace had the greatest relative abundance of endophytic (4.52 ± 0.56) and parasitic fungi (1.67 ± 0.30) compared to other cultivars.
Conclusions
Our findings provide evidence of crop cultivar’s effect in shaping fine-scale fungal community patterns in legume-based forage systems.
Graphical abstract
... In addition, legumes and gramineae tend to select speci c microbial taxa, which was probably advantageous for them (Bakker et al. 2013). Thus, legumes and gramineae differentially shaped the soil microbial community structure, resulting in different potential functions of microbial communities (Yang et al. 2017). Furthermore, we discovered that the predictive function related to chitin dissolution is prevalent in non-fertilization treatments. ...
Background and aims
Fertilization is a critical management practice for improving soil fertility and increasing agricultural production. We still don't fully understand how biotic and abiotic variables interact with soil multifunctionality in the rhizosphere soil of legume-Gramineae mixtures following fertilization. Studies on the effects of fertilization on the bacterial composition of legume-Gramineae mixtures in particular geographical areas are scarce.
Methods
To tackle this matter, we set up five treatments: no fertilizer zone (CK, N0P0K0), nitrogen-phosphorus-potassium zone (NPK, N2P2K2), nitrogen-less zone (PK, N0P2K2), phosphorus-less zone (NK, N2P0K2), and potassium-less zone (NP, N2P2K0). The soil data were measured to assess the response mechanism of legume-Gramineae mixtures to fertilization management.
Results
The fertilization treatment resulted in a beneficial impact on the rhizosphere soil nutrients, enzyme activity, and biological characteristics, reaching the maximum under N2P2K2 treatment. The analysis of the bacterial community revealed that the oligotrophic taxa decreased primarily due to fertilizer addition, including Acidobacteria, and enhancing the copiotrophic taxa, such as Bacteroidetes and Proteobacteria, in the soil. Furthermore, according to FAPROTAX analysis, the results indicated variations in the function of the bacterial community in the rhizosphere soil of legumes and gramineae. Fertilization indirectly affected soil versatility by changing the diversity and composition of bacterial communities.
Conclusions
The bacterial community can be reshaped and the properties of the rhizosphere soil can be modified by different fertilization treatments, thus impacting the potential function of the bacterial community. This study has the potential to offer scientific guidance for the rational management of fertilization in legume-Gramineae mixtures.
... Legumes incorporated into grasslands often enhance soil bacterial diversity and community composition directly through the supply of N from biological N 2 fixation and the release of N-rich root exudates and plant litter [13,35,36]. Increased microbial diversity in agroecosystems has been linked to increases in ecosystem services, such as nutrient cycling and nutrient availability [24,37], as well as resilience to environmental disturbances [38,39]. ...
... Reasons for the shift are not well understood, but Firmicutes have been reported in older, stable agroecosystems [45]. Different plant species have been linked to unique microbial taxa due to differences in plant litter quality and root exudate composition [36,44]. Guerra et al. [10] showed that Bryobacter, which is associated more with abundant C substrates, dominated a bahiagrass system, while RP had a greater relative abundance of Crossiella. ...
The introduction of rhizoma peanut (RP Arachis glabrata Benth) into bahiagrass (Paspalum notatum Flüggé) may require time to develop stable plant–soil microbe interactions as the microbial legacy of the previous plant community may be long-lasting. A previous study showed that <2 years of introducing rhizoma peanut into bahiagrass pastures minimally affected soil bacterial diversity and community composition. In this study, we compared the effects of the long-term inclusion of rhizoma peanut (>8 years) into bahiagrass on soil bacterial diversity and community composition against their monocultures at 0 to 15 and 15 to 30 cm soil depths using next-generation sequencing to target bacterial 16S V3–V4 regions. We observed that a well-established RP–bahiagrass mixed stand led to a 36% increase in bacterial alpha diversity compared to the bahiagrass monoculture. There was a shift from a soil bacterial community dominated by Proteobacteria (~26%) reported in other bahiagrass and rhizoma peanut studies to a soil bacterial community dominated by Firmicutes (39%) in our study. The relative abundance of the bacterial genus Crossiella, known for its antimicrobial traits, was enhanced in the presence of RP. Differences in soil bacterial diversity and community composition were substantial between 0 to 15 and 15 to 30 cm soil layers, with N2-fixing bacteria belonging to the phylum Proteobacteria concentrated in 0 to 15 cm. Introducing RP into bahiagrass pastures is a highly sustainable alternative to mineral N fertilizer inputs. Our results provide evidence that this system also promotes greater soil microbial diversity and is associated with unique taxa that require further study to better understand their contributions to healthy pastures.
