The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature

A positive feedback to climate change: The effect of temperature on the respiration of key wood-decomposing fungi does not decline with time

Heterotrophic soil microorganisms are responsible for ~50% of the carbon dioxide released by respiration from the terrestrial biosphere each year. The respiratory response of soil microbial communities to warming, and the control mechanisms, remains uncertain, yet is critical to understanding the future land carbon (C)-climate feedback. Individuals of nine species of fungi decomposing wood were exposed to 90 days of cooling to evaluate the medium-term effect of temperature on respiration. Overall, the effect of temperature on respiration increased in the medium term, with no evidence of compensation. However, the increasing effect of temperature on respiration was lost after correcting for changes in biomass. These results indicate that C loss through respiration of wood-decomposing fungi will increase beyond the direct effects of temperature on respiration, potentially promoting greater C losses from terrestrial ecosystems and a positive feedback to climate change.

Applications of Fourier Transform-Infrared spectroscopy in microbial cell biology and environmental microbiology: advances, challenges, and future perspectives

Microorganisms play pivotal roles in shaping ecosystems and biogeochemical cycles. Their intricate interactions involve complex biochemical processes. Fourier Transform-Infrared (FT-IR) spectroscopy is a powerful tool for monitoring these interactions, revealing microorganism composition and responses to the environment. This review explores the diversity of applications of FT-IR spectroscopy within the field of microbiology, highlighting its specific utility in microbial cell biology and environmental microbiology. It emphasizes key applications such as microbial identification, process monitoring, cell wall analysis, biofilm examination, stress response assessment, and environmental interaction investigation, showcasing the crucial role of FT-IR in advancing our understanding of microbial systems. Furthermore, we address challenges including sample complexity, data interpretation nuances, and the need for integration with complementary techniques. Future prospects for FT-IR in environmental microbiology include a wide range of transformative applications and advancements. These include the development of comprehensive and standardized FT-IR libraries for precise microbial identification, the integration of advanced analytical techniques, the adoption of high-throughput and single-cell analysis, real-time environmental monitoring using portable FT-IR systems and the incorporation of FT-IR data into ecological modeling for predictive insights into microbial responses to environmental changes. These innovative avenues promise to significantly advance our understanding of microorganisms and their complex interactions within various ecosystems.

Temperature and organic carbon quality control the anaerobic carbon mineralization in peat profiles via modulating microbes: A case study of Changbai Mountain

Peatlands account for a significant fraction of the global carbon stock. However, the complex interplay of abiotic and biotic factors governing anaerobic carbon mineralization in response to warming remains unclear. In this study, peat sediments were collected from a typical northern peatland-Changbai Mountain to investigate the behavior and mechanism of anaerobic carbon mineralization in response to depth (0-200 cm) and temperature (5 °C, 15 °C and 20 °C), by integrating geochemical and microbial analysis. Several indices including humification indexes (HI), aromaticity, and water extractable organic carbon (WEOC) components were applied to evaluate carbon quality, while 16S rRNA sequencing was used to measure microbial composition. Regardless of temperature, degradations of carbon quality and associated reduction in microbial abundance as well as diversity resulted in a decrease in anaerobic carbon mineralization (both CO2 and CH4) towards greater depth. Warming either from 5 °C to 15 °C or 20 °C significantly increased anaerobic carbon mineralization in all depth profiles by improving carbon availability. Enhanced carbon availabilities were mediated by the change in microbial composition (p < 0.01) and an increase in metabolic activities, which was particularly evident in the enhanced β-glucosidase activity and microbial collaborations. A remarkable increase of over 10-fold in the relative abundance of the Geothrix genus was observed under warming. Overall, warming resulted in an enhanced contribution of CH4 emission and a higher ratio of hydrogenotrophic methanogenesis, as evidenced by carbon isotope fractionation factors. In addition, deep peat soils (>100 cm) with recalcitrant carbon demonstrated greater temperature sensitivity (Q10: ∼2.0) than shallow peat soils (Q10:∼1.2) when temperature increased from 15 °C to 20 °C. The findings of this study have significantly deepened our understanding for mechanisms of carbon quality and microbe-driven anaerobic carbon mineralization in peatlands under global warming.

