Micro on a macroscale: relating microbial-scale soil processes to global ecosystem function

Estimating the Importance of Viral Contributions to Soil Carbon Dynamics

Biogeochemical models for predicting carbon dynamics increasingly include microbial processes, reflecting the importance of microorganisms in regulating the movement of carbon between soils and the atmosphere. Soil viruses can redirect carbon among various chemical pools, indicating a need for quantification and development soil carbon models that explicitly represent viral dynamics. In this opinion, we derive a global estimate of carbon potentially released from microbial biomass by viral infections in soils and synthesize a quantitative soil carbon budget from existing literature that explicitly includes viral impacts. We then adapt known mechanisms by which viruses influence carbon cycles in marine ecosystems into a soil-explicit framework. Finally, we explore the diversity of virus-host interactions during infection and conceptualize how infection mode may impact soil carbon fate. Our synthesis highlights key knowledge gaps hindering the incorporation of viruses into soil carbon cycling research and generates specific hypotheses to test in the pursuit of better quantifying microbial dynamics that explain ecosystem-scale carbon fluxes. The importance of identifying critical drivers behind soil carbon dynamics, including these elusive but likely pervasive viral mechanisms of carbon redistribution, becomes more pressing with climate change.

The soil-borne white root rot pathogen Rosellinia necatrix expresses antimicrobial proteins during host colonization

Rosellinia necatrix is a prevalent soil-borne plant-pathogenic fungus that is the causal agent of white root rot disease in a broad range of host plants. The limited availability of genomic resources for R. necatrix has complicated a thorough understanding of its infection biology. Here, we sequenced nine R. necatrix strains with Oxford Nanopore sequencing technology, and with DNA proximity ligation we generated a gapless assembly of one of the genomes into ten chromosomes. Whereas many filamentous pathogens display a so-called two-speed genome with more dynamic and more conserved compartments, the R. necatrix genome does not display such genome compartmentalization. It has recently been proposed that fungal plant pathogens may employ effectors with antimicrobial activity to manipulate the host microbiota to promote infection. In the predicted secretome of R. necatrix, 26 putative antimicrobial effector proteins were identified, nine of which are expressed during plant colonization. Two of the candidates were tested, both of which were found to possess selective antimicrobial activity. Intriguingly, some of the inhibited bacteria are antagonists of R. necatrix growth in vitro and can alleviate R. necatrix infection on cotton plants. Collectively, our data show that R. necatrix encodes antimicrobials that are expressed during host colonization and that may contribute to modulation of host-associated microbiota to stimulate disease development.

Exposure to polystyrene nanoplastics reduces bacterial and fungal biomass in microfabricated soil models

Nanoplastics have been proven to induce toxicity in diverse organisms, yet their effect on soil microbes like bacteria and fungi remains largely unexplored. In this paper, we used micro-engineered soil models to investigate the effect of polystyrene (PS) nanospheres on Pseudomonas putida and Coprinopsis cinerea. Specifically, we explored the effects of increasing concentrations of 60 nm carboxylated bovine serum albumin (BSA) coated nanospheres (0, 0.5, 2, and 10 mg/L) on these bacterial and fungal model organisms respectively, over time. We found that both microorganisms could disperse through the PS solution, but long-distance dispersal was reduced by high concentrations. Microbial biomass decreased in all treatments, in which bacteria showed a linear dose response with the strongest effect at 10 mg/L concentration, and fungi showed a non-linear response with the strongest effect at 2 mg/L concentration. At the highest nanoplastics concentration, the first colonizing fungal hyphae adsorbed most of the PS nanospheres present in their vicinity, in a process that we termed the 'vacuum cleaner effect'. As a result, the toxicity effect of the original treatment on subsequently growing fungal hyphae was reduced to a growth level indistinguishable from the control. We did not find evidence that nanoplastics are able to penetrate bacterial nor fungal cell walls. Overall, our findings provide evidence that nanoplastics can cause a direct negative effect on soil microbes and highlight the need for further studies that can explain how the microbial stress response might affect soil functions.

