Metatranscriptomic Sequencing of a Cyanobacterial Soil-Surface Consortium with and without a Diverse Underlying Soil Microbiome.

Soil surface consortia are easily observed and sampled, allowing examination of their interactions with soil microbiomes. Here, we present metatranscriptomic sequences from Dark Green 1 (DG1), a cyanobacterium-based soil surface consortium, in the presence and absence of an underlying soil microbiome and/or urea

Soil microbiome manipulation triggers direct and possible indirect suppression against <i>Ralstonia solanacearum</i> and <i>Fusarium oxysporum</i>

Soil microbiome manipulation can potentially reduce the use of pesticides by improving the ability of soils to resist or recover from pathogen infestation, thus generating natural suppressiveness. We simulated disturbance through soil fumigation and investigated how the subsequent application of bio-organic and organic amendments reshapes the taxonomic and functional potential of the soil microbiome to suppress the pathogens Ralstonia solanacearum and Fusarium oxysporum in tomato monocultures. The use of organic amendment alone generated smaller shifts in bacterial and fungal community composition and no suppressiveness. Fumigation directly decreased F. oxysporum and induced drastic changes in the soil microbiome. This was further converted from a disease conducive to a suppressive soil microbiome due to the application of organic amendment, which affected the way the bacterial and fungal communities were reassembled. These direct and possibly indirect effects resulted in a highly efficient disease control rate, providing a promising strategy for the control of the diseases caused by multiple pathogens

Impacts of wildfire on soil microbiome in Boreal environments

The temperature changes for the future climate are predicted to be the most pronounced in boreal and arctic regions, affecting the stability of permafrost and fire dynamics of these areas. Fires can affect soil microbiome (archaea, bacteria, fungi, and protists) directly via generated heat, whereas fire-altered soil properties have an indirect effect on soil microbiome. Fires usually decrease microbial biomass and alter microbial community composition. These changes can take decades to recover to prefire states. As the fire occurrence times are expected to change in the future, and the fire return intervals, intensity, and severity are expected to increase in boreal environments, the fire-related changes in the soil microbiome, including its recovery and resilience, are inevitable.Peer reviewe

Global meta-analysis and metagenomics approach on the soil microbiome associated with cover cropping

Soil nutrient loss is one of the major causes of soil degradation that threatens future global food security. Cover cropping is a promising sustainable agricultural method with the potential to enhance soil health and mitigate consequences of soil degradation. As one of the agricultural practices that can affect cover cropping, effects of tillage on cover cropping have been widely researched as well. Because cover cropping and tillage can form an agroecosystem distinct from that of bare fallow, the soil microbiome is hypothesized to respond to the altered environmental circumstances. Therefore, studying their impact on the soil microbiome is necessary because the soil microbes are important drivers of soil processes including those relevant to soil health. The objectives of this MS research were i) estimate the baseline effect size of cover cropping on soil microbial abundance, activity, and diversity, ii) identify environmental and agricultural factors that affect the cover crop effects sizes on the soil microbiome, iii) further understand the cover crop effects on the soil microbial diversity by investigating the shifts in the soil microbial compositions, and iv) contribute to understanding how the relationship between cover cropping and the soil microbiome may affect the soil health. A meta-analysis was conducted to estimate the global average effects of cover cropping on the soil microbiome. This study compiled the results of 60 relevant studies reporting cover cropping effects on soil microbial properties to estimate global effect sizes and explore the current landscape of this topic. Overall, cover cropping significantly increased parameters of soil microbial abundance, activity, and diversity by 27%, 22%, and 2.5% respectively, compared to those of bare fallow. Moreover, cover cropping effect sizes varied by agricultural covariates like cover crop termination or tillage methods. Notably, cover cropping effects were less pronounced under conditions like continental climate, chemical cover crop termination, and conservation tillage. This meta-analysis showed that the soil microbiome can become more robust under cover cropping when properly managed with other agricultural practices. However, more primary research is still needed to control between-study heterogeneity and to more elaborately assess the relationships between cover cropping and the soil microbiome. This meta-analysis revealed that cover cropping affect the overall soil microbial diversity and that tillage is a major cofactor that affect this relationship. To further investigate the cover cropping and tillage effects on the soil microbial diversity, a metagenomics study was conducted. This second part of the study was to observe compositional changes in the soil microbiome in response to cover cropping and tillage. Also, this study sought to identify microbial indicators that can be used to gauge responses of microbial guilds with functions relevant to soil health. This study used soil DNA data from a long-term cover cropping and tillage experiment on corn and soybean rotation in Illinois, USA. This study found that copiotrophic bacterial decomposers increased with legume cover crops and tillage, while oligotrophic and stress tolerant bacteria did so with bare fallow and no-till. Fungal groups responded to cover cropping and tillage based on their physiology, interaction with plant hosts, and nutrient strategies. This study also found an ammonia-oxidizing archaea species that increased with bare fallow. The consistent patterns that the microbial groups in this study display make them potential microbial indicators. Also, grass cover crops with no-till showed most potential for soil nutrient loss. Overall, this MS research found that cover cropping significantly enriches the soil microbiome. However, cover cropping effects may apply differential pressures on microbial groups with different adaptations so that the overall diversity is not changed significantly. This research suggests that timing and other agricultural practices like tillage need to be carefully considered to direct the changes in the soil microbiome to benefit the soil health