Waterlogging stress alters the structure of sugar beet rhizosphere microbial community structure and recruiting potentially beneficial bacterial

Waterlogging has been shown to have a significant inhibitory effect on plant growth. However, the response mechanisms of the soil environment of sugar beet seedlings under waterlogging conditions still need to be fully understood. This study aimed to investigate the effects of waterlogging treatments on the content of effective nutrients and the microbial communities in the rhizosphere and non-rhizosphere using high-throughput sequencing. We set up waterlogging and non-waterlogging treatments, sampled sugar beet seedlings after 10 days of waterlogging, determined the effective soil nutrients in the rhizosphere and non-rhizosphere of the plants, and analyzed the differences in microbial diversity at ten days of waterlogging. The results showed that waterlogging significantly affected available potassium (AK) content. The Ak content of waterlogged soil was significantly higher than that of non-waterlogged soil. Waterlogging caused no significant difference in available nitrogen (AN) content and pH. Moreover, the plant growth-promoting bacteria Pseudomonas was significantly enriched in sugar beet waterlogged rhizospheres compared with the non-waterlogged ones. Similarly, the harmful fungi Gibellulopsis and Alternaria were enriched in sugar beet non-waterlogged rhizosphere. The network analysis revealed that waterlogging built a less complex root-microbial network than non-waterlogging. These findings implied that sugar beets subjected to waterlogging stress were enriched with beneficial microorganisms in the rhizosphere, potentially alleviating the stress.

Temperature fluctuation promotes the thermal adaptation of soil microbial respiration

The magnitude of the feedback between soil microbial respiration and increased mean temperature may decrease (a process called thermal adaptation) or increase over time, and accurately representing this feedback in models improves predictions of soil carbon loss rates. However, climate change entails changes not only in mean temperature but also in temperature fluctuation, and how this fluctuation regulates the thermal response of microbial respiration has never been systematically evaluated. By analysing subtropical forest soils from a 2,000 km transect across China, we showed that although a positive relationship between soil microbial biomass-specific respiration and temperature was observed under increased constant incubation temperature, an increasing temperature fluctuation had a stronger negative effect. Our results further indicated that changes in bacterial community composition and reduced activities of carbon degradation enzymes promoted the effect of temperature fluctuation. This adaptive response of soil microbial respiration suggests that climate warming may have a lesser exacerbating effect on atmospheric CO2 concentrations than predicted.

Microbial respiratory thermal adaptation is regulated by r-/K-strategy dominance

Microbial thermal adaptation is considered to be one of the core mechanisms affecting soil carbon cycling. However, the role of microbial community composition in controlling thermal adaptation is poorly understood. Using microbial communities from the rhizosphere and bulk soils in an 8-year warming experiment as a model, we experimentally demonstrate that respiratory thermal adaptation was much stronger in microbial K-strategist-dominated bulk soils than in microbial r-strategist-dominated rhizosphere soils. Soil carbon availability exerted strong selection on the dominant ecological strategy of the microbial community, indirectly influencing respiratory thermal adaptation. Our findings shed light on the linchpin of the dominant ecological strategy exhibited by the microbial community in determining its respiratory thermal adaptation, with implications for understanding soil carbon losses under warming.

Depth-resolved microbial diversity and functional profiles of trichloroethylene-contaminated soils for Biolog EcoPlate-based biostimulation strategy

This study explores the toxic effect of TCE at different depths of sub-surface soil and underpins microbial community-level suitable carbon (C)-sources that provided directionality to the in situ biostimulation effort via augmentation strategy for effective TCE remediation in soil. The impacts on resident microbial communities and their functional profiles that govern the TCE biodegradation process were identified. Highly contaminated PW01 soil (9 m depth) had severely limited microbial diversity and was enriched in Proteobacteria and Firmicutes. The abundance of TCE degradation-associated genera was observed in all contaminated samples, and the abundance of TCE-degradation-related taxa were positively correlated with soil TCE contamination levels. Community-level metabolic activity associated with the utilization of diverse external C-sources was directly influenced by TCE concentration and soil depth. Multivariate data analysis revealed that the functional genus, TCE concentration, and selected available C substrate uptake capacity correlated in soil samples. Pearson's correlation tests revealed that C sources such as L-arginine, phenylethylamine and γ-hydroxybutyric acid utilization trait exhibited significant positive correlations with chloroalkane and chloroalkene degradation pathway abundance. Ultimately, depth and TCE contamination level-associated soil microbiota and their most preferred C-source understanding could add to facilitate effective biostimulation via external nutrient amendment for efficient in situ TCE degradation.

