The Transition From Stochastic to Deterministic Bacterial Community Assembly During Permafrost Thaw Succession

Genomic insights into redox-driven microbial processes for carbon decomposition in thawing Arctic soils and permafrost

Climate change is rapidly transforming Arctic landscapes where increasing soil temperatures speed up permafrost thaw. This exposes large carbon stocks to microbial decomposition, possibly worsening climate change by releasing more greenhouse gases. Understanding how microbes break down soil carbon, especially under the anaerobic conditions of thawing permafrost, is important to determine future changes. Here, we studied the microbial community dynamics and soil carbon decomposition potential in permafrost and active layer soils under anaerobic laboratory conditions that simulated an Arctic summer thaw. The microbial and viral compositions in the samples were analyzed based on metagenomes, metagenome-assembled genomes, and metagenomic viral contigs (mVCs). Following the thawing of permafrost, there was a notable shift in microbial community structure, with fermentative Firmicutes and Bacteroidota taking over from Actinobacteria and Proteobacteria over the 60-day incubation period. The increase in iron and sulfate-reducing microbes had a significant role in limiting methane production from thawed permafrost, underscoring the competition within microbial communities. We explored the growth strategies of microbial communities and found that slow growth was the major strategy in both the active layer and permafrost. Our findings challenge the assumption that fast-growing microbes mainly respond to environmental changes like permafrost thaw. Instead, they indicate a common strategy of slow growth among microbial communities, likely due to the thermodynamic constraints of soil substrates and electron acceptors, and the need for microbes to adjust to post-thaw conditions. The mVCs harbored a wide range of auxiliary metabolic genes that may support cell protection from ice formation in virus-infected cells.

IMPORTANCE

As the Arctic warms, thawing permafrost unlocks carbon, potentially accelerating climate change by releasing greenhouse gases. Our research delves into the underlying biogeochemical processes likely mediated by the soil microbial community in response to the wet and anaerobic conditions, akin to an Arctic summer thaw. We observed a significant shift in the microbial community post-thaw, with fermentative bacteria like Firmicutes and Bacteroidota taking over and switching to different fermentation pathways. The dominance of iron and sulfate-reducing bacteria likely constrained methane production in the thawing permafrost. Slow-growing microbes outweighed fast-growing ones, even after thaw, upending the expectation that rapid microbial responses to dominate after permafrost thaws. This research highlights the nuanced and complex interactions within Arctic soil microbial communities and underscores the challenges in predicting microbial response to environmental change.

Microbial composition and function in reclaimed mine sites along a reclamation chronosequence become increasingly similar to undisturbed reference sites

Mine reclamation historically focuses on enhancing plant coverage to improve below and aboveground ecology. However, there is a great need to study the role of soil microorganisms in mine reclamation, particularly long-term studies that track the succession of microbial communities. Here, we investigate the trajectory of microbial communities of mining sites reclaimed between three and 26 years. We used high-throughput amplicon sequencing to characterize the bacterial and fungal communities. We quantified how similar the reclaimed sites were to unmined, undisturbed reference sites and explored the trajectory of microbial communities along the reclamation chronosequence. We also examined the ecological processes that shape the assembly of bacterial communities. Finally, we investigated the functional potential of the microbial communities through metagenomic sequencing. Our results reveal that the reclamation age significantly impacted the community compositions of bacterial and fungal communities. As the reclamation age increases, bacterial and fungal communities become similar to the unmined, undisturbed reference site, suggesting a favorable succession in microbial communities. The bacterial community assembly was also significantly impacted by reclamation age and was primarily driven by stochastic processes, indicating a lesser influence of environmental properties on the bacterial community. Furthermore, our read-based metagenomic analysis showed that the microbial communities' functional potential increasingly became similar to the reference sites. Additionally, we found that the plant richness increased with the reclamation age. Overall, our study shows that both above- and belowground ecological properties of reclaimed mine sites trend towards undisturbed sites with increasing reclamation age. Further, it demonstrates the importance of microbial genomics in tracking the trajectory of ecosystem reclamation.

