scholarly journals Phosphorus Reduces Negative Effects of Nitrogen Addition on Soil Microbial Communities and Functions

2020 ◽  
Vol 8 (11) ◽  
pp. 1828 ◽  
Author(s):  
Zongwei Xia ◽  
Jingyi Yang ◽  
Changpeng Sang ◽  
Xu Wang ◽  
Lifei Sun ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Diversity ◽  
Soil Microbial Communities ◽  
N Deposition ◽  
N Fixation ◽  
N Addition ◽  
Soil Bacterial Diversity ◽  
Soil Microbial ◽  
Soil Bacterial ◽  
P Addition

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.

scholarly journals Cover Cropping Impacts Soil Microbial Communities and Functions in Mango Orchards

Agriculture ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 343
Author(s):  
Zhiyuan Wei ◽  
Quanchao Zeng ◽  
Wenfeng Tan
Keyword(s):  
Bacterial Diversity ◽  
Fungal Diversity ◽  
Soil Microbial Communities ◽  
Soil Bacterial Diversity ◽  
Mango Fruit ◽  
Soil Biodiversity ◽  
Soil Microbial ◽  
Cover Cropping ◽  
Soil Bacterial ◽  
Soil Fungal Diversity

Soil microbes play critical roles in nutrient cycling, net primary production, food safety, and climate change in terrestrial ecosystems, yet their responses to cover cropping in agroforestry ecosystems remain unknown. Here, we conducted a field experiment to assess how changes in cover cropping with sown grass strips affect the fruit yields and quality, community composition, and diversity of soil microbial taxa in a mango orchard. The results showed that two-year cover cropping increased mango fruit yields and the contents of soluble solids. Cover cropping enhanced soil fungal diversity rather than soil bacterial diversity. Although cover cropping had no significant effects on soil bacterial diversity, it significantly influenced soil bacterial community compositions. These variations in the structures of soil fungal and bacterial communities were largely driven by soil nitrogen, which positively or negatively affected the relative abundance of both bacterial and fungal taxa. Cover cropping also altered fungal guilds, which enhanced the proportion of pathotrophic fungi and decreased saprotrophic fungi. The increase in fungal diversity and alterations in fungal guilds might be the main factors to consider for increasing mango fruit yields and quality. Our results indicate that cover cropping affects mango fruit yields and quality via alterations in soil fungal diversity, which bridges a critical gap in our understanding of the linkages between soil biodiversity and fruit quality in response to cover cropping in orchard ecosystems.

scholarly journals Agricultural practice negatively affects soil microbial diversity and nitrogen functional genes comparing to adjacent native forest soils

2021 ◽  
Author(s):  
Tiehang Wu ◽  
Michael Sabula ◽  
Holli Milner ◽  
Gary Strickland ◽  
Gan Liu
Keyword(s):  
Community Structure ◽  
Bacterial Diversity ◽  
Forest Soils ◽  
Agricultural Practices ◽  
Functional Genes ◽  
Agricultural Practice ◽  
Soil Bacterial Diversity ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Soil Bacterial

Soil microbial diversity and community are determined by anthropogenic activities and environmental conditions, which greatly affect the functioning of ecosystem. We investigated the soil bacterial diversity, communities, and nitrogen (N) functional genes with different disturbance intensity levels from crop, transition, to forest soils at three locations in the coastal region of Georgia, USA. Illumina high-throughput DNA sequencing based on bacterial 16S rRNA genes were performed for bacterial diversity and community analyses. Nitrifying (AOB amoA) and denitrifying (nirK) functional genes were further detected using quantitative PCR (qPCR) and Denaturing Gradient Gel Electrophoresis (DGGE). Soil bacterial community structure determined by Illumina sequences were significantly different between crop and forest soils (p < 0.01), as well as between crop and transition soils (p = 0.01). However, there is no difference between transition and forest soils. Compared to less disturbed forest, agricultural practice significantly decreased soil bacterial richness and Shannon diversity. Soil pH and nitrate contents together contributed highest for the observed different bacterial communities (Correlations = 0.381). Two OTUs (OTU5, OTU8) belonging to Acidobacteriales species decreased in crop soils, however, agricultural practices significantly increased an OTU (OTU4) of Nitrobacteraceae. The relative abundance of AOB amoA gene was significantly higher in crop soils than in forest and transition soils. Distinct grouping of soil denitrifying bacterial nirK communities was observed and agricultural practices significantly decreased the diversity of nirK gene compared to forest soils. Anthropogenic effects through agricultural practices negatively affecting the soil bacterial diversity, community structure, and N functional genes.

