Nitrogen fertilizer application alters the root endophyte bacterial microbiome in maize plants, but not in the stem or rhizosphere Soil

Plant-associated microorganisms that affect plant development, their composition, and their functionality are determined by the host, soil conditions, and agricultural practices. How agricultural practices affect the rhizosphere microbiome has been well studied, but less is known about how they might affect plant endophytes. In this study, the metagenomic DNA from the rhizosphere and endophyte communities of root and stem of maize plants was extracted and sequenced with the “diversity arrays technology sequencing,” while the bacterial community and functionality (organized by subsystems from general to specific functions) were investigated in crops cultivated with or without tillage and with or without N fertilizer application. Tillage had a small significant effect on the bacterial community in the rhizosphere, but N fertilizer had a highly significant effect on the roots, but not on the rhizosphere or stem. The relative abundance of many bacterial species was significantly different in the roots and stem of fertilized maize plants, but not in the unfertilized ones. The abundance of N cycle genes was affected by N fertilization application, most accentuated in the roots. How these changes in bacterial composition and N genes composition might affect plant development or crop yields has still to be unraveled

Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil

In this study the archaeal communities in extreme saline-alkaline soils of the former lake Texcoco, Mexico, with electrolytic conductivities (EC) ranging from 0.7 to 157.2 dS/m and pH from 8.5 to 10.5 were explored. Archaeal communities in the 0.7 dS/m pH 8.5 soil had the lowest alpha diversity values and were dominated by a limited number of phylotypes belonging to the mesophilic Candidatus Nitrososphaera. Diversity and species richness were higher in the soils with EC between 9.0 and 157.2 dS/m. The majority of OTUs detected in the hypersaline soil were members of the Halobacteriaceae family. Novel phylogenetic branches in the Halobacteriales class were detected in the soil, and more abundantly in soil with the higher pH (10.5), indicating that unknown and uncharacterized Archaea can be found in this soil. Thirteen different genera of the Halobacteriaceae family were identified and were distributed differently between the soils. Halobiforma, Halostagnicola, Haloterrigena, and Natronomonas were found in all soil samples. Methanogenic archaea were found only in soil with pH between 10.0 and 10.3. Retrieved methanogenic archaea belonged to the Methanosarcinales and Methanomicrobiales orders. The comparison of the archaeal community structures considering phylogenetic information (UniFrac distances) clearly clustered the communities by pH

Application of ammonium to a N limited arable soil enriches a succession of bacteria typically found in the rhizosphere

Crop residue management and tillage are known to affect the soil bacterial community, but when and which bacterial groups are enriched by application of ammonium in soil under different agricultural practices from a semi-arid ecosystem is still poorly understood. Soil was sampled from a long-term agronomic experiment with conventional tilled beds and crop residue retention (CT treatment), permanent beds with crop residue burned (PBB treatment) or retained (PBC) left unfertilized or fertilized with 300 kg urea-N ha-1 and cultivated with wheat (Triticum durum L.)/maize (Zea mays L.) rotation. Soil samples, fertilized or unfertilized, were amended or not (control) with a solution of (NH4)2SO4 (300 kg N ha-1) and were incubated aerobically at 25 ± 2 °C for 56 days, while CO2 emission, mineral N and the bacterial community were monitored. Application of NH4+ significantly increased the C mineralization independent of tillage-residue management or N fertilizer. Oxidation of NH4+ and NO2- was faster in the fertilized soil than in the unfertilized soil. The relative abundance of Nitrosovibrio, the sole ammonium oxidizer detected, was higher in the fertilized than in the unfertilized soil; and similarly, that of Nitrospira, the sole nitrite oxidizer. Application of NH4+ enriched Pseudomonas, Flavisolibacter, Enterobacter and Pseudoxanthomonas in the first week and Rheinheimera, Acinetobacter and Achromobacter between day 7 and 28. The application of ammonium to a soil cultivated with wheat and maize enriched a sequence of bacterial genera characterized as rhizospheric and/or endophytic independent of the application of urea, retention or burning of the crop residue, or tillage

Changes in the bacterial and microeukaryotic communities in the bioreactor upon increasing heavy metal concentrations

Heavy metals are necessary at low concentration for biological activity, but they are often toxic for microorganisms at high concentrations. Amplicon sequencing of 16S rRNA and 18S rRNA was used to investigate changes in the bacterial and microeukaryotic communities in an activated sludge bioreactor incrementally contaminated with nickel (Ni), copper (Cu), and zinc (Zn) with an IC50 value ranging from 0% to 100%, as previously determined, while an uncontaminated bioreactor served as a control. The chemical oxygen demand (COD) was on average 90% in the uncontaminated bioreactor but dropped to 49% when the heavy metal concentration was 100% IC50. The bacterial community in the uncontaminated bioreactor was dominated by Alphaproteobacteria (mostly Agrobacterium and Brevundimonas) when the heavy metal concentrations were low and Bacteroidetes (mostly Sphingobacterium) when the highest amounts of heavy metal concentrations were applied. The members of Ciliophora, Ascomycota, and Basidiomycota alternatively dominated in the uncontaminated bioreactor, while Ascomycota (mostly Fusarium) dominated in the contaminated bioreactor. The results revealed that increased concentrations of Ni, Cu, and Zn altered the bacterial and microeukaryotic communities and some putative metabolic functions

