Effects of Rotations With Legume on Soil Functional Microbial Communities Involved in Phosphorus Transformation
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ABSTRACT:
SUBMITTER: Yu H
PROVIDER: S-EPMC8519609 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Increased soil nitrogen (N) from atmospheric N deposition could change microbial communities and functions. However, the underlying mechanisms and whether soil phosphorus (P) status are responsible for these changes still have not been well explained. Here, we investigated the effects of N and P additions on soil bacterial and fungal communities and predicted their functional compositions in a temperate forest. We found that N addition significantly decreased soil bacterial diversity in the organic (O) horizon, but tended to increase bacterial diversity in the mineral (A) horizon soil. P addition alone did not significantly change soil bacterial diversity but mitigated the negative effect of N addition on bacterial diversity in the O horizon. Neither N addition nor P addition significantly influenced soil fungal diversity. Changes in soil microbial community composition under N and P additions were mainly due to the shifts in soil pH and NO3- contents. N addition can affect bacterial functional potentials, such as ureolysis, N fixation, respiration, decomposition of organic matter processes, and fungal guilds, such as pathogen, saprotroph, and mycorrhizal fungi, by which more C probably was lost in O horizon soil under increased N deposition. However, P addition can alleviate or switch the effects of increased N deposition on the microbial functional potentials in O horizon soil and may even be a benefit for more C sequestration in A horizon soil. Our results highlight the different responses of microorganisms to N and P additions between O and A horizons and provides an important insight for predicting the changes in forest C storage status under increasing N deposition in the future.
| S-EPMC7699539 | biostudies-literature
Project description:Elevated nitrogen (N) deposition in humid tropical regions may exacerbate phosphorus (P) deficiency in forests on highly weathered soils. However, it is not clear how P availability affects soil microbes and soil carbon (C), or how P processes interact with N deposition in tropical forests. We examined the effects of N and P additions on soil microbes and soil C pools in a N-saturated old-growth tropical forest in southern China to test the hypotheses that (1) N and P addition will have opposing effects on soil microbial biomass and activity, (2) N and P addition will alter the composition of the microbial community, (3) the addition of N and P will have interactive effects on soil microbes and (4) addition-mediated changes in microbial communities would feed back on soil C pools. Phospholipid fatty acid (PLFA) analysis was used to quantify the soil microbial community following four treatments: Control, N addition (15 g N m(-2) yr(-1)), P addition (15 g P m(-2) yr(-1)), and N&P addition (15 g N m(-2) yr(-1) plus 15 g P m(-2) yr(-1)). These were applied from 2007 to 2011. Whereas additions of P increased soil microbial biomass, additions of N reduced soil microbial biomass. These effects, however, were transient, disappearing over longer periods. Moreover, N additions significantly increased relative abundance of fungal PLFAs and P additions significantly increased relative abundance of arbuscular mycorrhizal (AM) fungi PLFAs. Nitrogen addition had a negative effect on light fraction C, but no effect on heavy fraction C and total soil C. In contrast, P addition significantly decreased both light fraction C and total soil C. However, there were no interactions between N addition and P addition on soil microbes. Our results suggest that these nutrients are not co-limiting, and that P rather than N is limiting in this tropical forest.
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Project description:To study the soil mcirobial functional communities and the nutrient cycles couplings changes after exposure to different contaminant
2020-12-31 | GSE135153 | GEO
Project description:Soybean continuous cropping (SC) leads to continuous cropping obstacles, and soil-borne fungal diseases occur frequently. Rotation can alleviate continuous cropping obstacles. However, the long-term effects of continuous cropping and rotation on the structure and function of the fungal community in soil are not clear. In this study, five cropping systems, SC, fallow (CK), fallow-soybean (FS), corn-soybean (CS), and wheat-soybean (WS), were implemented in the long-term continuous cropping area of soybean. After 13 years of planting, high-throughput sequencing was used to evaluate the structure and diversity of soil fungal communities and to study the relationship between fungal communities and soil environmental factors. The results showed that the abundance and diversity of fungal flora in SC soil were the highest. There were significant differences in the formation of soil fungal communities between soybean continuous cropping and the other treatments. There were 355 species of endemic fungi in SC soil. There were 231 and 120 endemic species in WS and CS, respectively. The relative abundance of the potential pathogens Lectera, Gibberella, and Fusarium in the SC treatment soil was significantly high, and the abundance of all potential pathogens in CK was significantly the lowest. The abundance of Lectera and Fusarium in CS was significantly the lowest. There was a positive correlation between potential pathogens in the soil. The relative abundance of potential pathogens in the soil was significantly positively correlated with the relative abundance of Ascomycetes and negatively correlated with the relative abundance of Basidiomycetes. Potential pathogenic genera had a significant negative correlation with soil OM, available Mn, K and soil pH and a significant positive correlation with the contents of soil available Cu, Fe, and Zn. In general, the fungal communities of SC, FS, WS, and CS were divided into one group, which was significantly different from CK. WS and CS were more similar in fungal community structure. The CK and CS treatments reduced the relative abundance of soil fungi and potential pathogens. Our study shows that SC and FS lead to selective stress on fungi and pathogenic fungi and lead to the development of fungal community abundance and diversity, while CK and CS can reduce this development, which is conducive to plant health.