Opening Pandora's Box: Neglected Biochemical Potential of Permafrost-Associated Fungal Communities in a Warming Climate

Permafrost, a vast storage reservoir of frozen organic matter, is rapidly thawing due to climate change, releasing previously preserved carbon into the environment. This phenomenon has significant consequences for microbial communities, including fungi, inhabiting permafrost-associated regions. In this review, we delve into the intricate interplay between permafrost thawing and fungal diversity and functionality with an emphasis on thermokarst lakes. We explore how the release of organic carbon from thawing permafrost alters the composition and activities of fungal communities, emphasizing the potential for shifts in taxonomic diversity and functional gene expression. We discuss the formation of thermokarst lakes, as an example of permafrost thaw-induced ecological disruptions and their impact on fungal communities. Furthermore, we analyze the repercussions of these changes, including effects on nutrient cycling, plant productivity, and greenhouse gas (GHG) emissions. By elucidating the multifaceted relationship between permafrost thaw and aquatic fungi, this review provides valuable insights into the ecological consequences of ongoing climate change in permafrost-affected regions.

Genomic evidence that microbial carbon degradation is dominated by iron redox metabolism in thawing permafrost

Microorganisms drive many aspects of organic carbon cycling in thawing permafrost soils, but the compositional trajectory of the post-thaw microbiome and its metabolic activity remain uncertain, which limits our ability to predict permafrost-climate feedbacks in a warming world. Using quantitative metabarcoding and metagenomic sequencing, we determined relative and absolute changes in microbiome composition and functional gene abundance during thaw incubations of wet sedge tundra collected from northern Alaska, USA. Organic soils from the tundra active-layer (0-50 cm), transition-zone (50-70 cm), and permafrost (70+ cm) depths were incubated under reducing conditions at 4 °C for 30 days to mimic an extended thaw duration. Following extended thaw, we found that iron (Fe)-cycling Gammaproteobacteria, specifically the heterotrophic Fe(III)-reducing Rhodoferax sp. and chemoautotrophic Fe(II)-oxidizing Gallionella sp., increased by 3-5 orders of magnitude in absolute abundance within the transition-zone and permafrost microbiomes, accounting for 65% of community abundance. We also found that the abundance of genes for Fe(III) reduction (e.g., MtrE) and Fe(II) oxidation (e.g., Cyc1) increased concurrently with genes for benzoate degradation and pyruvate metabolism, in which pyruvate is used to generate acetate that can be oxidized, along with benzoate, to CO2 when coupled with Fe(III) reduction. Gene abundance for CH4 metabolism decreased following extended thaw, suggesting dissimilatory Fe(III) reduction suppresses acetoclastic methanogenesis under reducing conditions. Our genomic evidence indicates that microbial carbon degradation is dominated by iron redox metabolism via an increase in gene abundance associated with Fe(III) reduction and Fe(II) oxidation during initial permafrost thaw, likely increasing microbial respiration while suppressing methanogenesis in wet sedge tundra.

Biological Interactions and Environmental Influences Shift Microeukaryotes in Permafrost Active Layer Soil Across the Qinghai-Tibet Plateau