... The distinct abundance and composition of the root fungal communities in the main crops as a result of the CC legacy may be due to differences in CC root properties such as root biomass, root length and root exudates, which modulate root and soil fungal communities (Broeckling et al., 2008). Thereby, different CC species can select for distinct soil and root associated microbial populations (Finney et al., 2017;Zhou et al., 2017) which can be carried over to the next crop. Soil texture together with cover crops have been shown to shape soil fungal communities in crop rotations (Cloutier et al., 2020;Wakelin et al., 2008). ...
Cover crops (CC) can promote nutrient retention and recycling for main crops, yet may also promote soil‐borne pathogens or suppress beneficial root symbionts such as arbuscular mycorrhizal fungi (AMF). We investigated how root fungal communities of main crop are affected by preceding CC monocultures and mixtures and by main crop identity. We expected that AMF abundance and diversity in main crops are promoted by AM‐host CC, and suppressed by non‐AM host CC, and that mixtures of CC species can promote beneficial and suppress pathogenic root fungi. Our full‐factorial field experiment comprised a crop rotation in a sand soil with different CC treatments (monocultures of radish (AM non‐host), ryegrass, clover, vetch (AM‐hosts), mixtures of radish+vetch, ryegrass+clover, and fallow), and two main crops (oat and endive). At peak crop growth we investigated the root fungal communities in the main crops using microscopy and high throughput sequencing (Illumina MiSeq). Cover crop identity was of prime importance and CC legacy overruled main crop identity in determining root fungal communities in main crops. Compared to fallow CC with ryegrass increased AMF colonization and richness in both main crops and of non‐AMF in oat. Legacies of ryegrass, ryegrass+clover and vetch resulted in distinct root fungal communities in the main crops, while the legacy of CC with radish were similar to the legacy of fallow. Root fungal community in crops after clover had highest abundance of representative fungal pathogens in contrast with the other CC treatments that resulted in fungal communities where pathogens were scarce. Oppositely to expected, CC mixtures did not enhance fungal symbionts or suppressed pathogens. Overall, fungal communities in roots of the main crops in our field experiment, were determined by the preceding CC species in monoculture, rather than by the CC AMF preference or functional group. This research highlights that the choice of CC determines the root fungal community in main crop which may influence crop quality.
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... Legumes supply N through biological nitrogen fixation (BNF), and they can alter soil chemical properties by releasing N-rich root exudates [10,11]. As a result, soil microbial communities are also altered, in part, by enhancing soil microbial mediated N cycling processes [12,13]. Legumes have been reported to enhance the relative abundance of soil BNF bacteria [14,15] but also promote the activities of denitrifying microbial populations [16,17]. ...
... can also live non-symbiotically in soils, where they assimilate simple sugars and organic and amino acids, and it has been shown that growth of rhizobia is stimulated by the presence of legumes and non-leguminous dicots, whereas grasses maintain smaller numbers of rhizobia (Tuzimura and Watanabe 1962). In this study, the nitrifying Nitrospira sp. and an unclassified genus of the Comamonadaceae family containing denitrifiers (Patureau et al. 1996;Khan et al. 2002) were also less abundant in grass soils at low N than in legume soils, consistent with a study showing that legume species enriched Nitrospira in the soil microbiome (Zhou et al. 2017). These findings indicate that N fixed by Rhizobium associated with legumes might not only promote plant growth but also provide soil with N-containing substrates that promote propagation of the Nitrospira and denitrifiers in the soils. ...