Plant Growth-Promoting Bacteria of Soil: Designing of Consortia Beneficial for Crop Production

Plant growth-promoting bacteria are commonly used in agriculture, particularly for seed inoculation. Multispecies consortia are believed to be the most promising form of these bacteria. However, designing and modeling bacterial consortia to achieve desired phenotypic outcomes in plants is challenging. This review aims to address this challenge by exploring key antimicrobial interactions. Special attention is given to approaches for developing soil plant growth-promoting bacteria consortia. Additionally, advanced omics-based methods are analyzed that allow soil microbiomes to be characterized, providing an understanding of the molecular and functional aspects of these microbial communities. A comprehensive discussion explores the utilization of bacterial preparations in biofertilizers for agricultural applications, focusing on the intricate design of synthetic bacterial consortia with these preparations. Overall, the review provides valuable insights and strategies for intentionally designing bacterial consortia to enhance plant growth and development.

Challenges in upscaling laboratory studies to ecosystems in soil microbiology research

Soil microbiology has entered into the big data era, but the challenges in bridging laboratory-, field-, and model-based studies of ecosystem functions still remain. Indeed, the limitation of factors in laboratory experiments disregards interactions of a broad range of in situ environmental drivers leading to frequent contradictions between laboratory- and field-based studies, which may consequently mislead model development and projections. Upscaling soil microbiology research from laboratory to ecosystems represents one of the grand challenges facing environmental scientists, but with great potential to inform policymakers toward climate-smart and resource-efficient ecosystems. The upscaling is not only a scale problem, but also requires disentangling functional relationships and processes on each level. We point to three potential reasons for the gaps between laboratory- and field-based studies (i.e., spatiotemporal dynamics, sampling disturbances, and plant-soil-microbial feedbacks), and three key issues of caution when bridging observations and model predictions (i.e., across-scale effect, complex-process coupling, and multi-factor regulation). Field-based studies only cover a limited range of environmental variation that must be supplemented by laboratory and mesocosm manipulative studies when revealing the underlying mechanisms. The knowledge gaps in upscaling soil microbiology from laboratory to ecosystems should motivate interdisciplinary collaboration across experimental, observational, theoretic, and modeling research.

Insights into accumulation of active ingredients and rhizosphere microorganisms between Salvia miltiorrhiza and S. castanea

Salvia miltiorrhiza is an important traditional herbal medicine, and its extracts could be used for treating cardiovascular disease. Although these medicinal compounds are functionally similar, their wild relative, S. castanea, produces significantly different concentrations of these compounds. The reason for their differences is still unknown. In a series of soil and plant-based analyses, we explored and compared the rhizosphere microbiome of S. miltiorrhiza and S. castanea. To further investigate the geographical distribution of S. castanea, MaxEnt models were used to predict the future suitable habitat areas of S. castanea in China. Results revealed the distributions and structure of the rhizosphere microbial community of S. miltiorrhiza and S. castanea at different times. In addition, differences in altitude and soil moisture resulting from changes in climate and geographical location are also critical environmental factors in the distribution of S. castanea. The findings of this study increase our understanding of plant adaptation to their geographical environment through secondary metabolites. It also highlights the complex interplay between rhizospheric factors and plant metabolism, which provides the theoretical basis for the cultivation of S. miltiorrhiza and the use of S. castanea resources.

Interaction Networks Are Driven by Community-Responsive Phenotypes in a Chitin-Degrading Consortium of Soil Microbes