Conversion of a High-Altitude Temperate Forest for Agriculture Reduced Alpha and Beta Diversity of the Soil Fungal Communities as Revealed by a Metabarcoding Analysis

Land-use change is one of the most important drivers of change in biodiversity. Deforestation for grazing or agriculture has transformed large areas of temperate forest in the central highlands of Mexico, but its impact on soil fungal communities is still largely unknown. In this study, we determined how deforestation of a high-altitude temperate forest for cultivation of maize (Zea mays L.) or husbandry altered the taxonomic, phylogenetic, functional, and beta diversity of soil fungal communities using a 18S rRNA metabarcoding analysis. The true taxonomic and phylogenetic diversity at order q = 1, i.e., considering frequent operational taxonomic units, decreased significantly in the arable, but not in the pasture soil. The beta diversity decreased in the order forest > pasture > arable soil. The ordination analysis showed a clear effect of intensity of land-use as the forest soil clustered closer to pasture than to the arable soil. The most abundant fungal phyla in the studied soils were Ascomycota, Basidiomycota, and Mucoromycota. Deforestation more than halved the relative abundance of Basidiomycota; mostly Agaricomycetes, such as Lactarius and Inocybe. The relative abundance of Glomeromycota decreased in the order pasture > forest > arable soil. Symbiotrophs, especially ectomycorrhizal fungi, were negatively affected by deforestation while pathotrophs, especially animal pathogens, were enriched in the pasture and arable soil. Ectomycorrhizal fungi were more abundant in the forest soil as they are usually associated with conifers. Arbuscular mycorrhizal fungi were more abundant in the pasture than in the arable soil as the higher plant diversity provided more suitable hosts. Changes in fungal communities resulting from land-use change can provide important information for soil management and the assessment of the environmental impact of deforestation and conversion of vulnerable ecosystems such as high-altitude temperate forests

The bacterial community structure in an alkaline saline soil spiked with anthracene

Background: The application of polycyclic aromatic hydrocarbons (PAHs) will affect the bacterial community structure as some groups will be favoured and others not. An alkaline saline soil with electrolytic conductivity (EC) 56 dS m-1 was spiked with anthracene and acetone while their effect on bacterial community structure was investigated. Results: The percentages of Acidobacteria and Actinobacteria decreased over time, while the percentage of Proteobacteria, mostly Xanthomonadales, increased. The percentage of the phylotypes belonging to the Nocardioides , Rhodococcus and Streptomyces , known degraders of PAHs, was larger in the anthracene-amended soil than in the acetone-amended and unamended soil at day 14. The phylotypes belonging to the genera Sphingomonas , also a known degrader of PAHs, however, was lower. Weighted and unweighted PCoA with UniFrac indicated that phylotypes were similar in the different treatments at day 0, but changed at day 1. After 14 days, phylotypes in the unamended and acetone-amended soil were similar, but different from those in the anthracene-spiked soil. Conclusions: It was found that incubating the soil and contaminating it with anthracene changed the bacterial community structure, but spiking the soil with acetone had little or no effect on the bacterial community structure compared to the unamended soil

The Bacterial Community Structure and Microbial Activity in a Traditional Organic Milpa Farming System Under Different Soil Moisture Conditions

Agricultural practices affect the bacterial community structure, but how they determine the response of the bacterial community to drought, is still largely unknown. Conventional cultivated soil, i.e., inorganic fertilization, tillage, crop residue removal and maize (Zea mays L.) monoculture, and traditional organic farmed soil “milpa,” i.e., minimum tillage, rotation of maize, pumpkin (Cucurbita sp.) and beans (Phaseolus vulgaris L.) and organic fertilization were sampled. Both soils from the central highlands of Mexico were characterized and incubated aerobically at 5% field capacity (5%FC) and 100% field capacity (FC) for 45 days, while the C and N mineralization, enzyme activity and the bacterial community structure were monitored. After applying the different agricultural practices 3 years, the organic C content was 1.8-times larger in the milpa than in the conventional cultivated soil, the microbial biomass C 1.3-times, and C and N mineralization 2.0-times (mean for soil incubated at 5%FC and FC). The dehydrogenase, activity was significantly higher in the conventional cultivated soil than in the milpa soil when incubated at 5%FC, but not when incubated at FC. The relative abundance of Gemmatimonadetes was larger in the conventional cultivated soil than in the milpa soil in soil both at 5%FC and FC, while that of Bacteroidetes showed an opposite trend. The relative abundance of other groups, such as Nitrospirae and Proteobacteria, was affected by cultivation technique, but controlled by soil water content. The relative abundance of other groups, e.g., FBP, Gemmatimonadetes and Proteobacteria, was affected by water content, but the effect depended on agricultural practice. For soil incubated at FC, the xenobiotics biodegradation and metabolism related functions were higher in the milpa soil than in the conventional cultivated soil, and carbohydrate metabolism showed an opposite trend. It was found that agricultural practices and soil water content had a strong effect on soil characteristics, C and N mineralization, enzyme activity, and the bacterial community structure and its functionality. Decreases or increases in the relative abundance of bacterial groups when the soil water content decreased, i.e., from FC to 5%FC, was defined often by the cultivation technique, and the larger organic matter content in the milpa soil did not prevent large changes in the bacterial community structure when the soil was dried

Silver and Hematite Nanoparticles Had a Limited Effect on the Bacterial Community Structure in Soil Cultivated with <i>Phaseolus vulgaris</i> L.