Context There is concern that the introduction of ‘novel’ plant germplasm/traits could outpace our capacity to measure and so assess their impacts on soil microbial communities and function. Aim This study aimed to investigate the effects of plant species/functional traits, nitrogen (N) fertilisation and endophyte infection on grassland soil microbial communities within a short time span of 2 years. Methods Two field experiments with monoculture plots were conducted in a common soil. Experiment 1 compared grasses and legumes, using two cultivars of perennial ryegrass (Lolium perenne) that varied in fructan content, along with the legumes white clover (Trifolium repens) and bird’s-foot trefoil (Lotus pedunculatus) that varied in tannin content. Grass treatments received high and low N application levels. Experiment 2 compared the presence/absence of Epichloë strains in ryegrass, tall fescue (Schedonorus phoenix) and meadow fescue (Schedonorus pratensis). Soil microbial communities were analysed by using high-throughput sequencing of DNA isolated from bulk soil cores. Key results Higher abundance of ligninolytic fungi was found in grass soils and pectinolytic fungi in legume soils. Levels of N fertilisation and fructan in ryegrass had only minor effects on soil fungal communities. By contrast, N fertilisation or fixation had a strong effect on bacterial communities, with higher abundance of nitrifiers and denitrifiers in high-N grass soils and in legume soils than in low-N grass soils. Epichloë affected soil microbiota by reducing the abundance of certain fungal phytopathogens, increasing mycorrhizal fungi and reducing N-fixing bacteria. Conclusions Chemical composition of plant cell walls, which differs between grasses and legumes, and presence of Epichloë in grasses were the main drivers of shifts in soil microbial communities. Implications Impacts of farming practices such as mono- or poly-culture, N fertilisation and presence of Epichloë in grasses on soil microbial communities should be considered in pasture management.
... Plant species is an important factor influencing soil microbial diversity and community compositions through root exudates and morphology (Zhang et al. 1991;Berg and Smalla 2009;Shi et al. 2011;Turner et al. 2013;Zhou et al. 2017). In nitrogen (N) limited pastures, legumes supply N through biological N fixation (BNF) and release root compounds that are richer in N than grasses (Paynel et al. 2001;Jalonen et al. 2009;Jaramillo et al. 2021). ...
... In nitrogen (N) limited pastures, legumes supply N through biological N fixation (BNF) and release root compounds that are richer in N than grasses (Paynel et al. 2001;Jalonen et al. 2009;Jaramillo et al. 2021). As a result, legumes have been shown to have a greater influence on soil bacterial diversity and their community composition than grass species (Zhou et al. 2017). Integrating legumes into pastures can modify soil microbial communities and even stimulate beneficial microbial taxa involved in nutrient cycling and plant promotion (Guerra et al. 2022). ...
... This highlights the role of plant specificity in regulating these microbes in diverse environments (Wang et al. 2019b). The importance of plant functional groups in selecting for specific microbial taxa in soils has been established in several studies (Zhou et al. 2017;Hellequin et al. 2021). Compared to BG-RP mixture, BG promoted the relative abundance of the bacterial group, Hyphomicrobiaceae (Fig. S6A). ...
Rhizoma peanut (RP) (Arachis glabrata Benth.) is a sustainable warm-season perennial forage option in Florida that reduces the reliance on nitrogen (N) fertilizers. This forage legume has been demonstrated to improve bahiagrass (BG) (Paspalum notatum Flüggé) production under low fertilization inputs and promote beneficial soil microorganisms like N2 fixing bacteria. However, whether such microbial characteristics are consistent across different locations and growing seasons is unknown. We applied amplicon sequencing to target soil bacteria and fungi from surface soil (0–20 cm) collected from BG monoculture and BG-RP mixtures in May and July at North, Central, and South farms in Florida. The effect of BG or BG-RP mixtures on bacterial and fungal alpha and beta diversity was impacted by sampling time/location or their interactions. Bacterial alpha diversity was only greater in BG-RP mixtures than BG in May at North farm. Across all farm locations, fungal alpha diversity was greater in the mixtures than BG in July. Rhizoma peanut promoted the relative abundance of the fungal family Didymellaceae, across sampling time and location. However, the effect of RP on Nectriceae was dependent on farm location. Generally, location was a major factor driving the changes in soil microbial community composition, which was explained by soil chemical properties, especially soil pH. Our findings demonstrated that the impact of forage systems on microbial communities in Florida soil is mainly contextual, depending on soil properties, locations, and seasons, a given forage system may differentially affect soil microbial diversity and community composition.
... Legumes have evolved to exude compounds like flavonoids that serve as chemo-attractants for N 2 -fixing bacteria, while cereals are known to produce complex organic compounds that promote formation of rhizosheaths (Galloway et al., 2020). Legumes have been shown to secrete more low molecular-weight compounds (amino acids, sugars, flavonoids) than grass species (Isobe et al. (2001), and the range of variability in root exudates among legume species is greater than for cereals (Zhou et al., 2017). In our study, soybean rhizospheres had lower alpha-diversity than corn, having unique bacterial compositions clearly discernible from the soybean bulk soils. ...
