Agricultural land use determines functional genetic diversity of soil microbial communities

Manoharan, Lokeshwaran; Kushwaha, Sandeep; Ahrén, Dag; Hedlund, Katarina

doi:10.1016/j.soilbio.2017.09.011

Cited by 47 publications

(29 citation statements)

References 65 publications

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“…The spores and species of arbuscular mycorrhizal fungi were strongly associated with grassland patches, followed by low- and moderate arable lands and the lowest in the high-input maize monocropping ( Oehl et al, 2003 ). In another study of soil microbial communities, Eurotiales were abundant in grassland soils and Glomerellales in wheat fields ( Manoharan et al, 2017 ). Similarly, we found that Eurotiales were strongly correlated with grassland and stems, and that Glomerellales negatively correlated with semi-natural habitats but positively associated with cultivated land in the landscape.…”

Section: Discussionmentioning

confidence: 99%

Fungal Endophyte Communities of Crucifer Crops Are Seasonally Dynamic and Structured by Plant Identity, Plant Tissue and Environmental Factors

et al. 2020

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Endophytic fungi are important in diverse plant functions but knowledge of the factors that shape assemblages of these symbionts is lacking. Here, using a culture-dependent approach, we report 4,178 endophytic fungal isolates representing 16 orders isolated from stems, roots and leaves of three cruciferous plant species, Chinese cabbage ( Brassica rapa L.), radish ( Raphanus sativus L.) and white cabbage ( B. olerocea L.), collected from 21 focal fields with different landscape contexts and pesticide uses during four seasons (summer, autumn, winter and spring). The colonization rate of fungi was found to be most strongly affected by season, plant identity and plant tissue. The colonization was highest during autumn, followed by summer, spring and lowest during winter. The colonization was highest in B. olerocea (53.2%), followed by B. rapa (42.6%), and lowest in R. sativus (35.0%). The colonization was highest in stems (51.9%) in all plant types, followed by leaves (42.4%) and roots (37.5%). Hypocreales was the dominant order (33.3% of all the isolates), followed by Glomerellales (26.5%), Eurotiales (12.1%), Pleosporales (9.8%) and Capnodiales (6.0%). Fungal endophyte abundance (number of isolates) followed the same pattern as colonization rate, while species richness varied with season and host plant tissue. Ordination analyses showed that the abundance and richness of Hypocreales, Eurotiales and Sordariales were associated with plant roots, while Capnodiales, Pleosporales and Trichosphaeriales were associated with spring. Other environmental factors, elevation, and the proportions of grassland, forest, orchard and waterbodies in the surrounding landscape also exerted effects within some categories of other main effects or for certain fungal taxa. Our results indicate that while fungal endophyte communities of crucifer crops vary strongly with the season, they are also strongly structured by plant identity and plant tissue, to a lesser extent by pesticide use and only weakly by landscape composition. The understanding of the ecological roles of fungal endophytes could contribute to habitat management and consequently improve crop pest management.

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Section: Discussionmentioning

confidence: 99%

Fungal Endophyte Communities of Crucifer Crops Are Seasonally Dynamic and Structured by Plant Identity, Plant Tissue and Environmental Factors

et al. 2020

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“…Within 90 days, myclobutanil degraded faster in alluvial soil (62.40%-95.80% degradation) than in so-called cinnamon soil (36.20%-47.50% degradation). According to Manoharan et al (2017), an excessively high dose of pesticides can destroy indigenous microorganisms colonizing the soil ecosystem and therefore lead to their increased persistence in soil. In our research, changes in the community structure of bacterial groups and the enzyme activity may be evidence of the varied rate at which the tested fungicides disappeared from soil environment.…”