Soil microorganisms provide key ecological functions that often rely on metabolic interactions between individual populations of the soil microbiome. To better understand these interactions and community processes, we used chitin, a major carbon and nitrogen source in soil, as a test substrate to investigate microbial interactions during its decomposition. Chitin was applied to a model soil consortium that we developed, "model soil consortium-2" (MSC-2), consisting of eight members of diverse phyla and including both chitin degraders and nondegraders. A multiomics approach revealed how MSC-2 community-level processes during chitin decomposition differ from monocultures of the constituent species. Emergent properties of both species and the community were found, including changes in the chitin degradation potential of Streptomyces species and organization of all species into distinct roles in the chitin degradation process. The members of MSC-2 were further evaluated via metatranscriptomics and community metabolomics. Intriguingly, the most abundant members of MSC-2 were not those that were able to metabolize chitin itself, but rather those that were able to take full advantage of interspecies interactions to grow on chitin decomposition products. Using a model soil consortium greatly increased our knowledge of how carbon is decomposed and metabolized in a community setting, showing that niche size, rather than species metabolic capacity, can drive success and that certain species become active carbon degraders only in the context of their surrounding community. These conclusions fill important knowledge gaps that are key to our understanding of community interactions that support carbon and nitrogen cycling in soil. IMPORTANCE The soil microbiome performs many functions that are key to ecology, agriculture, and nutrient cycling. However, because of the complexity of this ecosystem we do not know the molecular details of the interactions between microbial species that lead to these important functions. Here, we use a representative but simplified model community of bacteria to understand the details of these interactions. We show that certain species act as primary degraders of carbon sources and that the most successful species are likely those that can take the most advantage of breakdown products, not necessarily the primary degraders. We also show that a species phenotype, including whether it is a primary degrader or not, is driven in large part by the membership of the community it resides in. These conclusions are critical to a better understanding of the soil microbial interaction network and how these interactions drive central soil microbiome functions.

Limited effect of thermal pruning on wild blueberry crop and its root-associated microbiota

Thermal pruning was a common pruning method in the past but has progressively been replaced by mechanical pruning for economic reasons. Both practices are known to enhance and maintain high yields; however, thermal pruning was documented to have an additional sanitation effect by reducing weeds and fungal diseases outbreaks. Nevertheless, there is no clear consensus on the optimal fire intensity required to observe these outcomes. Furthermore, fire is known to alter the soil microbiome as it impacts the soil organic layer and chemistry. Thus far, no study has investigated into the effect of thermal pruning intensity on the wild blueberry microbiome in agricultural settings. This project aimed to document the effects of four gradual thermal pruning intensities on the wild blueberry performance, weeds, diseases, as well as the rhizosphere fungal and bacterial communities. A field trial was conducted using a block design where agronomic variables were documented throughout the 2-year growing period. MiSeq amplicon sequencing was used to determine the diversity as well as the structure of the bacterial and fungal communities. Overall, yield, fruit ripeness, and several other agronomical variables were not significantly impacted by the burning treatments. Soil phosphorus was the only parameter with a significant albeit temporary change (1 month after thermal pruning) for soil chemistry. Our results also showed that bacterial and fungal communities did not significantly change between burning treatments. The fungal community was dominated by ericoid mycorrhizal fungi, while the bacterial community was mainly composed of Acidobacteriales, Isosphaerales, Frankiales, and Rhizobiales. However, burning at high intensities temporarily reduced Septoria leaf spot disease in the season following thermal pruning. According to our study, thermal pruning has a limited short-term influence on the wild blueberry ecosystem but may have a potential impact on pests (notably Septoria infection), which should be explored in future studies to determine the burning frequency necessary to control this disease.

Bulk and Spatially Resolved Extracellular Metabolome of Free-Living Nitrogen Fixation

Soil nitrogen (N) transformations constrain terrestrial net primary productivity and are driven by the activity of soil microorganisms. Free-living N fixation (FLNF) is an important soil N transformation and key N input to terrestrial systems, but the forms of N contributed to soil by FLNF are poorly understood. To address this knowledge gap, a focus on microorganisms and microbial scale processes is needed that links N-fixing bacteria and their contributed N sources to FLNF process rates. However, studying the activity of soil microorganisms in situ poses inherent challenges, including differences in sampling scale between microorganism and process rates, which can be addressed with culture-based studies and an emphasis on microbial-scale measurements. Culture conditions can differ significantly from soil conditions, so it also important that such studies include multiple culture conditions like liquid and solid media as proxies for soil environments like soil pore water and soil aggregate surfaces. Here we characterized extracellular N-containing metabolites produced by two common, diazotrophic soil bacteria in liquid and solid media, with or without N, across two sampling scales (bulk via GC-MS and spatially resolved via MALDI mass spec imaging). We found extracellular production of inorganic and organic N during FLNF, indicating terrestrial N contributions from FLNF occur in multiple forms not only as ammonium as previously thought. Extracellular metabolite profiles differed between liquid and solid media supporting previous work indicating environmental structure influences microbial function. Metabolite profiles also differed between sampling scales underscoring the need to quantify microbial scale conditions to accurately interpret microbial function.

