An Assessment of Climate Induced Increase in Soil Water Availability for Soil Bacterial Communities Exposed to Long-Term Differential Phosphorus Fertilization.

The fate of future food productivity depends primarily upon the health of soil used for cultivation. For Atlantic Europe, increased precipitation is predicted during both winter and summer months. Interactions between climate change and the fertilization of land used for agriculture are therefore vital to understand. This is particularly relevant for inorganic phosphorus (P) fertilization, which already suffers from resource and sustainability issues. The soil microbiota are a key indicator of soil health and their functioning is critical to plant productivity, playing an important role in nutrient acquisition, particularly when plant available nutrients are limited. A multifactorial, mesocosm study was established to assess the effects of increased soil water availability and inorganic P fertilization, on spring wheat biomass, soil enzymatic activity (dehydrogenase and acid phosphomonoesterase) and soil bacterial community assemblages. Our results highlight the significance of the spring wheat rhizosphere in shaping soil bacterial community assemblages and specific taxa under a moderate soil water content (60%), which was diminished under a higher level of soil water availability (80%). In addition, an interaction between soil water availability and plant presence overrode a long-term bacterial sensitivity to inorganic P fertilization. Together this may have implications for developing sustainable P mobilization through the use of the soil microbiota in future. Spring wheat biomass grown under the higher soil water regime (80%) was reduced compared to the constant water regime (60%) and a reduction in yield could be exacerbated in the future when grown in cultivated soil that have been fertilized with inorganic P. The potential feedback mechanisms for this need now need exploration to understand how future management of crop productivity may be impacted.

Sulfate fertilization supports growth of ryegrass in soil columns but changes microbial community structures and reduces abundances of nematodes and arbuscular mycorrhiza.

The increased use of sulfate fertilizers to compensate for soil sulphur (S) limitation in agricultural soils may affect soil microbes and micro-fauna involved in S mobilization. Here, columns with podzolic soil material and ryegrass (Lolium perenne) were fertilized with 0, 5, 10 and 20 kg ha-1 (S0/S5/S10/S20) inorganic sulfate-S alongside a full complement of other nutrients. In the S10 and S20 columns, significantly higher amounts of sulfate were present in soil solution. After two grass cuts (14 weeks in total), there was a significant decrease in arylsulfatase activity, bacterial-feeding nematode abundances and mycorrhizal colonization in the S10 and S20 columns compared to the S0. Bacterial, fungal and AM community structures shifted significantly across the treatments. After final harvest, the S10 and S20 columns had significantly higher grass dry matter yield and uptake of S, N, K, Ca and Mg compared to the S0. While the overall bacterial diversity was reduced in the S20 treatment, abundance (asfA) and diversity (ssuD and atsA) of bacterial genes involved in S cycling were not significantly affected by one-time sulfate fertilization. These results indicate that short-term sulfate fertilization benefits to plant growth outweighed the negative feedback from parts of the soil biota. To improve nutrient use efficiencies in a sustainable manner, future studies should consider alternative S fertilizers which may be beneficial to both, the soil biota and plants in the long-term.

Opportunistic Bacteria Dominate the Soil Microbiome Response to Phenanthrene in a Microcosm-Based Study.

Bioremediation offers a sustainable approach for removal of polycyclic aromatic hydrocarbons (PAHs) from the environment; however, information regarding the microbial communities involved remains limited. In this study, microbial community dynamics and the abundance of the key gene (PAH-RHDα) encoding a ring hydroxylating dioxygenase involved in PAH degradation were examined during degradation of phenanthrene in a podzolic soil from the site of a former timber treatment facility. The 10,000-fold greater abundance of this gene associated with Gram-positive bacteria found in phenanthrene-amended soil compared to unamended soil indicated the likely role of Gram-positive bacteria in PAH degradation. In contrast, the abundance of the Gram-negative PAHs-RHDα gene was very low throughout the experiment. While phenanthrene induced increases in the abundance of a small number of OTUs from the Actinomycetales and Sphingomonadale, most of the remainder of the community remained stable. A single unclassified OTU from the Micrococcaceae family increased ~20-fold in relative abundance, reaching 32% of the total sequences in amended microcosms on day 7 of the experiment. The relative abundance of this same OTU increased 4.5-fold in unamended soils, and a similar pattern was observed for the second most abundant PAH-responsive OTU, classified into the Sphingomonas genus. Furthermore, the relative abundance of both of these OTUs decreased substantially between days 7 and 17 in the phenanthrene-amended and control microcosms. This suggests that their opportunistic phenotype, in addition to likely PAH-degrading ability, was determinant in the vigorous growth of dominant PAH-responsive OTUs following phenanthrene amendment. This study provides new information on the temporal response of soil microbial communities to the presence and degradation of a significant environmental pollutant, and as such has the potential to inform the design of PAH bioremediation protocols.

Concentration-dependent responses of soil bacterial, fungal and nitrifying communities to silver nano and micron particles.