Evaluation of Bacteria and Fungi DNA Abundance in Human Tissues

Whereas targeted and shotgun sequencing approaches are both powerful in allowing the study of tissue-associated microbiota, the human: microorganism abundance ratios in tissues of interest will ultimately determine the most suitable sequencing approach. In addition, it is possible that the knowledge of the relative abundance of bacteria and fungi during a treatment course or in pathological conditions can be relevant in many medical conditions. Here, we present a qPCR-targeted approach to determine the absolute and relative amounts of bacteria and fungi and demonstrate their relative DNA abundance in nine different human tissue types for a total of 87 samples. In these tissues, fungi genomes are more abundant in stool and skin samples but have much lower levels in other tissues. Bacteria genomes prevail in stool, skin, oral swabs, saliva, and gastric fluids. These findings were confirmed by shotgun sequencing for stool and gastric fluids. This approach may contribute to a more comprehensive view of the human microbiota in targeted studies for assessing the abundance levels of microorganisms during disease treatment/progression and to indicate the most informative methods for studying microbial composition (shotgun versus targeted sequencing) for various samples types.

Long-Term Amelioration Practices Reshape the Soil Microbiome in a Coastal Saline Soil and Alter the Richness and Vertical Distribution Differently Among Bacterial, Archaeal, and Fungal Communities

Globally soil salinity is one of the most devastating environmental stresses affecting agricultural systems and causes huge economic losses each year. High soil salinity causes osmotic stress, nutritional imbalance and ion toxicity to plants and severely affects crop productivity in farming systems. Freezing saline water irrigation and plastic mulching techniques were successfully developed in our previous study to desalinize costal saline soil. Understanding how microbial communities respond during saline soil amelioration is crucial, given the key roles soil microbes play in ecosystem succession. In the present study, the community composition, diversity, assembly and potential ecological functions of archaea, bacteria and fungi in coastal saline soil under amelioration practices of freezing saline water irrigation, plastic mulching and the combination of freezing saline water irrigation and plastic mulching were assessed through high-throughput sequencing. These amelioration practices decreased archaeal and increased bacterial richness while leaving fungal richness little changed in the surface soil. Functional prediction revealed that the amelioration practices, especially winter irrigation with saline water and film mulched in spring, promoted a community harboring heterotrophic features. β-null deviation analysis illustrated that amelioration practices weakened the deterministic processes in structuring coastal saline soil microbial communities. These results advanced our understanding of the responses of the soil microbiome to amelioration practices and provided useful information for developing microbe-based remediation approaches in coastal saline soils.

Soil microbial sensitivity to temperature remains unchanged despite community compositional shifts along geothermal gradients

Climate warming may be exacerbated if rising temperatures stimulate losses of soil carbon to the atmosphere. The direction and magnitude of this carbon-climate feedback are uncertain, largely due to lack of knowledge of the thermal adaptation of the physiology and composition of soil microbial communities. Here, we applied the macromolecular rate theory (MMRT) to describe the temperature response of the microbial decomposition of soil organic matter (SOM) in a natural long-term warming experiment in a geothermally active area in New Zealand. Our objective was to test whether microbial communities adapt to long-term warming with a shift in their composition and their temperature response that are consistent with evolutionary theory of trade-offs between enzyme structure and function. We characterized the microbial community composition (using metabarcoding) and the temperature response of microbial decomposition of SOM (using MMRT) of soils sampled along transects of increasing distance from a geothermally active zone comprising two biomes (a shrubland and a grassland) and sampled at two depths (0-50 and 50-100 mm), such that ambient soil temperature and soil carbon concentration varied widely and independently. We found that the different environments were hosting microbial communities with distinct compositions, with thermophile and thermotolerant genera increasing in relative abundance with increasing ambient temperature. However, the ambient temperature had no detectable influence on the MMRT parameters or the relative temperature sensitivity of decomposition (Q₁₀ ). MMRT parameters were, however, strongly correlated with soil carbon concentration and carbon:nitrogen ratio. Our findings suggest that, while long-term warming selects for warm-adapted taxa, substrate quality and quantity exert a stronger influence than temperature in selecting for distinct thermal traits. The results have major implications for our understanding of the role of soil microbial processes in the long-term effects of climate warming on soil carbon dynamics and will help increase confidence in carbon-climate feedback projections.