scholarly journals Activation of the SA-Associated Plant Defense Pathway Alters the Composition of Soil Bacterial Communities

2021 ◽  
Author(s):  
Jing Zhang ◽  
Peter G.L. Klinkhamer ◽  
Klaas Vrieling ◽  
T. Martijn Bezemer
Keyword(s):  
Plant Growth ◽  
Microbial Communities ◽  
Signaling Pathway ◽  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Soil Microbial Communities ◽  
Core Microbiome ◽  
Soil Microbial ◽  
Soil Bacterial ◽  
Sa Signaling

Abstract Background and aimsMany plant species grow better in sterilized than in live soil. Foliar application of SA mitigates this negative effect of live soil on the growth of the plant Jacobaea vulgaris. To examine what causes the positive effect of SA application on plant growth in live soils, we analyzed the effects of SA application on the composition of active rhizosphere bacteria in the live soil. Methods We studied this over four consecutive plant cycles (generations), using mRNA sequencing of the microbial communities in the rhizosphere of J. vulgaris. ResultsOur study shows that the composition of the rhizosphere bacterial communities of J. vulgaris greatly differed among generations. Application of SA resulted in both increases and decreases in a number of active bacterial genera in the rhizosphere soil, but the genera that were affected by the treatment differed among generations. In the first generation, there were no genera that were significantly affected by the SA treatment, indicating that induction of the SA defense pathway in plants does not lead to immediate changes in the soil microbial community. 89 species out of the total 270 (32.4%) were present in all generations in all soils of SA-treated and control plants suggesting that these make up the “core” microbiome. On average in each generation, 72.9% of all genera were present in both soils. Application of SA to plants significantly up-regulated genera of Caballeronia, unclassified Cytophagaceae, Crinalium and Candidatus Thermofonsia Clade 2, and down-regulated genera of Thermomicrobiales, unclassified Rhodobacterales, Paracoccus and Flavihumibacter. While the functions of many of these bacteria are poorly understood, bacteria of the genus Caballeronia play an important role in fixing nitrogen and promoting plant growth, and hence this suggests that activation of the SA signaling pathway in J. vulgaris plants may select for bacterial genera that are beneficial to the plant. ConclusionsOverall, our study shows that aboveground activation of defenses in the plant affects soil microbial communities and, as soil microbes can greatly influence plant performance, this implies that induction of plant defenses can lead to complex above-belowground feedbacks. Further studies should examine how activation of the SA signaling pathway in the plant changes the functional genes of the rhizosphere soil bacterial community.

scholarly journals Management and Soil Conditions Influence Common Scab Severity on Potato Tubers Via Indirect Effects on Soil Microbial Communities

2020 ◽  
Vol 110 (5) ◽  
pp. 1049-1055
Author(s):  
Emily W. Lankau ◽  
Dianne Xue ◽  
Rachel Christensen ◽  
Amanda J. Gevens ◽  
Richard A. Lankau
Keyword(s):  
Microbial Communities ◽  
Indirect Effects ◽  
Common Scab ◽  
Soil Microbial Communities ◽  
Farm Management ◽  
Equation Modeling ◽  
Soil Conditions ◽  
Potato Market ◽  
Soil Microbial ◽  
Soil Bacterial