Permafrost active layer soils are harsh environments with thaw/freeze cycles and sub-zero temperatures, harboring diverse microorganisms. However, the distribution patterns, assembly mechanism, and driving forces of soil microeukaryotes in permafrost remain largely unknown. In this study, we investigated microeukaryotes in permafrost active layer across the Qinghai-Tibet Plateau (QTP) using 18S rRNA gene sequencing. The results showed that the microbial eukaryotic communities were dominated by Nematozoa, Ciliophora, Ascomycota, Cercozoa, Arthropoda, and Basidiomycota in terms of relative abundance and operational taxonomic unit (OTU) richness. Nematozoa had the highest relative abundance, while Ciliophora had the highest OTU richness. These phyla had strong interactions between each other. Their alpha diversity and community structure were differently influenced by the factors associated to location, climate, and soil properties, particularly the soil properties. Significant but weak distance-decay relationships with different slopes were established for the communities of these dominant phyla, except for Basidiomycota. According to the null model, community assemblies of Nematozoa and Cercozoa were dominated by heterogeneous selection, Ciliophora and Ascomycota were dominated by dispersal limitation, while Arthropoda and Basidiomycota were highly dominated by non-dominant processes. The assembly mechanisms can be jointly explained by biotic interactions, organism treats, and environmental influences. Modules in the co-occurrence network of the microeukaryotes were composed by members from different taxonomic groups. These modules also had interactions and responded to different environmental factors, within which, soil properties had strong influences on these modules. The results suggested the importance of biological interactions and soil properties in structuring microbial eukaryotic communities in permafrost active layer soil across the QTP.

Abrupt permafrost thaw triggers activity of copiotrophs and microbiome predators

Permafrost soils store a substantial part of the global soil carbon and nitrogen. However, global warming causes abrupt erosion and gradual thaw, which make these stocks vulnerable to microbial decomposition into greenhouse gases. Here, we investigated the microbial response to abrupt in situ permafrost thaw. We sequenced the total RNA of a 1 m deep soil core consisting of up to 26 500-year-old permafrost material from an active abrupt erosion site. We analysed the microbial community in the active layer soil, the recently thawed, and the intact permafrost, and found maximum RNA:DNA ratios in recently thawed permafrost indicating a high microbial activity. In thawed permafrost, potentially copiotrophic Burkholderiales and Sphingobacteriales, but also microbiome predators dominated the community. Overall, both thaw-dependent and long-term soil properties significantly correlated with changes in community composition, as did microbiome predator abundance. Bacterial predators were dominated in shallower depths by Myxococcota, while protozoa, especially Cercozoa and Ciliophora, almost tripled in relative abundance in thawed layers. Our findings highlight the ecological importance of a diverse interkingdom and active microbial community highly abundant in abruptly thawing permafrost, as well as predation as potential biological control mechanism.

Microbially mediated climate feedbacks from wetland ecosystems

Wetlands are crucial nodes in the carbon cycle, emitting approximately 20% of global CH4 while also sequestering 20%-30% of all soil carbon. Both greenhouse gas fluxes and carbon storage are driven by microbial communities in wetland soils. However, these key players are often overlooked or overly simplified in current global climate models. Here, we first integrate microbial metabolisms with biological, chemical, and physical processes occurring at scales from individual microbial cells to ecosystems. This conceptual scale-bridging framework guides the development of feedback loops describing how wetland-specific climate impacts (i.e., sea level rise in estuarine wetlands, droughts and floods in inland wetlands) will affect future climate trajectories. These feedback loops highlight knowledge gaps that need to be addressed to develop predictive models of future climates capturing microbial contributions. We propose a roadmap connecting environmental scientific disciplines to address these knowledge gaps and improve the representation of microbial processes in climate models. Together, this paves the way to understand how microbially mediated climate feedbacks from wetlands will impact future climate change.

Current advances in microbiome sciences within the US Department of Defense: part 2 - enabling technologies and environmental microbiomes