Section: Resultsmentioning

confidence: 99%

Changes in microbiological properties of soil during fungicide degradation

Baćmaga

Kucharski

Kaczyński

2018

Soil Science Annual

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Laboratory tests were performed on sandy loamy soil to establish the relations between bacterial diversity, soil enzyme activity and degradation of Amistar 250 SC, Falcon 460 EC and Gwarant 500 SC fungicides. Apart from carrying out microbiological and biochemical analyses, the residues of active substances from the tested fungicides were determined. Structural diversity of was determined based on the next-generation sequencing (NGS) method, and fungicide residues the liquid chromatography tandem-mass spectrometry (LC-MS/MS). It was found that changes in bacterial diversity occurred in the soil subject to fungicide treatment, particularly at the family and genus level. Proteobacteria, Firmicutes and Actinobacteria were prevailing in all soil samples. Bacillus occurred both in the control soil and in the soil treated with fungicides, while Pseudonocardia occurred only in the fungicide-treated soil. Of all the fungicides tested, the biggest changes in bacterial diversity were caused by Gwarant 500 SC. The preparations tested not only affected the composition of soil microbiota, but also contributed to changes in the biochemical properties of soil by inhibiting the activity of almost all tested enzymes, with the exception of alkaline phosphatase and β-glucosidase. Chlorothalinil was the fastest degraded in the soil and spiroxamine at the slowest.

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“…However, detailed studies on microbial communities considering functional genes, carbohydrate metabolism pathways, and carbohydrate-active enzymes under different tillage methods is lacking. It was also argued that the information about the microbial taxonomic composition itself is usually insufficient to predict the various functions [24].…”

Section: Introductionmentioning

confidence: 99%

“…Metagenomics is used to directly detect and quantify DNA sequences, thus avoiding the trouble of PCR amplification bias and providing annotation of functional capabilities via gene enrichment analysis [26,27]. Metagenomics allows researchers to answer questions about what the microbial communities do, how soil functions change, and how soil functions respond to the microenvironment through quantifying the functional composition of those communities [24,28]. The metagenomics technique is based on using the available gene sequences to reveal taxonomic structures according to the NR database [29], providing functional annotation according to the unsupervised orthologous groups database [30], elucidating the metabolic pathway using the KEGG database [31], and examining the carbohydrate-active enzymes and carbohydrate metabolism pathway using the CAZy database [32].…”

Section: Introductionmentioning

confidence: 99%

“…The metagenomics technique is based on using the available gene sequences to reveal taxonomic structures according to the NR database [29], providing functional annotation according to the unsupervised orthologous groups database [30], elucidating the metabolic pathway using the KEGG database [31], and examining the carbohydrate-active enzymes and carbohydrate metabolism pathway using the CAZy database [32]. Therefore, based on knowledge of the soil microbial community composition, we can generalize about the functional gene composition and carbohydrate metabolism pathways related to SOC cycling [15,24,33]. Metagenomic sequencing analysis provides an opportunity to explore the functional genes related to SOC cycling, where crop residues and root exudates are the main C sources.…”

Section: Introductionmentioning

confidence: 99%

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Tillage Practice Impacts on the Carbon Sequestration Potential of Topsoil Microbial Communities in an Agricultural Field

Dai

Zhang

et al. 2020

Agronomy

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Soil microorganisms are the core force driving the conversion of plant residues into soil organic carbon (SOC). Identifying the changes in soil microorganism responses to tillage practices is a key step in understanding the SOC sequestration potential. The aim of this study is to assess the impacts of different tillage practices on microbial communities and functions in agricultural soils. A field experiment involving no tillage (NT), rotary tillage (RT), and deep tillage (DT) in winter wheat-summer maize double cropping was performed to determine the structure of the microbial community and its functions using metagenomics. We found that tillage practices changed the composition of soil microbial communities and their functions related to the C cycle. The relative abundance of fungi in DT was significantly higher than that of the NT and RT treatments and primarily facilitated the growth of the fungi community. Moreover, DT treatment increased the relative abundance of genes involved in carbohydrate transport and metabolism genes and carbohydrate metabolism pathway genes, in addition to those encoding carbohydrate-binding modules. Therefore, we concluded that DT increases the transformation potential of straw-C to SOC in the North China Plain where large amounts of wheat and maize straw are returned to the field every year.

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Agricultural land use determines functional genetic diversity of soil microbial communities

Cited by 47 publications

References 65 publications

Fungal Endophyte Communities of Crucifer Crops Are Seasonally Dynamic and Structured by Plant Identity, Plant Tissue and Environmental Factors

Fungal Endophyte Communities of Crucifer Crops Are Seasonally Dynamic and Structured by Plant Identity, Plant Tissue and Environmental Factors

Changes in microbiological properties of soil during fungicide degradation

Tillage Practice Impacts on the Carbon Sequestration Potential of Topsoil Microbial Communities in an Agricultural Field

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