Common scab, caused by Streptomyces scabies and related species, is a potato tuber blemish disease that causes reductions in marketable yield worldwide. Evidence of suppression of common scab by indigenous soil microbial populations has been found in several studies. However, we lack a comprehensive understanding of how common scab severity relates functionally to potato varieties, farming systems, soil physical and chemical properties, and soil microbial communities. These factors may affect disease directly or indirectly by affecting one of the other variables. We performed a survey of 30 sampling locations across 12 fields in Wisconsin and used structural equation modeling to disentangle the direct effects of potato market classes, farm management (conventional versus organic), and soil physiochemical properties on common scab severity from their indirect effects mediated through soil bacterial and fungal communities. We found that, although potato market classes affected disease severity directly, the effects of farm management and soil physiochemistry were best explained as indirect, mediated by their impacts on soil bacterial communities. This suggests that evaluating the consequences of specific management practices for soil microbial communities may be useful for understanding disease pressure across fields.

scholarly journals Impact of Land Use on Bacterial Diversity and Community Structure in Temperate Pine and Indigenous Forest Soils

Diversity ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 217 ◽  
Author(s):  
Adenike Eunice Amoo ◽  
Olubukola Oluranti Babalola
Keyword(s):  
Land Use ◽  
Microbial Communities ◽  
Bacterial Diversity ◽  
Correspondence Analysis ◽  
Canonical Correspondence Analysis ◽  
Bacterial Communities ◽  
Soil Microbial Communities ◽  
Soil Characteristics ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

Soil microbial communities are an important part of ecosystems that possess the capability to improve ecosystem services; however, several aspects of the ecology of forest soil bacterial communities are still unknown. Here, we investigated the impact of land-use change on soil bacterial communities and the soil characteristics. High-throughput sequencing was used to ascertain the bacterial diversity and canonical correspondence analysis was used to determine relationships between the bacterial communities and environmental variables. Our results show spatial heterogeneity in the distribution of the microbial communities and significant relationships between the microbes and soil characteristics (axis 1 of the canonical correspondence analysis (CCA) plot explained 64.55% of the total variance while axis 2 described 24.49%). Knowledge of this is essential as it has direct consequences for the functioning of the soil ecosystem.

scholarly journals Agricultural practice altering soil microbial diversity and nitrogen functional genes comparing to adjacent native forest soils

2021 ◽  
Author(s):  
Tiehang Wu ◽  
Michael Sabula ◽  
Holli Milner ◽  
Gary Strickland ◽  
Gan Liu
Keyword(s):  
Community Structure ◽  
Bacterial Diversity ◽  
Forest Soils ◽  
Agricultural Practices ◽  
Functional Genes ◽  
Agricultural Practice ◽  
Soil Bacterial Diversity ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Soil Bacterial

Soil microbial diversity and community are determined by anthropogenic activities and environmental conditions, which greatly affect the functioning of ecosystem. We investigated the soil bacterial diversity, communities, and nitrogen (N) functional genes with different disturbance intensity levels from crop, transition, to forest soils at three locations in the coastal region of Georgia, USA. Illumina high-throughput DNA sequencing based on bacterial 16S rRNA genes were performed for bacterial diversity and community analyses. Nitrifying (AOB amoA) and denitrifying (nirK) functional genes were further detected using quantitative PCR (qPCR) and Denaturing Gradient Gel Electrophoresis (DGGE). Soil bacterial community structure determined by Illumina sequences were significantly different between crop and forest soils (p < 0.01), as well as between crop and transition soils (p = 0.01). However, there is no difference between transition and forest soils. Compared to less disturbed forest, agricultural practice significantly decreased soil bacterial richness and Shannon diversity. Soil pH and nitrate contents together contributed highest for the observed different bacterial communities (Correlations = 0.381). Two OTUs (OTU5, OTU8) belonging to Acidobacteriales species decreased in crop soils, however, agricultural practices significantly increased an OTU (OTU4) of Nitrobacteraceae. The relative abundance of AOB amoA gene was significantly higher in crop soils than in forest and transition soils. Distinct grouping of soil denitrifying bacterial nirK communities was observed and agricultural practices significantly decreased the diversity of nirK gene compared to forest soils. Anthropogenic effects through agricultural practices negatively affecting the soil bacterial diversity, community structure, and N functional genes.