Microbiomes involve complex microbial communities wherein the micro-organisms interact with one another as well as their associated hosts or environmental niches. Much of the characterisation of these communities and the associations have been achieved through 'omics' technologies, such as metagenomics, metaproteomics and metametabolomics, and model systems. Recent research in host-associated microbiomes has been aimed at understanding the role microbes may play in host fitness or conversely how host activities/conditions may perturb the microbial community, which can further affect host health. These studies have led to the investigation of detection, intervention or modulation methods, which may serve to provide benefits to the host and advance our understanding of microbiome associations. With the clear implications on human health and disease, the US Department of Defense (DoD) has made microbiome research a priority, with the founding of the Tri-Service Microbiome Consortium (TSMC) to enhance collaboration, coordination,and communication of microbiome research among DoD organisations and partners in academia and industry. DoD microbiome research focuses mainly on the following themes: (1) human health and performance, (2) environmental microbiomes and (3) enabling technologies. This review provides an update of current DoD microbiome research efforts centred on enabling technologies and environmental microbiomes and highlights innovative research being done in academia and industry that can be leveraged by the DoD. These topics were also communicated and further discussed in the Fifth Annual TSMC Symposium. This paper forms part of the special issue of BMJ Military Health dedicated to personalised digital technology for mental health in the Armed Forces.

Distinct patterns of soil bacterial and fungal community assemblages in subtropical forest ecosystems under warming

Climate change globally affects soil microbial community assembly across ecosystems. However, little is known about the impact of warming on the structure of soil microbial communities or underlying mechanisms that shape microbial community composition in subtropical forest ecosystems. To address this gap, we utilized natural variation in temperature via an altitudinal gradient to simulate ecosystem warming. After 6 years, microbial co-occurrence network complexity increased with warming, and changes in their taxonomic composition were asynchronous, likely due to contrasting community assembly processes. We found that while stochastic processes were drivers of bacterial community composition, warming led to a shift from stochastic to deterministic drivers in dry season. Structural equation modelling highlighted that soil temperature and water content positively influenced soil microbial communities during dry season and negatively during wet season. These results facilitate our understanding of the response of soil microbial communities to climate warming and may improve predictions of ecosystem function of soil microbes in subtropical forests.

Interannual dynamics of putative parasites (Syndiniales Group II) in a coastal ecosystem

Temporal dynamics of Syndiniales Group II were investigated combining 18S rDNA amplicon sequencing and direct microscopy counts (fluorescence in situ hybridization-tyramide signal amplification [FISH-TSA]) during 5 years. The study was undertaken in meso-eutrophic coastal ecosystem, dominated by diatoms, the haptophyte Phaeocystis globosa and exhibiting relatively low dinoflagellate abundance (max. 18.6 × 10³  cells L^-1 ). Consistent temporal patterns of Syndiniales Group II were observed over consecutive years highlighting the existence of local populations. According to sequencing data, Syndiniales Group II showed increasing abundance and richness in summer and autumn. Dinospores counted by microscopy, were present at low abundances and were punctuated by transient peaks. In summer dinospore highest abundance (559 × 10³  L^-1 ) and prevalence (38.5%) coincided with the peak abundance of the dinoflagellate Prorocentrum minimum (13 × 10³  L^-1 ) while in autumn Syndiniales Group II likely had more diversified hosts. Although, several peaks of dinospore and read abundances coincided, there was no consistent relation between them. Ecological assembly processes at a seasonal scale revealed that stochastic processes were the main drivers (80%) of the Group II community assembly, though deterministic processes were noticeable (20%) in June and July. This latter observation may reflect the specific Syndiniales-dinoflagellate interactions in summer.

Microbial communities in tree root-compartment niches under Cd and Zn pollution: Structure, assembly process and co-occurrence relationship

Woody plants have showed great potential in remediating severely contaminated soils by heavy metals (HMs) due to their cost-efficient and ecologically friendly trait. It is believed the root-associated microbiota plays a vital role in phytoremediation for HMs. However, the ecological process controlling the assembly and composition of tree root-associated microbial communities under HMs stress remains poorly understood. Herein, we profiled the bulk soil, rhizosphere and endosphere microbial communities of trees growing in heavily Cd and Zn polluted soil. The microbiota was gradually filtered from bulk soil to the tree roots and was selectively enriched in roots with specific taxa, such as Proteobacteria and Ascomycota. The microbial community assembly along the soil-root continuum was mainly controlled by deterministic processes from bulk soil to the endosphere, with the normalized stochasticity ratio (NST) indices of 67.16-31.05 % and 30.37-15.02 % for bacteria and fungi, respectively. Plant selection pressure sequentially increased from bulk soil to rhizosphere to endosphere, with the reduced bacterial alpha diversity accompanying the consequently reduced complexity of the co-occurrence network. Together, the findings provide new evidence for horizontal transmission of endophytic microbiome from soil to the host, which can shed light on the future screening and application of microbial-assisted phytoremediation.