The growing use of silver nanoparticles (AgNPs) is likely to result in increased environmental contamination. Although AgNPs have been reported to affect microbial communities in a range of ecosystems, there is still a lack of information concerning the effect of low concentrations of AgNPs on soil microbial community structures and functional groups involved in biogeochemical cycling. In this study, the concentration-dependent effects of AgNPs and silver micron particles (AgMPs) on bacterial and fungal community structures in an agricultural pastureland soil were examined in a microcosm-based experiment using enzyme analysis, molecular fingerprinting, qPCR and amplicon sequencing. Soil enzyme processes were impacted by Ag contamination, with soil dehydrogenase activity reduced by 1 mg kg-1 of AgNPs and AgMPs. Soil urease activity was less susceptible, but was inhibited by ≥ 10 mg kg-1 AgNPs. The significant (P ≤ 0.001) decrease in copy numbers of the amoA gene by 10 mg kg-1 AgNPs indicated that archaea ammonia oxidisers may be more sensitive to AgNP contamination than bacteria. Amplicon sequencing revealed the bacterial phyla Acidobacteria and Verrucomicrobia to be highly sensitive to AgNP contamination. A broad reduction in the relative abundance of Acidobacterial genera was observed, with the exception of the genus Geothrix which increased in response to AgNP and AgMP amendment. Broad tolerance to Ag was observed among the Bacteriodetes, with higher relative abundance of most genera observed in the presence of AgNPs and AgMPs. The proteobacterial genus Dyella was highly tolerant to AgNPs and AgMPs and relative abundance of this genus increased with Ag concentration. Soil fungal community structure responded to both AgNPs and AgMPs, but the nanoparticle had an impact at a lower concentration. This study demonstrates that pastureland soil microbial communities are highly sensitive to AgNP amendment and key functional processes may be disrupted by relatively low levels of contamination.

Linseed Oil Supplementation of Lambs' Diet in Early Life Leads to Persistent Changes in Rumen Microbiome Structure.

Diet has been shown to have a significant impact on microbial community composition in the rumen and could potentially be used to manipulate rumen microbiome structure to achieve specific outcomes. There is some evidence that a window may exist in early life, while the microbiome is being established, where manipulation through diet could lead to long-lasting results. The aim of this study was to test the hypothesis that dietary supplementation in early life will have an effect on rumen microbial composition that will persist even once supplementation is ceased. Twenty-seven new-born lambs were allocated to one of three dietary treatments; a control group receiving standard lamb meal, a group receiving lamb meal supplemented with 40 g kg-1 DM of linseed oil and a group receiving the supplement pre-weaning and standard lamb meal post-weaning. The supplement had no effect on average daily feed intake or average daily weight gain of lambs. Bacterial and archaeal community composition was significantly (p = 0.033 and 0.005, respectively) different in lambs fed linseed oil throughout the study compared to lambs on the control diet. Succinivibrionaceae, succinate producers, and Veillonellaceae, propionate producers, were in a higher relative abundance in the lambs fed linseed oil while Ruminococcaceae, a family linked with high CH4 emitters, were in a higher relative abundance in the control group. The relative abundance of Methanobrevibacter was reduced in the lambs receiving linseed compared to those that didn't. In contrast, the relative abundance of Methanosphaera was significantly higher in the animals receiving the supplement compared to animals receiving no supplement (40.82 and 26.67%, respectively). Furthermore, lambs fed linseed oil only in the pre-weaning period had a bacterial community composition significantly (p = 0.015) different to that of the control group, though archaeal diversity and community structure did not differ. Again, Succinivibrionaceae and Veillonellaceae were in a higher relative abundance in the group fed linseed oil pre-weaning while Ruminococcaceae were in a higher relative abundance in the control group. This study shows that lambs fed the dietary supplement short-term had a rumen microbiome that remained altered even after supplementation had ceased.

Benzo(a)pyrene degradation and microbial community responses in composted soil.

Benzo(a)pyrene degradation was compared in soil that was either composted, incubated at a constant temperature of 22 °C, or incubated under a temperature regime typical of a composting process. After 84 days, significantly more (61%) benzo(a)pyrene was removed from composted soil compared to soils incubated at a constant temperature (29%) or at composting temperatures (46%). Molecular fingerprinting approaches indicated that in composted soils, bacterial community changes were driven by both temperature and organic amendment, while fungal community changes were primarily driven by temperature. Next-generation sequencing data revealed that the bacterial community in composted soil was dominated by Actinobacteria (order Actinomycetales), Firmicutes (class Bacilli), and Proteobacteria (classes Gammaproteobacteria and Alphaproteobacteria), regardless of whether benzo(a)pyrene was present or not. The relative abundance of unclassified Actinomycetales (Actinobacteria) was significantly higher in composted soil when degradation was occurring, indicating a potential role for these organisms in benzo(a)pyrene metabolism. This study provides baseline data for employing straw-based composting strategies for the removal of high molecular weight PAHs from soil and contributes to the knowledge of how microbial communities respond to incubation conditions and pollutant degradation.

Comparison of bacterial succession in green waste composts amended with inorganic fertiliser and wastewater treatment plant sludge.

Replacing CAN with DWS resulted in a stable product capable of supporting similar levels of plant growth to conventional compost. Proteobacteria was the dominant phylum detected in both CAN- and DWS-amended composts with Actinobacteria, Bacteroidetes, Firmicutes and Chloroflexi present also. Proteobacteria in both composts negatively correlated with pH, NO3 concentration and temperature, but were positively influenced by NH4 levels. Sphaerobacter was the most abundant genus in the mature phase of both CAN- and DWS-amended composts but bacterial community structure in mature DWS-amended compost appeared more diverse than that present in mature compost made using CAN.