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Project description:Recent advancements in agricultural metagenomics allow for characterizing microbial indicators of soil health brought on by changes in management decisions, which ultimately affect the soil environment. Field-scale studies investigating the microbial taxa from agricultural experiments are sparse, with none investigating the long-term effect of crop rotation and tillage on microbial indicator species. Therefore, our goal was to determine the effect of rotations (continuous corn, CCC; continuous soybean, SSS; and each phase of a corn-soybean rotation, Cs and Sc) and tillage (no-till, NT; and chisel tillage, T) on the soil microbial community composition following 20 years of management. We found that crop rotation and tillage influence the soil environment by altering key soil properties, such as pH and soil organic matter (SOM). Monoculture corn lowered pH compared to SSS (5.9 vs. 6.9, respectively) but increased SOM (5.4% vs. 4.6%, respectively). Bacterial indicator microbes were categorized into two groups: SOM dependent and acidophile vs. N adverse and neutrophile. Fungi preferred the CCC rotation, characterized by low pH. Archaeal indicators were mainly ammonia oxidizers with species occupying niches at contrasting pHs. Numerous indicator microbes are involved with N cycling due to the fertilizer-rich environment, prone to aquatic or gaseous losses.
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Project description:Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Here, we identified important functional genes that characterize the rhizosphere microbial community to understand metabolic capabilities in the maize rhizosphere using the GeoChip-based functional gene array method. Significant differences in functional gene structure were apparent between rhizosphere and bulk soil microbial communities. Approximately half of the detected gene families were significantly (p<0.05) increased in the rhizosphere. Based on the detected gyrB genes, Gammaproteobacteria, Betaproteobacteria, Firmicutes, Bacteroidetes and Cyanobacteria were most enriched in the rhizosphere compared to those in the bulk soil. The rhizosphere niche also supported greater functional diversity in catabolic pathways. The maize rhizosphere had significantly enriched genes involved in carbon fixation and degradation (especially for hemicelluloses, aromatics and lignin), nitrogen fixation, ammonification, denitrification, polyphosphate biosynthesis and degradation, sulfur reduction and oxidation. This research demonstrates that the maize rhizosphere is a hotspot of genes, mostly originating from dominant soil microbial groups such as Proteobacteria, providing functional capacity for the transformation of labile and recalcitrant organic C, N, P and S compounds.
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Project description:The use of phosphorus (P) to alleviate soil nutrient deficiency alters resources in plant and microbial communities, but it remains unknown how mixed and monospecific planting of forest tree species shape soil microbial structure and functions in response to drought and its interplay with phosphorus addition. We investigated the microbial structure and chemical properties of forest soils planted with P. zhennan monoculture, A. cremastogyne monoculture, and their mixed cultures. The three planting systems were exposed to drought (30-35% water reduction) and the combination of drought with P. A well-watered treatment (80-85% water addition) of similar combinations was used as the control. Planting systems shaped the effects of drought on the soil microbial properties leading to an increase in nitrate nitrogen, urease activity, and microbial biomass carbon in the monocultures, but decrease in mixed cultures. In the monoculture of P. zhennan, addition of P to drought-treated soil increased enzyme activities, the concentration of dissolved organic nitrogen, and carbon, leading to increase in the total bacteria, G+ bacteria, and arbuscular mycorrhizal fungi. Except in the drought with P addition treatment, the impact of admixing on total phospholipid fatty acids (PLFAs), bacterial PLFA, and fungi PLFA was synergistic in all treatments. Our findings indicated that in monoculture of P. zhennan and its mixed planting with A. cremastogyne, greater biological activities could be established under drought conditions with the addition of P.