Stochastic and Deterministic Processes Regulate Phytoplankton Assemblages in a Temperate Coastal Ecosystem

Assessing the relative contributions of the interacting deterministic and stochastic ecological processes for phytoplankton community assembly is crucial in understanding and predicting community organization and succession at different temporal and spatial scales. In this study, we hypothesized that deterministic and stochastic ecological processes regulating phytoplankton, present seasonal and repeating patterns. This hypothesis was explored during a 5-year survey (287 samples) conducted at a small spatial scale (~15km) in a temperate coastal ecosystem (eastern English Channel). Microscopy and flow cytometry quantified phytoplankton abundance and biomass, while metabarcoding data allowed an extended evaluation of diversity and the exploration of the ecological processes regulating phytoplankton using null model analysis. Alpha diversity of phytoplankton was governed by the effect of environmental conditions (environmental filtering). Temporal community turnover (beta diversity) evidenced a consistent interannual pattern that determined the phytoplankton seasonal structure. In winter and early spring (from January to March), determinism (homogeneous selection) was the major process in the phytoplankton community assembly. The overall mean in the year was 38%. Stochastic processes (ecological drift) prevailed during the rest of the year from April to December, where the overall mean for the year was 55%. The maximum values were recorded in late spring and summer, which often presented recurrent and transient monospecific phytoplankton peaks. Overall, the prevalence of stochastic processes rendered less predictable seasonal dynamics of phytoplankton communities to future environmental change. IMPORTANCE While ecological deterministic processes are conducive to modeling, stochastic ones are far less predictable. Understanding the overall assembly processes of phytoplankton is critical in tracking and predicting future changes. The novelty of this study was that it addressed a long-posed question, on a pluriannual scale. Was seasonal phytoplankton succession influenced by deterministic processes (e.g., abiotic environment) or by stochastic ones (e.g., dispersal, or ecological drift)? Our results provided strong support for a seasonal and repeating pattern with stochastic processes (drift) prevailing during most of the year and periods with monospecific phytoplankton peaks.

Functional microbial ecology in arctic soils: the need for a year-round perspective

The microbial ecology of arctic and sub-arctic soils is an important aspect of the global carbon cycle, due to the sensitivity of the large soil carbon stocks to ongoing climate warming. These regions are characterized by strong climatic seasonality, but the emphasis of most studies on the short vegetation growing season could potentially limit our ability to predict year-round ecosystem functions. We compiled a database of studies from arctic, subarctic, and boreal environments that include sampling of microbial community and functions outside the growing season. We found that for studies comparing across seasons, in most environments, microbial biomass and community composition vary intra-annually, with the spring thaw period often identified by researchers as the most dynamic time of year. This seasonality of microbial communities will have consequences for predictions of ecosystem function under climate change if it results in: seasonality in process kinetics of microbe-mediated functions; intra-annual variation in the importance of different (a)biotic drivers; and/or potential temporal asynchrony between climate change-related perturbations and their corresponding effects. Future research should focus on (i) sampling throughout the entire year; (ii) linking these multi-season measures of microbial community composition with corresponding functional or physiological measurements to elucidate the temporal dynamics of the links between them; and (iii) identifying dominant biotic and abiotic drivers of intra-annual variation in different ecological contexts.