IMPORTANCE Free-living nitrogen-fixing bacteria contribute significantly to terrestrial nitrogen availability; however, the forms of nitrogen contributed by this process are poorly understood. This is in part because of inherent challenges to studying soil microorganisms in situ, such as vast differences in scale between microorganism and ecosystem and complexities of the soil system (e.g., opacity, chemical complexity). Thus, upscaling important ecosystem processes driven by soil microorganisms, like free-living nitrogen fixation, requires microbial-scale measurements in controlled systems. Our work generated bulk and spatially resolved measurements of nitrogen released during free-living nitrogen fixation under two contrasting growth conditions analogous to soil pores and aggregates. This work allowed us to determine that diverse forms of nitrogen are likely contributed to terrestrial systems by free-living nitrogen bacteria. We also demonstrated that microbial habitat (e.g., liquid versus solid media) alters microbial activity and that measurement of microbial activity is altered by sampling scale (e.g., bulk versus spatially resolved) highlighting the critical importance of quantifying microbial-scale processes to upscaling of ecosystem function.

Synthetic Soil Aggregates: Bioprinted Habitats for High-Throughput Microbial Metaphenomics

The dynamics of microbial processes are difficult to study in natural soil, owing to the small spatial scales on which microorganisms operate and to the opacity and chemical complexity of the soil habitat. To circumvent these challenges, we have created a 3D-bioprinted habitat that mimics aspects of natural soil aggregates while providing a chemically defined and translucent alternative culturing method for soil microorganisms. Our Synthetic Soil Aggregates (SSAs) retain the porosity, permeability, and patchy resource distribution of natural soil aggregates—parameters that are expected to influence emergent microbial community interactions. We demonstrate the printability and viability of several different microorganisms within SSAs and show how the SSAs can be integrated into a multi-omics workflow for single SSA resolution genomics, metabolomics, proteomics, lipidomics, and biogeochemical assays. We study the impact of the structured habitat on the distribution of a model co-culture microbial community and find that it is significantly different from the spatial organization of the same community in liquid culture, indicating a potential for SSAs to reproduce naturally occurring emergent community phenotypes. The SSAs have the potential as a tool to help researchers quantify microbial scale processes in situ and achieve high-resolution data from the interplay between environmental properties and microbial ecology.

N Addition Overwhelmed the Effects of P Addition on the Soil C, N, and P Cycling Genes in Alpine Meadow of the Qinghai-Tibetan Plateau

Although human activities have greatly increased nitrogen (N) and phosphorus (P) inputs to the alpine grassland ecosystems, how soil microbial functional genes involved in nutrient cycling respond to N and P input remains unknown. Based on a fertilization experiment established in an alpine meadow of the Qinghai-Tibetan Plateau, we investigated the response of the abundance of soil carbon (C), N, and P cycling genes to N and P addition and evaluated soil and plant factors related to the observed effects. Our results indicated that the abundance of C, N, and P cycling genes were hardly affected by N addition, while P addition significantly increased most of them, suggesting that the availability of P plays a more important role for soil microorganisms than N in this alpine meadow ecosystem. Meanwhile, when N and P were added together, the abundance of C, N, and P cycling genes did not change significantly, indicating that the promoting effects of P addition on microbial functional genes abundances were overwhelmed by N addition. The Mantel analysis and the variation partitioning analysis revealed the major role of shoot P concentration in regulating the abundance of C, N, and P cycling genes. These results suggest that soil P availability and plant traits are key in governing C, N, and P cycling genes at the functional gene level in the alpine grassland ecosystem.