Soil microbiome signatures are associated with pesticide residues in arable landscapes

Pesticides are widely applied in agriculture to combat disease, pests, and weeds, leading to long-lasting contamination of agricultural soils with pesticide residues. While classical risk assessment experiments have repeatedly addressed immediate pesticide effects, we employ an ecological approach to investigate how pesticide residues persisting in soils influence the soil microbiome under realistic agricultural conditions. We assessed a wide range of soil characteristics, including the occurrence of 48 widely-used pesticides in 60 fields under conventional, no-tillage and organic management. We then tested which factors best explain soil microbiome traits. Environmental factors, including climate, geography, and soil characteristics, were the soil microbiome's leading drivers. Remarkably, of all management factors, pesticide residues showed the strongest associations with soil microbiome traits, which were even more pronounced than the effects of cropping systems. Pesticide residues were almost exclusively positively associated with the relative abundance of 113 bacterial and 130 fungal taxa, many of them being assigned to taxa of known pesticide degraders. While fungal diversity and abundance were primarily positively associated with pesticide residues, bacterial diversity and abundance of the gene nifH - essential for biological nitrogen fixation - were negatively linked to the concentration of individual pesticide residues. Our results suggest that pesticide residues alter the soil microbiome, with potential long-term implications for the functioning of agricultural soils

Functional Traits Co-Occurring with Mobile Genetic Elements in the Microbiome of the Atacama Desert

Mobile genetic elements (MGEs) play an essential role in bacterial adaptation and evolution. These elements are enriched within bacterial communities from extreme environments. However, very little is known if specific genes co-occur with MGEs in extreme environments and, if so, what their function is. We used shotgun-sequencing to analyse the metagenomes of 12 soil samples and characterized the composition of MGEs and the genes co-occurring with them. The samples ranged from less arid coastal sites to the inland hyperarid core of the Atacama Desert, as well as from sediments below boulders, protected from UV-irradiation. MGEs were enriched at the hyperarid sites compared with sediments from below boulders and less arid sites. MGEs were mostly co-occurring with genes belonging to the Cluster Orthologous Group (COG) categories “replication, recombination and repair,” “transcription” and “signal transduction mechanisms.” In general, genes coding for transcriptional regulators and histidine kinases were the most abundant genes proximal to MGEs. Genes involved in energy production were significantly enriched close to MGEs at the hyperarid sites. For example, dehydrogenases, reductases, hydrolases and chlorite dismutase and other enzymes linked to nitrogen metabolism such as nitrite- and nitro-reductase. Stress response genes, including genes involved in antimicrobial and heavy metal resistance genes, were rarely found near MGEs. The present study suggests that MGEs could play an essential role in the adaptation of the soil microbiome in hyperarid desert soils by the modulation of housekeeping genes such as those involved in energy production.EC/FP7/339231/EU/Habitability of Martian Environments: Exploring the Physiological and Environmental Limits of Life/HOM

Soil Viruses: A New Hope.

As abundant members of microbial communities, viruses impact microbial mortality, carbon and nutrient cycling, and food web dynamics. Although most of our information about viral communities comes from marine systems, evidence is mounting to suggest that viruses are similarly important in soil. Here I outline soil viral metagenomic approaches and the current state of soil viral ecology as a field, and then I highlight existing knowledge gaps that we can begin to fill. We are poised to elucidate soil viral contributions to terrestrial ecosystem processes, considering: the full suite of potential hosts across trophic scales, the ecological impacts of different viral replication strategies, links to economically relevant outcomes like crop productivity, and measurable in situ virus-host population dynamics across spatiotemporal scales and environmental conditions. Soon, we will learn how soil viruses contribute to food webs linked to organic matter decomposition, carbon and nutrient cycling, greenhouse gas emissions, and agricultural productivity