High-throughput molecular technologies for unraveling the mystery of soil microbial community: challenges and future prospects

Soil microbial communities play a crucial role in soil fertility, sustainability, and plant health. However, intensive agriculture with increasing chemical inputs and changing environments have influenced native soil microbial communities. Approaches have been developed to study the structure, diversity, and activity of soil microbes to better understand the biology and plant-microbe interactions in soils. Unfortunately, a good understanding of soil microbial community remains a challenge due to the complexity of community composition, interactions of the soil environment, and limitations of technologies, especially related to the functionality of some taxa rarely detected using conventional techniques. Culture-based methods have been shown unable and sometimes are biased for assessing soil microbial communities. To gain further knowledge, culture-independent methods relying on direct analysis of nucleic acids, proteins, and lipids are worth exploring. In recent years, metagenomics, metaproteomics, metatranscriptomics, and proteogenomics have been increasingly used in studying microbial ecology. In this review, we examined the importance of microbial community to soil quality, the mystery of rhizosphere and plant-microbe interactions, and the biodiversity and multi-trophic interactions that influence the soil structure and functionality. The impact of the cropping system and climate change on the soil microbial community was also explored. Importantly, progresses in molecular biology, especially in the development of high-throughput biotechnological tools, were extensively assessed for potential uses to decipher the diversity and dynamics of soil microbial communities, with the highlighted advantages/limitations.

Carbon Dynamics of Fruit and Vegetable Wastes and Biodegradable Municipal Waste Compost-Amended Oxisol

Recycling of wastes via composting is advocated as a means to reduce environmental hazards due to the dumping of wastes. Composting also creates a vital source of organic matter that is important in nutrient and soil moisture retention, soil fertility preservation and improving the physical and chemical properties of soils. This study was conducted to evaluate the short-term effects of four compost amendments in an Oxisol on carbon dynamics (carbon dioxide evolution and carbon transformation). The composts were prepared in 3:1 and 1:2 of fruit and vegetable waste (FVW) to biodegradable municipal waste (BMW) with and without indigenous microorganisms (IMO) (3:1 +IMO, 1:2 +IMO, 3:1 −IMO, 1:2 −IMO). Soil incubation studies were carried out for 35 days at three compost application rates of 0, 5 and 10 Mg ha−1, with measurements done including the CO2 evolution, dehydrogenase enzyme (DHA) assay and compost Fourier transform infrared (FTIR) spectroscopy spectral analysis. At 10 Mg ha−1 compost application rate, increased soil respiration rate was obtained at 3:1 +IMO compost, mostly due to increased labile organic matter and higher amount of FVW in the compost mixture, which stimulated soil microorganisms and/or their activities reflected by increased evolution of CO2 in the process of decomposition of the added composts in the compost-amended soils. The DHA activity increased with compost application rates, and significantly, the highest DHA activity was recorded at 3:1 +IMO compost applied at 10 Mg ha−1 soil at 1.38 triphenylformazan (TPF)/g dry soil/24 h. The compost FTIR spectral analysis showed transformations that occurred due to the composting that was carried out. A broadband between 3279–3347 cm wavelength in the FTIR spectroscopy indicated the presence of carboxylic and hydroxyl functional groups because of carbon transformation that occurred in the composts.

