An ecological perspective on microbial genes of unknown function in soil

Genes that remain hypothetical, uncharacterized, and unannotated comprise a substantial portion of metagenomic datasets and are likely to be particularly prevalent in soils where poorly characterized taxa predominate. Documenting the prevalence, distribution, and potential roles of these genes of unknown function is an important first step to understanding their functional contributions in soil communities. We identified genes of unknown function from 50 soil metagenomes and analyzed their environmental distributions and ecological associations. We found that genes of unknown function are prevalent in soils, particularly fine-textured, higher pH soils that harbor greater abundances of Crenarchaeota, Gemmatimonadota, Nitrospirota, and Methylomirabilota. We identified 43 dominant (abundant and ubiquitous) gene clusters of unknown function and determined their associations with soil microbial phyla and other “known” genes. We found that these dominant unknown genes were commonly associated with microbial phyla that are relatively uncharacterized, with the majority of these dominant unknown genes associated with mobile genetic elements. This work demonstrates a strategy for investigating genes of unknown function in soils, emphasizes the biological insights that can be learned by adopting this strategy, and highlights specific hypotheses that warrant further investigation regarding the functional roles of abundant and ubiquitous genes of unknown function in soil metagenomes.

Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics

Microbial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing and assembly of metagenomes from biological soil crusts, a group of soil communities that are rich in BGCs. Taking advantage of the unusually long assemblies produced by this approach, we recovered nearly 3,000 BGCs for analysis, including 712 full-length BGCs. Functional exploration through metatranscriptome analysis of a 3-day wetting experiment uncovered phylum-specific BGC expression upon activation from dormancy, elucidating distinct roles and complex phylogenetic and temporal dynamics in wetting processes. For example, a pronounced increase in BGC transcription occurs at night primarily in cyanobacteria, implicating BGCs in nutrient scavenging roles and niche competition. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional dynamics of BGCs in environmental processes and suggests a central role of secondary metabolites in maintaining phylogenetically conserved niches within biocrusts.

Disentangling nematode and arbuscular mycorrhizal fungal community effect on the growth of range-expanding Centaurea stoebe in original and new range soil

Aims Numerous organisms show range expansions in response to current climate change. Differences in expansion rates, such as between plants and soil biota, may lead to altered interactions in the new compared to the original range. While plant-soil interactions influence plant performance and stress tolerance, the roles of specific soil organisms driving these responses remain unknown. Methods We manipulated the abundances of nematodes and arbuscular mycorrhizal fungi (AMF), collected from original and new range soils, and examined their effects on the biomass of range-expanding Centaurea stoebe and native Centaurea jacea. In the first approach, nematode and AMF communities were extracted from field soils, and inoculated to sterilized soil. In the second approach, the abundance of soil organisms in soil inocula was reduced by wet sieving; at first, plants were grown to condition the soil, and then plant-soil feedback was determined under ambient and drought conditions. Results The origin of soil communities did not influence the biomass production of range-expanding or native plant species, neither by addition nor by (partial) removal. However, after conditioning and under drought, range expanding C. stoebe produced more biomass with soil communities from the original range while C. jacea, native to both ranges, produced more biomass with new range soil communities. Conclusions We show that nematode and AMF communities from original and new range have similar effect on the growth of range expanding C. stoebe. Our results highlight that the effect of soil communities on plant growth increases after soil conditioning and under drought stress.

COMMIT: Consideration of metabolite leakage and community composition improves microbial community models

Composition and functions of microbial communities affect important traits in diverse hosts, from crops to humans. Yet, mechanistic understanding of how metabolism of individual microbes is affected by the community composition and metabolite leakage is lacking. Here, we first show that the consensus of automatically generated metabolic models improves the quality of the draft models, measured by the genomic evidence for considered enzymatic reactions. We then devise an approach for gap filling, termed COMMIT, that considers exchangeable metabolites based on their permeability and the composition of the community. By applying COMMIT with two soil communities from the Arabidopsis thaliana culture collection, we could significantly reduce the gap-filling solution in comparison to filling gaps in individual models. Inspection of the metabolic interactions in the soil communities allows us to identify microbes with community roles of helpers and beneficiaries. Therefore, COMMIT offers a versatile automated solution for large-scale modelling of microbial communities for diverse biotechnological applications.

