Insight into how organic amendments can shape the soil microbiome in long-term field experiments as revealed by network analysis

Soil Biology and Biochemistry, Journal Year: 2016, Volume and Issue: 99, P. 137 - 149

Published: May 18, 2016

Language: Английский

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Bacterial Community Structure after Long-term Organic and Inorganic Fertilization Reveals Important Associations between Soil Nutrients and Specific Taxa Involved in Nutrient Transformations

Frontiers in Microbiology, Journal Year: 2017, Volume and Issue: 8

Published: Feb. 9, 2017

Fertilization has a large impact on the soil microbial communities, which play pivotal roles in biogeochemical cycling and ecological processes. While effects of changes nutrient availability due to fertilization communities have received considerable attention, specific taxa strongly influenced by long-term organic inorganic fertilization, their potential associations with nutrients remain unclear. Here we use deep 16S amplicon sequencing investigate bacterial community characteristics fluvo-aquic treated for 24 years fertilizers organics (manure straw)-inorganic fertilizers, uncover links between parameters taxa. Our results showed that combined organic-inorganic increased carbon (SOC) total nitrogen (TN) contents altered composition, while had little composition. SOC TN emerged as major determinants The abundances taxa, especially Arenimonas, Gemmatimonas an unclassified member Xanthomonadaceae, were substantially amendments rather than only. A co-occurrence based network analysis demonstrated strong positive some (Gemmatimonas members Acidobacteria subgroup 6, Myxococcales, Betaproteobacteria Bacteroidetes), Gemmatimonas, Flavobacterium Verrucomicrobia identified keystone These above are implicated decomposition complex matters carbon, phosphorus transformations. present work strengthens our current understanding structure functions under management provides certain theoretical support selection rational strategies.

Language: Английский

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Distinct roles for soil fungal and bacterial communities associated with the suppression of vanilla Fusarium wilt disease

Soil Biology and Biochemistry, Journal Year: 2017, Volume and Issue: 107, P. 198 - 207

Published: Jan. 22, 2017

Language: Английский

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Soil carbon content drives the biogeographical distribution of fungal communities in the black soil zone of northeast China

Soil Biology and Biochemistry, Journal Year: 2015, Volume and Issue: 83, P. 29 - 39

Published: Jan. 24, 2015

Language: Английский

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Spatial scale drives patterns in soil bacterial diversity

Environmental Microbiology, Journal Year: 2016, Volume and Issue: 18(6), P. 2039 - 2051

Published: Feb. 26, 2016

Soil microbial communities are essential for ecosystem function, but linking community composition to biogeochemical processes is challenging because of high diversity and large spatial variability most soil characteristics. We investigated bacterial structure in a switchgrass stand planted on with history grassland vegetation at resolution determine whether biogeographic trends occurred the centimeter scale. Moreover, we tested such heterogeneity, if present, influenced within or among ecosystems. Pronounced heterogeneity was observed scales, abrupt changes relative abundance phyla from sample sample. At scale (> 10 m), however, were subtly, significantly, altered by fertilization, higher alpha fertilized plots. comparing these data 1772 soils Earth Microbiome Project, it found that 20% taxa shared between their site diverse globally sourced samples, while approximately 40% operational taxonomic units current study. By spanning several orders magnitude, analysis suggested extreme patchiness characterized smaller scales coherent patterns emerged larger length scales.

Language: Английский

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Rhizosphere-associated bacterial network structure and spatial distribution differ significantly from bulk soil in wheat crop fields

Soil Biology and Biochemistry, Journal Year: 2017, Volume and Issue: 113, P. 275 - 284

Published: June 26, 2017

Language: Английский

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Fertilization Shapes Bacterial Community Structure by Alteration of Soil pH