Castro I, Soares R, Brito DRA, Mbanze AA, Chaúque A, Máguas C, Ezeokoli OT, Ribeiro NS, Marques I, Ribeiro-Barros AI. The Nexus between Fire and Soil Bacterial Diversity in the African Miombo Woodlands of Niassa Special Reserve, Mozambique

(1) Background: the Miombo woodlands comprise the most important vegetation from southern Africa and are dominated by tree legumes with an ecology highly driven by fires. Here, we report on the characterization of bacterial communities from the rhizosphere of Brachystegia boehmii in different soil types from areas subjected to different regimes. (2) Methods: bacterial communities were identified through Illumina MiSeq sequencing (16S rRNA). Vigna unguiculata was used as a trap to capture nitrogen-fixing bacteria and culture-dependent methods in selective media were used to isolate plant growth promoting bacteria (PGPB). PGP traits were analysed and molecular taxonomy of the purified isolates was performed. (3) Results: Bacterial communities in the Miombo rhizosphere are highly diverse and driven by soil type and fire regime. Independent of the soil or fire regime, the functional diversity was high, and the different consortia maintained the general functions. A diverse pool of diazotrophs was isolated, and included symbiotic (e.g., Mesorhizobium sp., Neorhizobium galegae, Rhizobium sp., and Ensifer adhaerens), and non-symbiotic (e.g., Agrobacterium sp., Burkholderia sp., Cohnella sp., Microvirga sp., Pseudomonas sp., and Stenotrophomonas sp.) bacteria. Several isolates presented cumulative PGP traits. (4) Conclusions: Although the dynamics of bacterial communities from the Miombo rhizosphere is driven by fire, the maintenance of high levels of diversity and functions remain unchanged, constituting a source of promising bacteria in terms of plant-beneficial activities such as mobilization and acquisition of nutrients, mitigation of abiotic stress, and modulation of plant hormone levels.

The thermal response of soil microbial methanogenesis decreases in magnitude with changing temperature

Microbial methanogenesis in anaerobic soils contributes greatly to global methane (CH₄) release, and understanding its response to temperature is fundamental to predicting the feedback between this potent greenhouse gas and climate change. A compensatory thermal response in microbial activity over time can reduce the response of respiratory carbon (C) release to temperature change, as shown for carbon dioxide (CO₂) in aerobic soils. However, whether microbial methanogenesis also shows a compensatory response to temperature change remains unknown. Here, we used anaerobic wetland soils from the Greater Khingan Range and the Tibetan Plateau to investigate how 160 days of experimental warming (+4°C) and cooling (−4°C) affect the thermal response of microbial CH₄ respiration and whether these responses correspond to changes in microbial community dynamics. The mass-specific CH₄ respiration rates of methanogens decreased with warming and increased with cooling, suggesting that microbial methanogenesis exhibited compensatory responses to temperature changes. Furthermore, changes in the species composition of methanogenic community under warming and cooling largely explained the compensatory response in the soils. The stimulatory effect of climate warming on soil microbe-driven CH₄ emissions may thus be smaller than that currently predicted, with important consequences for atmospheric CH₄ concentrations.

Soil microbes produce more methane as temperatures warm, but it is unclear if they acclimate to heat, or keep producing more of the greenhouse gas. Here the authors use artificial wetland warming experiments to show that after initial spikes in methane emissions after warming, emissions level out over time.

Cross-biome patterns in soil microbial respiration predictable from evolutionary theory on thermal adaptation

Climate warming may stimulate microbial metabolism of soil carbon, causing a carbon-cycle-climate feedback whereby carbon is redistributed from the soil to atmospheric CO₂. The magnitude of this feedback is uncertain, in part because warming-induced shifts in microbial physiology and/or community composition could retard or accelerate soil carbon losses. Here, we measure microbial respiration rates for soils collected from 22 sites in each of 3 years, at locations spanning boreal to tropical climates. Respiration was measured in the laboratory with standard temperatures, moisture and excess carbon substrate, to allow physiological and community effects to be detected independent of the influence of these abiotic controls. Patterns in respiration for soils collected across the climate gradient are consistent with evolutionary theory on physiological responses that compensate for positive effects of temperature on metabolism. Respiration rates per unit microbial biomass were as much as 2.6 times higher for soils sampled from sites with a mean annual temperature of -2.0 versus 21.7 °C. Subsequent 100-d incubations suggested differences in the plasticity of the thermal response among microbial communities, with communities sampled from sites with higher mean annual temperature having a more plastic response. Our findings are consistent with adaptive metabolic responses to contrasting thermal regimes that are also observed in plants and animals. These results may help build confidence in soil-carbon-climate feedback projections by improving understanding of microbial processes represented in biogeochemical models.