Oxygen isotope exchange between water and carbon dioxide in soils is controlled by pH, nitrate and microbial biomass through links to carbonic anhydrase activity

The oxygen isotope composition of atmospheric carbon dioxide (CO2) is intimately linked to large-scale variations in the cycling of CO2 and water across the Earth's surface. Understanding the role the biosphere plays in modifying the oxygen isotope composition of atmospheric CO2 is particularly important as this isotopic tracer has the potential to constrain estimates of important processes such as gross primary production at large scales. However, constraining the atmospheric mass budget for the oxygen isotope composition of CO2 also requires that we understand better the contribution of soil communities and how they influence the rate of oxygen isotope exchange between soil water and CO2 (kiso) across a wide range of soil types and climatic zones. As the carbonic anhydrases (CAs) group of enzymes enhances the rate of CO2 hydration within the water-filled pore spaces of soils, it is important to develop understanding of how environmental drivers can impact kiso through changes in their activity. Here we estimate kiso and measure associated soil properties in laboratory incubation experiments using 44 soils sampled from sites across western Eurasia and north-eastern Australia. Observed values for kiso always exceeded theoretically derived uncatalysed rates, indicating a significant influence of CAs on the variability of kiso across the soils studied. We identify soil pH as the principal source of variation, with greater kiso under alkaline conditions suggesting that shifts in microbial community composition or intra–extra-cellular dissolved inorganic carbon gradients induce the expression of more or higher activity forms of CAs. We also show for the first time in soils that the presence of nitrate under naturally acidic conditions reduces kiso, potentially reflecting a direct or indirect inhibition of CAs. This effect appears to be supported by a supplementary ammonium nitrate fertilisation experiment conducted on a subset of the soils. Greater microbial biomass also increased kiso under a given set of chemical conditions, highlighting a putative link between CA expression and the abundance of soil microbes. These data provide the most extensive analysis of spatial variations in soil kiso to date and indicate the key soil trait datasets required to predict variations in kiso at large spatial scales, a necessary next step to constrain the important role of soil communities in the atmospheric mass budget of the oxygen isotope composition of CO2.

Manure Microbial Communities and Resistance Profiles Reconfigure after Transition to Manure Pits and Differ from Those in Fertilized Field Soil

ABSTRACT In agricultural settings, microbes and antimicrobial resistance genes (ARGs) have the potential to be transferred across diverse environments and ecosystems. The consequences of these microbial transfers are unclear and understudied. On dairy farms, the storage of cow manure in manure pits and subsequent application to field soil as a fertilizer may facilitate the spread of the mammalian gut microbiome and its associated ARGs to the environment. To determine the extent of both taxonomic and resistance similarity during these transitions, we collected fresh manure, manure from pits, and field soil across 15 different dairy farms for three consecutive seasons. We used a combination of shotgun metagenomic sequencing and functional metagenomics to quantitatively interrogate taxonomic and ARG compositional variation on farms. We found that as the microbiome transitions from fresh dairy cow manure to manure pits, microbial taxonomic compositions and resistance profiles experience distinct restructuring, including decreases in alpha diversity and shifts in specific ARG abundances that potentially correspond to fresh manure going from a gut-structured community to an environment-structured community. Further, we did not find evidence of shared microbial community or a transfer of ARGs between manure and field soil microbiomes. Our results suggest that fresh manure experiences a compositional change in manure pits during storage and that the storage of manure in manure pits does not result in a depletion of ARGs. We did not find evidence of taxonomic or ARG restructuring of soil microbiota with the application of manure to field soils, as soil communities remained resilient to manure-induced perturbation. IMPORTANCE The addition of dairy cow manure—stored in manure pits—to field soil has the potential to introduce not only organic nutrients but also mammalian microbial communities and antimicrobial resistance genes (ARGs) to soil communities. Using shotgun sequencing paired with functional metagenomics, we showed that microbial community composition changed between fresh manure and manure pit samples with a decrease in gut-associated pathobionts, while ARG abundance and diversity remained high. However, field soil communities were distinct from those in manure in both microbial taxonomic and ARG composition. These results broaden our understanding of the transfer of microbial communities in agricultural settings and suggest that field soil microbial communities are resilient against the deposition of ARGs or microbial communities from manure.

Entangled Materialities

This paper discusses craft and design practices through their impact on the environment. We consider how to act concerning the consequences of the craft and design industry. Also, we reflect on the agency of our field of practice in changing how we perceive the environment. We present three case studies of the European glass industry sites in Sweden, Italy and Finland, where we study contamination of the soil with participatory, speculative and craft methods. Through these cases, we reflect on our role in soil communities and ask how we may act in them with responsibility, hope and care. We conclude by proposing to act locally, to share our practices and make them visible, expanding our situated, personal skills and knowledge towards the political.