Microbial Community in the Permafrost Thaw Gradient in the South of the Vitim Plateau (Buryatia, Russia)

Soil microbial communities play key roles in biogeochemical cycles and greenhouse gas formation during the decomposition of the released organic matter in the thawing permafrost. The aim of our research was to assess the taxonomic prokaryotic diversity in soil-ecological niches of the Darkhituy-Khaimisan transect during the initial period of soil thawing. We investigated changes in the microbial communities present in the active layer of four sites representing distinct habitats (larch forest, birch forest, meadow steppe and thermokarst lake). We explore the relationship between the biogeochemical differences among habitats and the active layer microbial community via a spatial (across habitats, and with depth through the active layer) community survey using high-throughput Illumina sequencing. Microbial communities showed significant differences between active and frozen layers and across ecosystem types, including a high relative abundance of Alphaproteobacteria, Firmicutes, Crenarchaeota, Bacteroidota and Gemmatimonadota in the active layer and a high relative abundance of Actinobacteriota and Desulfobacterota in the frozen layer. Soil pH, temperature and moisture were the most significant parameters underlying the variations in the microbial community composition. CCA suggested that the differing environmental conditions between the four soil habitats had strong influences on microbial distribution and diversity and further explained the variability of soil microbial community structures.

Microbiome assembly in thawing permafrost and its feedbacks to climate

The physical and chemical changes that accompany permafrost thaw directly influence the microbial communities that mediate the decomposition of formerly frozen organic matter, leading to uncertainty in permafrost-climate feedbacks. Although changes to microbial metabolism and community structure are documented following thaw, the generality of post-thaw assembly patterns across permafrost soils of the world remains uncertain, limiting our ability to predict biogeochemistry and microbial community responses to climate change. Based on our review of the Arctic microbiome, permafrost microbiology, and community ecology, we propose that Assembly Theory provides a framework to better understand thaw-mediated microbiome changes and the implications for community function and climate feedbacks. This framework posits that the prevalence of deterministic or stochastic processes indicates whether the community is well-suited to thrive in changing environmental conditions. We predict that on a short timescale and following high-disturbance thaw (e.g., thermokarst), stochasticity dominates post-thaw microbiome assembly, suggesting that functional predictions will be aided by detailed information about the microbiome. At a longer timescale and lower-intensity disturbance (e.g., active layer deepening), deterministic processes likely dominate, making environmental parameters sufficient for predicting function. We propose that the contribution of stochastic and deterministic processes to post-thaw microbiome assembly depends on the characteristics of the thaw disturbance, as well as characteristics of the microbial community, such as the ecological and phylogenetic breadth of functional guilds, their functional redundancy, and biotic interactions. These propagate across space and time, potentially providing a means for predicting the microbial forcing of greenhouse gas feedbacks to global climate change.

Microbial Community Changes in 26,500-Year-Old Thawing Permafrost

Northern permafrost soils store more than half of the global soil carbon. Frozen for at least two consecutive years, but often for millennia, permafrost temperatures have increased drastically in the last decades. The resulting thermal erosion leads not only to gradual thaw, resulting in an increase of seasonally thawing soil thickness, but also to abrupt thaw events, such as sudden collapses of the soil surface. These could affect 20% of the permafrost zone and half of its organic carbon, increasing accessibility for deeper rooting vegetation and microbial decomposition into greenhouse gases. Knowledge gaps include the impact of permafrost thaw on the soil microfauna as well as key taxa to change the microbial mineralization of ancient permafrost carbon stocks during erosion. Here, we present the first sequencing study of an abrupt permafrost erosion microbiome in Northeast Greenland, where a thermal erosion gully collapsed in the summer of 2018, leading to the thawing of 26,500-year-old permafrost material. We investigated which soil parameters (pH, soil carbon content, age and moisture, organic and mineral horizons, and permafrost layers) most significantly drove changes of taxonomic diversity and the abundance of soil microorganisms in two consecutive years of intense erosion. Sequencing of the prokaryotic 16S rRNA and fungal ITS2 gene regions at finely scaled depth increments revealed decreasing alpha diversity with depth, soil age, and pH. The most significant drivers of variation were found in the soil age, horizons, and permafrost layer for prokaryotic and fungal beta diversity. Permafrost was mainly dominated by Proteobacteria and Firmicutes, with Polaromonas identified as the most abundant taxon. Thawed permafrost samples indicated increased abundance of several copiotrophic phyla, such as Bacteroidia, suggesting alterations of carbon utilization pathways within eroding permafrost.