Frontiers in Microbiology, Journal Year: 2017, Volume and Issue: 8

Published: July 18, 2017

Application of chemical fertilizer or manure can affect soil microorganisms directly by supplying nutrients and indirectly altering pH. However, it remains uncertain which effect mostly shapes microbial community structure. We determined bacterial diversity structure 454 pyrosequencing the V1-V3 regions 16S rRNA genes after 7-years (2007-2014) applying nitrogen, phosphorus potassium (NPK) fertilizers, composted their combination to acidic (pH 5.8), near-neutral 6.8) alkaline 8.4) Eutric Regosol in a maize-vegetable rotation southwest China. In soil, nutrient sources did not Operational Taxonomic Unit (OTU) richness Shannon index, despite higher available N, P, K, organic carbon fertilized than unfertilized soil. contrast, OTU index were significantly lower soils under NPK combination, corresponded with changes Permutational multivariate analysis variance showed that was affected across these three soils, but PCoA ordination patterns indicated less distinct among near-neural soils. Distance-based redundancy structures altered pH any properties The relative abundance (%) most phyla dominant Proteobacteria (24.6%), Actinobacteria (19.7%), Chloroflexi (15.3%) Acidobacteria (12.6%); medium Bacterioidetes (5.3%), Planctomycetes (4.8%), Gemmatimonadetes (4.5%), Firmicutes (3.4%), Cyanobacteria (2.1%), Nitrospirae (1.8%), candidate division TM7 (1.0%); least abundant Verrucomicrobia (0.7%), Armatimonadetes (0.6%), WS3 (0.4%) Fibrobacteres (0.3%). addition, more whereas Gemmatimonadetes, conclude fertilization, shaped rather direct addition.

Language: Английский

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Biogeography of soil bacteria and archaea across France

Science Advances, Journal Year: 2018, Volume and Issue: 4(7)

Published: July 4, 2018

Over the last two decades, a considerable effort has been made to decipher biogeography of soil microbial communities as whole, from small broad scales. In contrast, few studies have focused on taxonomic groups constituting these communities; thus, our knowledge their ecological attributes and drivers determining composition distribution is limited. We applied pyrosequencing approach targeting 16S ribosomal RNA (rRNA) genes in DNA set 2173 samples France reach comprehensive understanding spatial bacteria archaea identify processes environmental involved. Taxonomic assignment rRNA sequences indicated presence 32 bacterial phyla or subphyla 3 archaeal phyla. Twenty 35 were cosmopolitan abundant, with heterogeneous distributions structured patches ranging 43- 260-km radius. The hierarchy main was pH > land management texture nutrients climate. At lower level, 47 dominant genera belonging 12 aggregated 62.1% sequences. also showed that phylum-level can be determined largely by genus or, alternatively, reflect combined all phylum members. Together, study demonstrated present highly diverse biogeographical patterns nationwide scale based intensive systematic sampling wide provide promising contribution for elucidating biodiversity determinism.

Language: Английский

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From Benchtop to Desktop: Important Considerations when Designing Amplicon Sequencing Workflows

PLoS ONE, Journal Year: 2015, Volume and Issue: 10(4), P. e0124671 - e0124671

Published: April 22, 2015

Amplicon sequencing has been the method of choice in many high-throughput DNA (HTS) applications. To date there a heavy focus on means by which to analyse burgeoning amount data afforded HTS. In contrast, distinct lack attention paid considerations surrounding importance sample preparation and fidelity library generation. No high-end bioinformatics can compensate for poorly prepared samples it is therefore imperative that careful given generation within workflows, especially those involving multiple PCR steps. This paper redresses this imbalance focusing aspects pertaining benchtop typical amplicon workflows: screening, target region, Empirical provided illustrate scope problem. Lastly, impact various analysis parameters also investigated context how was initially generated. It hoped may serve highlight pre-analysis workflows achieving meaningful, future-proof be analysed appropriately. As gains traction variety diagnostic applications from forensics environmental (eDNA) paramount analytics are both fit purpose.

Language: Английский

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Impact of long-term N additions upon coupling between soil microbial community structure and activity, and nutrient-use efficiencies

Soil Biology and Biochemistry, Journal Year: 2015, Volume and Issue: 91, P. 151 - 159

Published: Sept. 13, 2015

Language: Английский

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