The amount of nanoparticles that enters the environment has increased substantially in the last years. How they might affect plant characteristics and the bacterial community structure when they enter the soil, however, is still debated, as there is a continuous interaction between them. In this study, we determined the effect of silver (Ag-NPs) and hematite (α-Fe2O3-NPs) nanoparticles (0.15 g kg−1) on the characteristics of common bean (Phaseolus vulgaris L.) and the rhizosphere, non-rhizosphere and uncultivated soil bacterial community. The application of Ag-NPs or α-Fe2O3-NPs did not affect plant growth, but changed the amount of some heavy metals in the roots and aerial parts. The application of nanoparticles had a limited effect on the diversity, structure and functional profile of the soil and rhizosphere bacterial communities, but they were altered by cultivation of the bean plants and changed over time. It was found that application of Ag-NPs or α-Fe2O3-NPs had no effect on bean plant growth and only a small effect on the bacterial community structure and its putative metabolic functions. These findings show that in a complex system, such as a soil, different factors might affect the bacterial community structure and alter the possible effect of nanoparticles on it

Bacterial Communities in Alkaline Saline Soils Amended with Young Maize Plants or Its (Hemi)Cellulose Fraction

We studied three soils of the former lake Texcoco with different electrolytic conductivity (1.9 dS m−1, 17.3 dS m−1, and 33.4 dS m−1) and pH (9.3, 10.4, and 10.3) amended with young maize plants and their neutral detergent fibre (NDF) fraction and aerobically incubated in the laboratory for 14 days while the soil bacterial community structure was monitored by means of 454-pyrosequencing of their 16S rRNA marker gene. We identified specific bacterial groups that showed adaptability to soil salinity, i.e., Prauseria in soil amended with young maize plants and Marinobacter in soil amended with NDF. An increase in soil salinity (17.3 dS m−1, 33.4 dS m−1) showed more bacterial genera enriched than soil with low salinity (1.9 dS m−1). Functional prediction showed that members of Alfa-, Gamma-, and Deltaproteobacteria, which are known to adapt to extreme conditions, such as salinity and low nutrient soil content, were involved in the lignocellulose degradation, e.g., Marinimicrobium and Pseudomonas as cellulose degraders, and Halomonas and Methylobacterium as lignin degraders. This research showed that the taxonomic annotation and their functional prediction both highlighted keystone bacterial groups with the ability to degrade complex C-compounds, such as lignin and (hemi)cellulose, in the extreme saline-alkaline soil of the former Lake of Texcoco

Changes in the Bacterial Community Structure of Remediated Anthracene-Contaminated Soils.

Mixing soil or adding earthworms (Eisenia fetida (Savigny, 1826)) accelerated the removal of anthracene, a polycyclic aromatic hydrocarbon, from a pasture and an arable soil, while a non-ionic surfactant (Surfynol® 485) inhibited the removal of the contaminant compared to the untreated soil. It was unclear if the treatments affected the soil bacterial community and consequently the removal of anthracene. Therefore, the bacterial community structure was monitored by means of 454 pyrosequencing of the 16S rRNA gene in the pasture and arable soil mixed weekly, amended with Surfynol® 485, E. fetida or organic material that served as food for the earthworms for 56 days. In both soils, the removal of anthracene was in the order: mixing soil weekly (100%) > earthworms applied (92%) > organic material applied (77%) > untreated soil (57%) > surfactant applied (34%) after 56 days. There was no clear link between removal of anthracene from soil and changes in the bacterial community structure. On the one hand, application of earthworms removed most of the contaminant from the arable soil and had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of the Acidobacteria, Chloroflexi and Gemmatimonadetes, and an increase in that of the Proteobacteria compared to the unamended soil. Mixing the soil weekly removed all anthracene from the arable soil, but had little or no effect on the bacterial community structure. On the other hand, application of the surfactant inhibited the removal of anthracene from the arable soil compared to the untreated soil, but had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of Cytophagia (Bacteroidetes), Chloroflexi, Gemmatimonadetes and Planctomycetes and an increase in that of the Flavobacteria (Bacteroidetes) and Proteobacteria. Additionally, the removal of anthracene was similar in the different treatments of both the arable and pasture soil, but the effect of application of carrot residue, earthworms or the surfactant on the bacterial community structure was more accentuated in the arable soil than in the pasture soil. It was found that removal of anthracene was not linked to changes in the bacterial community structure