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Project description:Plants in their natural and agricultural environments are continuously exposed to a plethora of diverse microorganisms resulting in microbial colonization of plants in the rhizosphere. This process is believed to be accompanied by an intricate network of ongoing simultaneous interactions. In this study, we compared transcriptional patterns of Arabidopsis thaliana roots and shoots in the presence and absence of whole microbial communities extracted from compost soil. The results show a clear growth promoting effect of Arabidopsis shoots in the presence of soil microbes compared to axenically grown plants under identical conditions. Element analyses showed that iron uptake was facilitated by these mixed microbial communities which also lead to transcriptional downregulation of genes required for iron transport. In addition, soil microbial communities suppressed the expression of marker genes involved in oxidative stress/redox signalling, cell wall modification and plant defense. While most previous studies have focussed on individual plant-microbe interactions, our data suggest that multi-species transcriptional profiling, using simultaneous plant and metatranscriptomics coupled to metagenomics may be required to further increase our understanding of the intricate networks underlying plant-microbe interactions in their diverse environments.
2013-03-09 | GSE44984 | GEO
Project description:Oomycetes are critically important in soil microbial communities, especially for agriculture, where they are responsible for major declines in yields. Unfortunately, oomycetes are vastly understudied compared to bacteria and fungi. As such, our understanding of how oomycete biodiversity and community structure vary through time in the soil remains poor. Soil history established by previous crops is one factor known to structure other soil microbes, but this has not been investigated for its influence on oomycetes. In this study, we established three different soil histories in field trials; the following year, these plots were planted with five different Brassicaceae crops. We hypothesized that the previously established soil histories would structure different oomycete communities, regardless of their current Brassicaceae crop host, in both the roots and rhizosphere. We used a nested internal transcribed spacer amplicon strategy incorporated with MiSeq metabarcoding, where the sequencing data was used to infer amplicon sequence variants of the oomycetes present in each sample. This allowed us to determine the impact of different soil histories on the structure and biodiversity of the oomycete root and rhizosphere communities from the five different Brassicaceae crops. We found that each soil history structured distinct oomycete rhizosphere communities, regardless of different Brassicaceae crop hosts, while soil chemistry structured the oomycete communities more during a dry year. Interestingly, soil history appeared specific to oomycetes but was less influential for bacterial communities previously identified from the same samples. These results advance our understanding of how different agricultural practices and inputs can alter edaphic factors to impact future oomycete communities. Examining how different soil histories endure and impact oomycete biodiversity will help clarify how these important communities may be assembled in agricultural soils. IMPORTANCE Oomycetes cause global plant diseases that result in substantial losses, yet they are highly understudied compared to other microbes, like fungi and bacteria. We wanted to investigate how past soil events, like changing crops in rotation, would impact subsequent oomycete communities. We planted different oilseed crops in three different soil histories and found that each soil history structured a distinct oomycete community regardless of which new oilseed crop was planted, e.g., oomycete communities from last year's lentil plots were still detected the following year regardless of which new oilseed crops we planted. This study demonstrated how different agricultural practices can impact future microbial communities differently. Our results also highlight the need for continued monitoring of oomycete biodiversity and quantification.
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Project description:Functional attributes of microbial communities are difficult to study, and most current techniques rely on DNA- and rRNA-based profiling of taxa and genes, including microarrays containing sequences of known microorganisms. To quantify gene expression in environmental samples in a culture-independent manner, we constructed an environmental functional gene microarray (E-FGA) consisting of 13,056 mRNA-enriched anonymous microbial clones from diverse microbial communities to profile microbial gene transcripts. A new normalization method using internal spot standards was devised to overcome spotting and hybridization bias, enabling direct comparisons of microarrays. To evaluate potential applications of this metatranscriptomic approach for studying microbes in environmental samples, we tested the E-FGA by profiling the microbial activity of agricultural soils with a low or high flux of N?O. A total of 109 genes displayed expression that differed significantly between soils with low and high N?O emissions. We conclude that mRNA-based approaches such as the one presented here may complement existing techniques for assessing functional attributes of microbial communities.
| S-EPMC2976231 | biostudies-literature