Glucose triggers strong taxon-specific responses in microbial growth and activity: insights from DNA and RNA qSIP

Soil warming increases the number of growing bacterial taxa but not their growth rates

Soil microorganisms control the fate of soil organic carbon. Warming may accelerate their activities putting large carbon stocks at risk of decomposition. Existing knowledge about microbial responses to warming is based on community-level measurements, leaving the underlying mechanisms unexplored and hindering predictions. In a long-term soil warming experiment in a Subarctic grassland, we investigated how active populations of bacteria and archaea responded to elevated soil temperatures (+6°C) and the influence of plant roots, by measuring taxon-specific growth rates using quantitative stable isotope probing and 18O water vapor equilibration. Contrary to prior assumptions, increased community growth was associated with a greater number of active bacterial taxa rather than generally faster-growing populations. We also found that root presence enhanced bacterial growth at ambient temperatures but not at elevated temperatures, indicating a shift in plant-microbe interactions. Our results, thus, reveal a mechanism of how soil bacteria respond to warming that cannot be inferred from community-level measurements.

Nitrogen fixation and transcriptome of a new diazotrophic Geomonas from paddy soils

IMPORTANCE

The ability of Geomonas species to fix nitrogen gas (N2) is an important metabolic feature for its application as a plant growth-promoting rhizobacterium. This research is of great importance as it provides the first comprehensive direct experimental evidence of nitrogen fixation by the genus Geomonas in pure culture. We isolated a number of Geomonas strains from paddy soils and determined that nifH was present in these strains. This study demonstrated that these Geomonas species harbored genes encoding nitrogenase, as do Geobacter and Anaeromyxobacter in the same class of Deltaproteobacteria. We demonstrated N2-dependent growth of Geomonas and determined regulation of gene expression associated with nitrogen fixation. The research establishes and advances our understanding of nitrogen fixation in Geomonas.

Low and high nucleic acid content bacteria play discrepant roles in response to various carbon supply modes

Planktonic bacteria can be grouped into 'high nucleic acid content (HNA) bacteria' and 'low nucleic acid content (LNA) bacteria.' Nutrient input modes vary in environments, causing nutrient availability heterogeneity. We incubated them with equal amounts of total glucose added in a continuous/pulsed mode. The pulse-treated LNA bacteria exhibited twice the cell abundance and four times the viability of the continuous-treated LNA, while HNA did not show an adaptation to pulsed treatment. In structural equation modelling, LNA bacteria had higher path coefficients than HNA, between growth and carbon-saving metabolic pathways, intracellular ATP and the inorganic energy storage polymer, polyphosphate, indicating their low-cost growth, and flexible energy storage and utilisation. After incubation, the pulse-treated LNA bacteria contained more proteins and polysaccharides (0.00064, 0.0012 ng cell-1 ) than the continuous-treated LNA (0.00014, 0.00014 ng cell-1 ), conferring endurance and rapid response to pulses. Compared to LNA, HNA keystone taxa had stronger correlations with the primary glucose metabolism step, glycolysis, and occupied leading positions to explain the random forest model. They are essential to introduce glucose into the element cycling of the whole community under both treatments. Our work outlines a systematic bacterial response to carbon input.

Advances and perspectives of using stable isotope probing (SIP)-based technologies in contaminant biodegradation

Stable isotope probing (SIP) is a powerful tool to study microbial community structure and function in both nature and engineered environments. Coupling with advanced genomics and other techniques, SIP studies have generated substantial information to allow researchers to draw a clearer picture of what is occurring in complex microbial ecosystems. This review provides an overview of the advances of SIP-based technologies over time, summarizes the status of SIP applications to contaminant biodegradation, provides critical perspectives on ecological interactions within the community, and important factors (controllable and non-controllable) to be considered in SIP experimental designs and data interpretation. Current trend and perspectives of adapting SIP techniques for environmental applications are also discussed.

Life history strategies among soil bacteria-dichotomy for few, continuum for many

Study of life history strategies may help predict the performance of microorganisms in nature by organizing the complexity of microbial communities into groups of organisms with similar strategies. Here, we tested the extent that one common application of life history theory, the copiotroph-oligotroph framework, could predict the relative population growth rate of bacterial taxa in soils from four different ecosystems. We measured the change of in situ relative growth rate to added glucose and ammonium using both ¹⁸O-H₂O and ¹³C quantitative stable isotope probing to test whether bacterial taxa sorted into copiotrophic and oligotrophic groups. We saw considerable overlap in nutrient responses across most bacteria regardless of phyla, with many taxa growing slowly and few taxa that grew quickly. To define plausible life history boundaries based on in situ relative growth rates, we applied Gaussian mixture models to organisms' joint ¹⁸O-¹³C signatures and found that across experimental replicates, few taxa could consistently be assigned as copiotrophs, despite their potential for fast growth. When life history classifications were assigned based on average relative growth rate at varying taxonomic levels, finer resolutions (e.g., genus level) were significantly more effective in capturing changes in nutrient response than broad taxonomic resolution (e.g., phylum level). Our results demonstrate the difficulty in generalizing bacterial life history strategies to broad lineages, and even to single organisms across a range of soils and experimental conditions. We conclude that there is a continued need for the direct measurement of microbial communities in soil to advance ecologically realistic frameworks.