Raman-Deuterium Isotope Probing and Metagenomics Reveal the Drought Tolerance of the Soil Microbiome and Its Promotion of Plant Growth

Drought has become a major agricultural threat leading crop yield loss. Although a few species of rhizobacteria have the ability to promote plant growth under drought, the drought tolerance of the soil microbiome and its relationship with the promotion of plant growth under drought are scarcely studied. This study aimed to develop a novel approach for assessing drought tolerance in agricultural land by quantitatively measuring microbial phenotypes using stable isotopes and Raman spectroscopy. Raman spectroscopy with deuterium isotope probing was used to identify the Raman signatures of drought effects from drought-tolerant bacteria. Counting drought-tolerant cells by applying these phenotypic properties to agricultural samples revealed that 0% to 52.2% of all measured single cells had drought-tolerant properties, depending on the soil sample. The proportions of drought-tolerant cells in each soil type showed similar tendencies to the numbers of revived pea plants cultivated under drought. The phenotype of the soil microbiome and plant behavior under drought conditions therefore appeared to be highly related. Studying metagenomics suggested that there was a reliable link between the phenotype and genotype of the soil microbiome that could explain mechanisms that promote plant growth in drought. In particular, the proportion of drought-tolerant cells was highly correlated with genes encoding phytohormone production, including tryptophan synthase and isopentenyl-diphosphate delta-isomerase; these enzymes are known to alleviate drought stress. Raman spectroscopy with deuterium isotope probing shows high potential as an alternative technology for quantitatively assessing drought tolerance through phenotypic analysis of the soil microbiome. IMPORTANCE Soil microbiome has played a critical role in the plant survival during drought. However, the drought tolerance of soil microbiome and its ability to promote plant growth under drought is still scarcely studied. In this study, we identified the Raman signature (i.e., phenotype) of drought effects from drought-tolerant bacteria in agricultural soil samples using Raman-deuterium isotope probing (Raman-DIP). Moreover, the number of drought-tolerant cells measured by Raman-DIP was highly related to the survival rate of plant cultivation under drought and the abundance of genes encoding phytohormone production alleviating drought stress in plant. These results suggest Raman-DIP is a promising technology for measuring drought tolerance of soil microbiome. This result give us important insight into further studies of a reliable link between phenotype and genotype of soil microbiome for future plant-bacteria interaction research.

Deciphering Succession and Assembly Patterns of Microbial Communities in a Two-Stage Solid-State Fermentation System

Although the importance of microbiota in the natural environment and in industrial production has been widely recognized, little is known about the formation and succession patterns of the microbial community, particularly secondary succession after disturbance. Here, we choose the Xiaoqu liquor brewing process as an experimental model in which sorghum grains were first aerobically saccharified and then anaerobically fermented after being stirred and acidified to explore multistage community succession patterns. We analyzed microbial composition, physicochemical factors, and metabolites of brewing grains inoculated with two different starters, pure starter and traditional starter, respectively. Two groups showed similar succession patterns where the saccharification microbiota was mainly derived from starters, while environmental microorganisms, mainly Lactobacillaceae and Saccharomyces, dominated the fermentation microbiota regardless of the original saccharification community composition. Species replacement shaped the bacterial community, while species replacement and loss both contributed to fungal community succession in both groups. Grain acidification and hypoxia led to the succession of bacterial and fungal communities during fermentation, respectively. Despite inoculation with starters containing different microorganisms, similar microbial communities during the fermentation stage of the two groups exhibited similar metabolite composition. However, higher abundance of Rhizopus in the saccharification of the pure starter group led to more alcohols, while higher abundance of Monascus and Saccharomycopsis in the traditional starter group promoted acid and ester metabolism. These results revealed the microbial succession patterns of two-stage liquor brewing and its influence on flavor metabolism, which could be used to regulate the microbial community in food fermentation to further promote the modernization of the fermented food industry.