The Legacy Effects of Winter Climate on Microbial Functioning After Snowmelt in a Subarctic Tundra

Warming-induced increases in microbial CO₂ release in northern tundra may positively feedback to climate change. However, shifts in microbial extracellular enzyme activities (EEAs) may alter the impacts of warming over the longer term. We investigated the in situ effects of 3 years of winter warming in combination with the in vitro effects of a rapid warming (6 days) on microbial CO₂ release and EEAs in a subarctic tundra heath after snowmelt in spring. Winter warming did not change microbial CO₂ release at ambient (10 °C) or at rapidly increased temperatures, i.e., a warm spell (18 °C) but induced changes (P < 0.1) in the Q₁₀ of microbial respiration and an oxidative EEA. Thus, although warmer winters may induce legacy effects in microbial temperature acclimation, we found no evidence for changes in potential carbon mineralization after spring thaw.

Spatial variations of soil respiration and temperature sensitivity along a steep slope of the semiarid Loess Plateau

The spatial heterogeneity of soil respiration and its temperature sensitivity pose a great challenge to accurately estimate the carbon flux in global carbon cycling, which has primarily been researched in flatlands versus hillslope ecosystems. On an eroded slope (35°) of the semiarid Loess Plateau, soil respiration, soil moisture and soil temperature were measured in situ at upper and lower slope positions in triplicate from 2014 until 2016, and the soil biochemical and microbial properties were determined. The results showed that soil respiration was significantly greater (by 44.2%) at the lower slope position (2.6 μmol m^–2 s^–1) than at the upper slope position, as were soil moisture, carbon, nitrogen fractions and root biomass. However, the temperature sensitivity was 13.2% greater at the upper slope position than at the lower slope position (P < 0.05). The soil fungal community changed from being Basidiomycota-dominant at the upper slope position to being Zygomycota-dominant at the lower slope position, corresponding with increased β-D-glucosidase activity at the upper slope position than at the lower slope position. We concluded that soil respiration was enhanced by the greater soil moisture, root biomass, carbon and nitrogen contents at the lower slope position than at the upper slope position. Moreover, the increased soil respiration and decreased temperature sensitivity at the lower slope position were partially due to copiotrophs replacing oligotrophs. Such spatial variations along slopes must be properly accounted for when estimating the carbon budget and feedback of future climate change on hillslope ecosystems.

Fast and Simple Analysis of MiSeq Amplicon Sequencing Data with MetaAmp

Microbial community profiling by barcoded 16S rRNA gene amplicon sequencing currently has many applications in microbial ecology. The low costs of the parallel sequencing of multiplexed samples, combined with the relative ease of data processing and interpretation (compared to shotgun metagenomes) have made this an entry-level approach. Here we present the MetaAmp pipeline for processing of SSU rRNA gene and other non-coding or protein-coding amplicon sequencing data by investigators that are inexperienced with bioinformatics procedures. It accepts single-end or paired-end sequences in fasta or fastq format from various sequencing platforms. It includes read quality control, and merging of forward and reverse reads of paired-end reads. It makes use of UPARSE, Mothur, and the SILVA database for clustering, removal of chimeric reads, taxonomic classification, and generation of diversity metrics. The pipeline has been validated with a mock community of known composition. MetaAmp provides a convenient web interface as well as command line interface. It is freely available at: http://ebg.ucalgary.ca/metaamp. Since its launch 2 years ago, MetaAmp has been used >2,800 times, by many users worldwide.

Plant-microbial interactions in agriculture and the use of farming systems to improve diversity and productivity

A thorough understanding of the services provided by microorganisms to the agricultural ecosystem is integral to understanding how management systems can improve or deteriorate soil health and production over the long term. Yet it is hampered by the difficulty in measuring the intersection of plant, microbe, and environment, in no small part because of the situational specificity to some plant-microbial interactions, related to soil moisture, nutrient content, climate, and local diversity. Despite this, perspective on soil microbiota in agricultural settings can inform management practices to improve the sustainability of agricultural production.