Effects of Tree Composition and Soil Depth on Structure and Functionality of Belowground Microbial Communities in Temperate European Forests

Depending on their tree species composition, forests recruit different soil microbial communities. Likewise, the vertical nutrient gradient along soil profiles impacts these communities and their activities. In forest soils, bacteria and fungi commonly compete, coexist, and interact, which is challenging for understanding the complex mechanisms behind microbial structuring. Using amplicon sequencing, we analyzed bacterial and fungal diversity in relation to forest composition and soil depth. Moreover, employing random forest models, we identified microbial indicator taxa of forest plots composed of either deciduous or evergreen trees, or their mixtures, as well as of three soil depths. We expected that forest composition and soil depth affect bacterial and fungal diversity and community structure differently. Indeed, relative abundances of microbial communities changed more across soil depths than in relation to forest composition. The microbial Shannon diversity was particularly affected by soil depth and by the proportion of evergreen trees. Our results also reflected that bacterial communities are primarily shaped by soil depth, while fungi were influenced by forest tree species composition. An increasing proportion of evergreen trees did not provoke differences in main bacterial metabolic functions, e.g., carbon fixation, degradation, or photosynthesis. However, significant responses related to specialized bacterial metabolisms were detected. Saprotrophic, arbuscular mycorrhizal, and plant pathogenic fungi were related to the proportion of evergreen trees, particularly in topsoil. Prominent microbial indicator taxa in the deciduous forests were characterized to be r-strategists, whereas K-strategists dominated evergreen plots. Considering simultaneously forest composition and soil depth to unravel differences in microbial communities, metabolic pathways and functional guilds have the potential to enlighten mechanisms that maintain forest soil functionality and provide resistance against disturbances.

Bridging Microbial Functional Traits With Localized Process Rates at Soil Interfaces

In this review, we introduce microbially-mediated soil processes, players, their functional traits, and their links to processes at biogeochemical interfaces [e.g., rhizosphere, detritusphere, (bio)-pores, and aggregate surfaces]. A conceptual view emphasizes the central role of the rhizosphere in interactions with other biogeochemical interfaces, considering biotic and abiotic dynamic drivers. We discuss the applicability of three groups of traits based on microbial physiology, activity state, and genomic functional traits to reflect microbial growth in soil. The sensitivity and credibility of modern molecular approaches to estimate microbial-specific growth rates require further development. A link between functional traits determined by physiological (e.g., respiration, biomarkers) and genomic (e.g., genome size, number of ribosomal gene copies per genome, expression of catabolic versus biosynthetic genes) approaches is strongly affected by environmental conditions such as carbon, nutrient availability, and ecosystem type. Therefore, we address the role of soil physico-chemical conditions and trophic interactions as drivers of microbially-mediated soil processes at relevant scales for process localization. The strengths and weaknesses of current approaches (destructive, non-destructive, and predictive) for assessing process localization and the corresponding estimates of process rates are linked to the challenges for modeling microbially-mediated processes in heterogeneous soil microhabitats. Finally, we introduce a conceptual self-regulatory mechanism based on the flexible structure of active microbial communities. Microbial taxa best suited to each successional stage of substrate decomposition become dominant and alter the community structure. The rates of decomposition of organic compounds, therefore, are dependent on the functional traits of dominant taxa and microbial strategies, which are selected and driven by the local environment.

Rapid Response of Nitrogen Cycling Gene Transcription to Labile Carbon Amendments in a Soil Microbial Community

A large portion of activity in soil microbial communities occurs in short time frames in response to an increase in C availability, affecting the biogeochemical cycling of nitrogen. These changes are of particular importance as nitrogen represents both a limiting nutrient for terrestrial plants as well as a potential pollutant.

Episodic inputs of labile carbon (C) to soil can rapidly stimulate nitrogen (N) immobilization by soil microorganisms. However, the transcriptional patterns that underlie this process remain unclear. In order to better understand the regulation of N cycling in soil microbial communities, we conducted a 48-h laboratory incubation with agricultural soil where we stimulated the uptake of inorganic N by amending the soil with glucose. We analyzed the metagenome and metatranscriptome of the microbial communities at four time points that corresponded with changes in N availability. The relative abundances of genes remained largely unchanged throughout the incubation. In contrast, glucose addition rapidly increased the transcription of genes encoding ammonium and nitrate transporters, enzymes responsible for N assimilation into biomass, and genes associated with the N regulatory network. This upregulation coincided with an increase in transcripts associated with glucose breakdown and oxoglutarate production, demonstrating a connection between C and N metabolism. When concentrations of ammonium were low, we observed a transient upregulation of genes associated with the nitrogen-fixing enzyme nitrogenase. Transcripts for nitrification and denitrification were downregulated throughout the incubation, suggesting that dissimilatory transformations of N may be suppressed in response to labile C inputs in these soils. These results demonstrate that soil microbial communities can respond rapidly to changes in C availability by drastically altering the transcription of N cycling genes.

IMPORTANCE A large portion of activity in soil microbial communities occurs in short time frames in response to an increase in C availability, affecting the biogeochemical cycling of nitrogen. These changes are of particular importance as nitrogen represents both a limiting nutrient for terrestrial plants as well as a potential pollutant. However, we lack a full understanding of the short-term effects of labile carbon inputs on the metabolism of microbes living in soil. Here, we found that soil microbial communities responded to labile carbon addition by rapidly transcribing genes encoding proteins and enzymes responsible for inorganic nitrogen acquisition, including nitrogen fixation. This work demonstrates that soil microbial communities respond within hours to carbon inputs through altered gene expression. These insights are essential for an improved understanding of the microbial processes governing soil organic matter production, decomposition, and nutrient cycling in natural and agricultural ecosystems.

Metagenomes and Metatranscriptomes of a Glucose-Amended Agricultural Soil

The addition of glucose to soil has long been used to study the metabolic activity of microbes in soil; however, the response of the microbial ecophysiology remains poorly characterized. To address this, we sequenced the metagenomes and metatranscriptomes of glucose-amended soil microbial communities in a laboratory incubation.