Agroecosystem management practices, plant-microbe interactions, and climate are all factors that influence soil microbial community diversity and functionality. Herein, we assessed diversity of soil bacterial-archaeal assemblages and denitrification gene markers in a long-term tillage field experiment. We evaluated bulk and rhizosphere soils from two crop years (corn and soybean) of a three-year rotation of corn-soybean-small grain + cover crop. Soil samples were collected at three growth stages from corn and soybean plants and across three tillage practices that had been applied every year for 40 years. Tillage practices represented three levels of disturbance intensity ranging from low (no-till) to intermediate (chisel-disk) to high (moldboard plow) intensities. Bacterial assemblage diversity differed in soils having contrasting tillage histories and from bulk or rhizosphere soil (compartments), crop year, and growth stage. Compared to plowed and chisel-disked soils, no-till soils had lower abundances of denitrification genes, higher abundances of genes for dissimilatory nitrate reduction to ammonium (DNRA), and higher abundances of family-level taxa associated with archaeal nitrification and anammox. Soybean rhizospheres exerted stronger selection on bacterial-archaeal composition and diversity relative to corn rhizospheres. Abundances of N genes were grouped by factors related to weather, as well as management and soil compartment, which could impact activity related to denitrification and DNRA. Low intensity tillage may provide an option to reduce potential ‘hot spots’ or ‘hot moments’ for N losses in agricultural soils, although weather and crop type are also important factors that can influence how tillage affects microbial assemblages and microbial N use.
... Soil microbes have vital rule in a variety of ecological activities, including organic matter decomposition, nitrogen cycling, and plant productivity [73,74]. The study of how different plant species and their configurations, such as forbs, grasses, and legumes, regulate their collaborated microbial association is receiving more consideration (e.g., [75,76]). Within a particular soil type, distinct plant species found to assemblage-distinguished configuration of microbial colonization [77]. ...
This chapter discusses concerning land use shifting influences to the soil microorganisms dynamic, especially in Indonesia where the biggest tropical rain forest established. Indonesia is among the region with largest tropical rain forest in the world. The country is also rich in plants biodiversity associated with the biophysical and the climate conditions forming the tropical rain forest. The high of plant diversity of Indonesia forest is illustrated by Malik et al. (Jurnal Ilmiah Pendidikan Sains 1:35–42, 2020), in Kalimantan in a hectar of forest can be identified more than 150 species.
... Variation in rhizobia populations can be attributed to the influence of root exudates, plant age, soil biogeochemical and physicochemical properties, and environmental conditions (Wieland et al., 2011). Balota and Chaves (2011) and Zhou et al. 2017 also reported the greatest variation in microbial populations with respect to legumes. ...
The rhizosphere contains a host of microorganisms that are affected by both abiotic stress and biotic stress. Low fertility is a major problem in establishing vegetation in degraded areas. Nitrogen (N) is an important plant nutrient needed for plant growth in abundance in the earth's atmosphere however; most tropical soils are deficient in available N. In low-lying ecosystems and without human fertilization or supplementation, the nutrients found in plants come from organic matter or organic matter. The amount of fixed nitrogen depends on the nitrogen level of the soil, the type of rhizobia that attacks the pods, the growth of the plant and the length of the growing season. Nitrogen-fixing tree species can play an important role in stabilizing sandy and eroded soils, utilizing deep groundwater due to its broad roots and thus helping to increase soil fertility. Among the indigenous legume species Albizia procera is best known for the traditional legume species, which are associated with Rhizobium and this association leads to nitrogen fixation in the atmosphere. Soil rhizobial value calculations showed high number of bacteria in the soil sample of Baddi (297.21 cfu g-1) and a small amount in Solan (243.46 cfu g-1). On the basis of verification tests namely, congo red test, ketolactose testing and plant infection testing in all isolated areas, more than 70.58 per cent (26 of 34) were confirmed as rhizoba. All isolates are tested for factors that promote the growth of different plants, namely, p-solubilizers, siderophore producers and IAA producers. Of these 26 rhizobial isolate, 82.38 per cent were p-solubilizers, 54.45 per cent were siderophore producers and 75.47 per cent were IAA producers. This approach was to improve the bio-inoculum to increase soil fertility by injecting the most suitable type of bacteria that would bring the best plant into the natural environment without adding fertilizer from the outside. Rhizobia is very important in improving the availability of nitrogen in the soil.