IMPORTANCE Revealing formation and assembly mechanisms of microbiota can help us to understand and further regulate its roles in the ecosystems. The Xiaoqu liquor brewing system is a tractable microbial ecosystem with low complexity. This two-stage microbial ecosystem can be used as an experimental model to analyze the multistage temporal succession pattern of microbial communities. Our results demonstrated the dynamic composition and succession pattern of a microbial community in the two-stage liquor brewing system. The results also revealed the microbial origins determining community composition, the ecological processes dominating microbial community succession patterns, the determinants affecting microbial community successions, and the effect of microbial community changes on metabolite synthesis. Overall, our study not only provides an insight into multistage succession patterns of microbial communities in liquor brewing systems but also provides reference for optimizing the quality of fermented products, which will be helpful to understand the succession patterns of microbial communities in other natural ecosystems.

Meeting report of the fourth annual Tri-Service Microbiome Consortium symposium

The Tri-Service Microbiome Consortium (TSMC) was founded to enhance collaboration, coordination, and communication of microbiome research among U.S. Department of Defense (DoD) organizations. The annual TSMC symposium is designed to enable information sharing between DoD scientists and leaders in the field of microbiome science, thereby keeping DoD consortium members informed of the latest advances within the microbiome community and facilitating the development of new collaborative research opportunities. The 2020 annual symposium was held virtually on 24-25 September 2020. Presentations and discussions centered on microbiome-related topics within four broad thematic areas: (1) Enabling Technologies; (2) Microbiome for Health and Performance; (3) Environmental Microbiome; and (4) Microbiome Analysis and Discovery. This report summarizes the presentations and outcomes of the 4th annual TSMC symposium.

Rainfall Alters Permafrost Soil Redox Conditions, but Meta-Omics Show Divergent Microbial Community Responses by Tundra Type in the Arctic

Soil anoxia is common in the annually thawed surface (‘active’) layer of permafrost soils, particularly when soils are saturated, and supports anaerobic microbial metabolism and methane (CH4) production. Rainfall contributes to soil saturation, but can also introduce oxygen, causing soil oxidation and altering anoxic conditions. We simulated a rainfall event in soil mesocosms from two dominant tundra types, tussock tundra and wet sedge tundra, to test the impacts of rainfall-induced soil oxidation on microbial communities and their metabolic capacity for anaerobic CH4 production and aerobic respiration following soil oxidation. In both types, rainfall increased total soil O2 concentration, but in tussock tundra there was a 2.5-fold greater increase in soil O2 compared to wet sedge tundra due to differences in soil drainage. Metagenomic and metatranscriptomic analyses found divergent microbial responses to rainfall between tundra types. Active microbial taxa in the tussock tundra community, including bacteria and fungi, responded to rainfall with a decline in gene expression for anaerobic metabolism and a concurrent increase in gene expression for cellular growth. In contrast, the wet sedge tundra community showed no significant changes in microbial gene expression from anaerobic metabolism, fermentation, or methanogenesis following rainfall, despite an initial increase in soil O2 concentration. These results suggest that rainfall induces soil oxidation and enhances aerobic microbial respiration in tussock tundra communities but may not accumulate or remain in wet sedge tundra soils long enough to induce a community-wide shift from anaerobic metabolism. Thus, rainfall may serve only to maintain saturated soil conditions that promote CH4 production in low-lying wet sedge tundra soils across the Arctic.