scholarly journals Organic manure managements increases soil microbial community structure and diversity in double-cropping paddy field of Southern China

2020 ◽  
Author(s):  
Haiming Tang ◽  
Xiaoping Xiao ◽  
Chao Li ◽  
Xiaochen Pan ◽  
Kaikai Cheng ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Rice Straw ◽  
Paddy Field ◽  
Southern China ◽  
Soil Microbial Communities ◽  
Organic Manure ◽  
Chemical Fertilizer ◽  
Soil Microbial ◽  
Double Cropping ◽  
Soil Bacterial

AbstractThe soil physicochemical properties were affected by different fertilizer managements, and the soil microbial communities were changed. Fertilizer regimes were closely relative to the soil texture and nutrient status in a double-cropping paddy field of southern China. However, there was limited information about the influence of different long-term fertilizer management practices on the soil microbial communities in a double-cropping rice (Oryza sativa L.) fields. Therefore, the 39-year long-term fertilizer regimes on soil bacterial and fungal diversity in a double-cropping paddy field of southern China were studied by using Illumina sequencing and quantitative PCR technology in the present paper. The filed experiment were including chemical fertilizer alone (MF), rice straw residue and chemical fertilizer (RF), 30% organic manure and 70% chemical fertilizer (OM), and without fertilizer input as a control (CK). The results showed that diversity indices of soil microbial communities with application of organic manure and rice straw residue treatments were higher than that without fertilizer input treatment. Application of organic manure and rice straw residue managements increase soil bacterial abundance of the phylum Proteobacteria, Actinobacteria, and Gammaproteobacteria, and soil fungi abundance of the phylum Basidiomycota, Zygomycota and Tremellales were also increased. Compared with CK treatment, the value of Richness, Shannon and McIntosh indices, and taxonomic diversity were increased with RF and OM treatments. This finding demonstrated that RF and OM treatments modify soil bacterial and fungal diversity. Therefore, the combined application of organic manure or rice straw residue with chemical fertilizer managements could significantly increase the abundance of profitable functional bacteria and fungi species in double-cropping rice fields of southern China.

scholarly journals Long-Term Drought and Warming Alter Soil Bacterial and Fungal Communities in an Upland Heathland

Ecosystems ◽  
2021 ◽  
Author(s):  
Fiona M. Seaton ◽  
Sabine Reinsch ◽  
Tim Goodall ◽  
Nicola White ◽  
Davey L. Jones ◽  
...  
Keyword(s):  
Climate Change ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Fungal Communities ◽  
Its2 Region ◽  
Rrna Gene ◽  
Summer Drought ◽  
Soil Microbial ◽  
Soil Bacterial

AbstractThe response of soil microbial communities to a changing climate will impact global biogeochemical cycles, potentially leading to positive and negative feedbacks. However, our understanding of how soil microbial communities respond to climate change and the implications of these changes for future soil function is limited. Here, we assess the response of soil bacterial and fungal communities to long-term experimental climate change in a heathland organo-mineral soil. We analysed microbial communities using Illumina sequencing of the 16S rRNA gene and ITS2 region at two depths, from plots undergoing 4 and 18 years of in situ summer drought or warming. We also assessed the colonisation of Calluna vulgaris roots by ericoid and dark septate endophytic (DSE) fungi using microscopy after 16 years of climate treatment. We found significant changes in both the bacterial and fungal communities in response to drought and warming, likely mediated by changes in soil pH and electrical conductivity. Changes in the microbial communities were more pronounced after a longer period of climate manipulation. Additionally, the subsoil communities of the long-term warmed plots became similar to the topsoil. Ericoid mycorrhizal colonisation decreased with depth while DSEs increased; however, these trends with depth were removed by warming. We largely ascribe the observed changes in microbial communities to shifts in plant cover and subsequent feedback on soil physicochemical properties, especially pH. Our results demonstrate the importance of considering changes in soil microbial responses to climate change across different soil depths and after extended periods of time.

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